1
|
Zouagui R, Zouagui H, Aurag J, Ibrahimi A, Sbabou L. Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere. BMC Genomics 2024; 25:289. [PMID: 38500021 PMCID: PMC10946135 DOI: 10.1186/s12864-024-10088-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/03/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted. RESULTS Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera. CONCLUSIONS The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.
Collapse
Affiliation(s)
- Rahma Zouagui
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Houda Zouagui
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Jamal Aurag
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Laila Sbabou
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
| |
Collapse
|
2
|
Boumajdi N, Bendani H, Kartti S, Alouane T, Belyamani L, Ibrahimi A. A Comprehensive Analysis of 3 Moroccan Genomes Revealed Contributions From Both African and European Ancestries. Evol Bioinform Online 2024; 20:11769343241229278. [PMID: 38327511 PMCID: PMC10848790 DOI: 10.1177/11769343241229278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Genetic variations in the human genome represent the differences in DNA sequence within individuals. This highlights the important role of whole human genome sequencing which has become the keystone for precision medicine and disease prediction. Morocco is an important hub for studying human population migration and mixing history. This study presents the analysis of 3 Moroccan genomes; the variant analysis revealed 6 379 606 single nucleotide variants (SNVs) and 1 050 577 small InDels. Of those identified SNVs, 219 152 were novel, with 1233 occurring in coding regions, and 5580 non-synonymous single nucleotide variants (nsSNP) variants were predicted to affect protein functions. The InDels produced 1055 coding variants and 454 non-3n length variants, and their size ranged from -49 and 49 bp. We further analysed the gene pathways of 8 novel coding variants found in the 3 genomes and revealed 5 genes involved in various diseases and biological pathways. We found that the Moroccan genomes share 92.78% of African ancestry, and 92.86% of Non-Finnish European ancestry, according to the gnomAD database. Then, population structure inference, by admixture analysis and network-based approach, revealed that the studied genomes form a mixed population structure, highlighting the increased genetic diversity in Morocco.
Collapse
Affiliation(s)
- Nasma Boumajdi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation (CM6), Rabat, Morocco
| | - Houda Bendani
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation (CM6), Rabat, Morocco
| | - Souad Kartti
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation (CM6), Rabat, Morocco
| | - Tarek Alouane
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Mohammed VI Center for Research & Innovation (CM6), Rabat, Morocco
- Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation (CM6), Rabat, Morocco
- Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| |
Collapse
|
3
|
Essabbar A, El Mazouri S, Boumajdi N, Bendani H, Aanniz T, Mouna O, Lahcen B, Ibrahimi A. Temporal Dynamics and Genomic Landscape of SARS-CoV-2 After Four Years of Evolution. Cureus 2024; 16:e53654. [PMID: 38327721 PMCID: PMC10849819 DOI: 10.7759/cureus.53654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2024] [Indexed: 02/09/2024] Open
Abstract
Introduction Since its emergence, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone extensive genomic evolution, impacting public health policies, diagnosis, medication, and vaccine development. This study leverages advanced bioinformatics to assess the virus's temporal and regional genomic evolution from December 2019 to October 2023. Methods Our analysis incorporates 16,575 complete SARS-CoV-2 sequences collected from 214 countries. These samples were comparatively analyzed, with a detailed characterization of nucleic mutations, lineages, distribution, and evolutionary patterns during each year, using the Wuhan-Hu-1 strain as the reference. Results Our analysis has identified a total of 21,580 mutations that we classified into transient mutations, which diminished over time, and persistent mutations with steadily increasing frequencies. This mutation landscape led to a notable surge in the evolutionary rate, rising from 13 mutations per sample in 2020 to 96 by 2023, with minor geographic variations. The phylogenetic analysis unveiled three distinct evolutionary branches, each representing unique viral evolution pathways. These lineages exhibited a tendency for a reduced duration of dominance with a shortening prevalence period over time, as dominant strains were consistently replaced by more fit variants. Notably, the emergence of the Alpha and Delta variants in 2021 was followed by the subsequent dominance of Omicron clade variants that have branched into several recombinant variants in 2022, marking a significant shift in the viral landscape. Conclusion This study sheds light on the dynamic nature of SARS-CoV-2 evolution, emphasizing the importance of continuous and vigilant genomic surveillance. The dominance of recombinant lineages, coupled with the disappearance of local variants, underscores the virus's adaptability.
Collapse
Affiliation(s)
- Abdelmounim Essabbar
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
- Toulouse Cancer Research Center, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, FRA
| | - Safae El Mazouri
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Nassma Boumajdi
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Houda Bendani
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Tarik Aanniz
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Ouadghiri Mouna
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Belyamani Lahcen
- Émergency Department, Military Hospital Rabat Morocco, Rabat, MAR
- Mohammed VI Center For Research and Innovation, Mohammed VI University of Sciences and Health, Rabat, MAR
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| |
Collapse
|
4
|
Boutahar M, Belaouni M, Ibrahimi A, Eljaoudi R, Aanniz T, Er-Rami M. Prevalence of Blastocystis sp. in Morocco: Comparative assessment of three diagnostic methods and characterization of parasite forms in Jones' culture medium. Parasite 2023; 30:64. [PMID: 38117274 PMCID: PMC10732137 DOI: 10.1051/parasite/2023065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023] Open
Abstract
Blastocystosis is an infection caused by Blastocystis sp., which colonizes the digestive tract of various hosts, including humans, although its pathogenicity is debated. It is crucial to detect and distinguish the different forms of Blastocystis to understand better its impact on human health and its epidemiological evolution. This study evaluated three diagnostic methods on 105 stool samples: direct examination, culture in Jones' medium, and conventional PCR. PCR is considered the gold standard and revealed a high prevalence of Blastocystis (67.62%) compared to direct examination (20.95%) and culture in Jones' medium (51.43%). Although the sensitivity of direct examination and culture was 31% and 76.1%, respectively, their specificity was 100%. No significant risk factors were identified. A statistically significant association was observed between Blastocystis infection and abdominal pain. Microscopic analysis revealed various morphological forms. Molecular diagnosis is an essential tool to determine the true prevalence of Blastocystis, and studying the different forms of this microorganism will contribute to a better understanding of its biological cycle and, therefore, the impact of this emerging infection on human health.
Collapse
Affiliation(s)
- Mounia Boutahar
- Human Pathology, Biomedicine and Environment Laboratory, Faculty of Science and Technology of Fez, B.P. 2202 - Route d'Imouzzer, Fez, Morocco
| | - Mourad Belaouni
- Parasitology-Mycology Laboratory, Moulay Ismaïl Military Hospital, Meknes 50007, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat 10100, Morocco - Mohammed VI Center for Research & Innovation (CM6), Rabat 10000, Morocco - Mohammed VI University of Health Sciences, Casablanca 20000, Morocco
| | - Rachid Eljaoudi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat 10100, Morocco - Mohammed VI Center for Research & Innovation (CM6), Rabat 10000, Morocco - Emergency Department, Military Hospital Mohammed V, Rabat 10000, Morocco
| | - Tarik Aanniz
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat 10100, Morocco
| | - Mohammed Er-Rami
- Parasitology-Mycology Laboratory, Moulay Ismaïl Military Hospital, Meknes 50007, Morocco - Human Pathology, Biomedicine and Environment Laboratory, Faculty of Medicine and Pharmacy, Fez 30070, Morocco
| |
Collapse
|
5
|
Kandoussi I, Abbou H, Haddoumi GEL, Mansouri M, Belyamani L, Ibrahimi A. Virtual docking screening and quantitative structure-activity relationship studies to explore AKT and PI3K inhibitors acting on mTOR in cancers by theoretical biology and medical modeling. Contemp Oncol (Pozn) 2023; 27:155-162. [PMID: 38239868 PMCID: PMC10793616 DOI: 10.5114/wo.2023.133709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 10/04/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction The mechanistic target of rapamycin (mTOR) coordinates the growth and metabolism of eukaryotic cells with a central role in the regulation of many fundamental cellular processes. It is strongly connected to phosphatidylinositol 3-kinase (PI3K) and AKT signaling. Activation of the PI3K/AKT/mTOR pathway leads to a profound disruption in the control of cell growth and survival, which ultimately leads to competitive growth advantage, metastatic competence, angiogenesis and therapeutic resistance. Material and methods To explore the common competitive adenosine triphosphate (ATP) inhibitors PI3K/AKT and PI3K/mTOR, we built a 2D mTOR-SAR model that predicted the bioactivity of AKT and PI3K inhibitors towards mTOR. The interaction of the best inhibitors was evaluated by docking analysis and compared to that of the standard AZ8055 and XL388 inhibitors. Results A mechanistic target of rapamycin-quantitative structure-activity relationship (mTOR-QSAR) model with a correlation coefficient (R2) of 0.80813 and a root mean square error of 0.17756 was obtained, validated and evaluated by a cross-validation leave-one-out method. The best predicted AKT and PI3K inhibitor pIC50 activities were 9.36-9.95 and 9.23-9.87 respectively. Conclusions After docking and several comparisons, the inhibitors with better predictions showed better affinity and interaction with mTOR compared to AZ8055 and XL388, so we have found that 2 AKT inhibitors and 9 mTOR inhibitors met the Lipinski and Veber criteria and could be future drugs.
Collapse
Affiliation(s)
- Ilham Kandoussi
- Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Morocco
- Centre Mohammed VI de la Recherche et de l’Innovation, Rabat, Morocco
| | - Hanane Abbou
- Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Morocco
- Centre Mohammed VI de la Recherche et de l’Innovation, Rabat, Morocco
| | - Ghyzlane EL Haddoumi
- Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Morocco
- Centre Mohammed VI de la Recherche et de l’Innovation, Rabat, Morocco
| | - Mariam Mansouri
- Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Morocco
- Centre Mohammed VI de la Recherche et de l’Innovation, Rabat, Morocco
| | - Lahcen Belyamani
- Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Morocco
- Centre Mohammed VI de la Recherche et de l’Innovation, Rabat, Morocco
- Emergency Department, Military Hospital Mohammed V, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Morocco
- Centre Mohammed VI de la Recherche et de l’Innovation, Rabat, Morocco
| |
Collapse
|
6
|
Magri M, Bouricha EM, Hakmi M, Jaoudi REL, Belyamani L, Ibrahimi A. In Silico Identification of Natural Food Compounds as Potential Quorum-Sensing Inhibitors Targeting the LasR Receptor of Pseudomonas aeruginosa. Bioinform Biol Insights 2023; 17:11779322231212755. [PMID: 38020496 PMCID: PMC10664429 DOI: 10.1177/11779322231212755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/21/2023] [Indexed: 12/01/2023] Open
Abstract
Pseudomonas aeruginosa is a major cause of nosocomial infections and is often associated with biofilm-mediated antibiotic resistance. The LasR protein is a key component of the quorum system in P. aeruginosa, allowing it to regulate its biofilm-induced pathogenicity. When the bacterial population reaches a sufficient density, the accumulation of N-(3-oxododecanoyl) acyl homoserine lactone (3O-C12-HSL) leads to the activation of the LasR receptor, which then acts as a transcriptional activator of target genes involved in biofilm formation and virulence, thereby increasing the bacteria's antibiotic resistance and enhancing its virulence. In this study, we performed a structure-based virtual screening of a natural food database of 10 997 compounds against the crystal structure of the ligand-binding domain of the LasR receptor (PDB ID: 3IX4). This allowed us to identify four molecules, namely ZINC000001580795, ZINC000014819517, ZINC000014708292, and ZINC000004098719, that exhibited a favorable binding mode and docking scores greater than -13 kcal/mol. Furthermore, the molecular dynamics simulation showed that these four molecules formed stable complexes with LasR during the 150-ns molecular dynamics (MD) simulation, indicating their potential for use as inhibitors of the LasR receptor in P. aeruginosa. However, further experimental validation is needed to confirm their activity.
Collapse
Affiliation(s)
- Meryam Magri
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Rabat, Morocco
| | - El Mehdi Bouricha
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Rabat, Morocco
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Rabat, Morocco
| | - Rachid EL Jaoudi
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Rabat, Morocco
- Emergency Department, Military Hospital Mohammed V, Rabat, Morocco
| | - Lahcen Belyamani
- Mohammed VI Center for Research & Innovation, Rabat, Morocco
- Emergency Department, Military Hospital Mohammed V, Rabat, Morocco
- Mohammed VI University of Sciences and Health, Casablanca, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Rabat, Morocco
- Mohammed VI University of Sciences and Health, Casablanca, Morocco
| |
Collapse
|
7
|
El Mazouri S, Essabbar A, Aanniz T, Eljaoudi R, Belyamani L, Ibrahimi A, Ouadghiri M. Genetic diversity and evolutionary dynamics of the Omicron variant of SARS-CoV-2 in Morocco. Pathog Glob Health 2023:1-12. [PMID: 37635364 DOI: 10.1080/20477724.2023.2250942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
Among the numerous variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that have been reported worldwide, the emergence of the Omicron variant has drastically changed the landscape of the coronavirus disease (COVID-19) pandemic. Here, we analyzed the genetic diversity of Moroccan SARS-CoV-2 genomes with a focus on Omicron variant after one year of its detection in Morocco in order to understand its genomic dynamics, features and its potential introduction sources. From 937 Omicron genomes, we identified a total of 999 non-unique mutations distributed across 92 Omicron lineages, of which 13 were specific to the country. Our findings suggest multiple introductory sources of the Omicron variant to Morocco. In addition, we found that four Omicron clades are more infectious in comparison to other Omicron clades. Remarkably, a clade of Omicron is particularly more transmissible and has become the dominant variant worldwide. Moreover, our assessment of Receptor-Binding Domain (RBD) mutations showed that the Spike K444T and N460K mutations enabled a clade higher ability of immune vaccine escape. In conclusion, our analysis highlights the unique genetic diversity of the Omicron variant in Moroccan SARS-CoV-2 genomes, with multiple introductory sources and the emergence of highly transmissible clades. The distinctiveness of the Moroccan strains compared to global ones underscores the importance of ongoing surveillance and understanding of local genomic dynamics for effective response strategies in the evolving COVID-19 pandemic.
Collapse
Affiliation(s)
- Safae El Mazouri
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelmounim Essabbar
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarik Aanniz
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Rachid Eljaoudi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Lahcen Belyamani
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Emergency Department, Military Hospital Mohammed V, Rabat, Morocco
| | - Azeddine Ibrahimi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Mouna Ouadghiri
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| |
Collapse
|
8
|
El Yacoubi FA, Oukabli M, Ibrahimi A, Kisra H, Bensaid M. Unraveling the Role of Neuroligin3 in Autism Spectrum Disorders: Pathophysiological Insights and Targeted Therapies. CNS Neurol Disord Drug Targets 2023; 23:CNSNDDT-EPUB-133208. [PMID: 37497709 DOI: 10.2174/1871527323666230727102244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/28/2023]
Abstract
Autism Spectrum Disorder is a neurodevelopmental disorder characterized by impaired social and communication skills, repetitive behaviors, and/or restricted interests with a prevalence of as high as 1% of children. Autism spectrum has strongly associated with genetic factors and exhibits wide clinical and heterogeneous genetic architecture. Most genes associated with Autism are involved in neuronal and synaptic development. The neuroligin3, the sex-linked gene on the X chromosome, was the first gene to be associated with a monogenic form of Autism. Neuroligin3 is a postsynaptic cell adhesion protein involved in synapse transmission, brain formation, and neuronal development. In this review, we provide recent findings on different mutations in the Neuroligin3 gene linked to Autism spectrum disorder and their molecular pathway effect. We also give the behavioral, and synaptic alterations reported in the Neuroligin3 animal model of Autism and the potential therapeutic strategies targeting the biological processes and the main symptoms of autism spectrum disorder. In addition, we discuss the use of novel technologies like induced pluripotent stem cells from Autistic patients that have the potential to differentiate in human neurons and therefore have a variety of applications in therapy and biomedical studies to search specific biomarkers, and develop systems for screening chemical molecules in human cells to discover target therapies.
Collapse
Affiliation(s)
- Fatima Azzahrae El Yacoubi
- Laboratory of Immunology, Infectious Disease and Tropical Biotechnology, Faculty of Pharmacy, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Mohamed Oukabli
- Laboratory of Pathological Anatomy, Military Hospital Mohamed V, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Rabat Medical and Pharmacy School, University Mohammed V, Rabat, Morocco
| | - Hassan Kisra
- Medical and Pharmacy School, University Mohammed V, Rabat, Morocco
| | - Mounia Bensaid
- Laboratory of Pathological Anatomy, Military Hospital Mohamed V, Rabat, Morocco
| |
Collapse
|
9
|
Kartti S, Bouricha EM, Zarrik O, Aghlallou Y, Mounjid C, ELJaoudi R, Belyamani L, Ibrahimi A, EL khannoussi B. Targeted Gene Panel Sequencing Unveiled New Pathogenic Mutations in Patients With Breast Cancer. Bioinform Biol Insights 2023; 17:11779322231182054. [PMID: 37377792 PMCID: PMC10291397 DOI: 10.1177/11779322231182054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
The increasing commercialization of new gene panels based on next-generation sequencing for clinical research has significantly improved our understanding of breast cancer genetics and has led to the discovery of new mutation variants. The study included 16 unselected Moroccan breast cancer patients tested with multi-gene panel (HEVA screen panel) using Illumina Miseq, followed by Sanger sequencing to validate the most relevant mutation. Mutational analysis revealed the presence of 13 mutations (11 single-nucleotide polymorphisms [SNPs] and 2 indels), and 6 of 11 identified SNPs were predicted as pathogenic. One of the 6 pathogenic mutations was c.7874G>C, a heterozygous SNP in HD-OB domain of BRCA2 gene, which led to the arginine to threonine change at codon 2625 of the protein. This work describes the first case of a patient with breast cancer harboring this pathogenic variant and analyzes its functional impact using molecular docking and molecular dynamics simulation. Further experimental investigations are needed to validate its pathogenicity and to verify its association with breast cancer.
Collapse
Affiliation(s)
- Souad Kartti
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
| | - El Mehdi Bouricha
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
| | - Oumaima Zarrik
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | | | - Chaimaa Mounjid
- Pathology Department, Oncology National Institute, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Rachid ELJaoudi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- Emergency Department, Military Hospital Mohammed V, Rabat, Morocco
| | - Lahcen Belyamani
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- Emergency Department, Military Hospital Mohammed V, Rabat, Morocco
- Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Basma EL khannoussi
- Pathology Department, Oncology National Institute, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| |
Collapse
|
10
|
El Ouali EM, Zouhal H, Bahije L, Ibrahimi A, Benamar B, Kartibou J, Saeidi A, Laher I, El Harane S, Granacher U, Mesfioui A. Effects of Malocclusion on Maximal Aerobic Capacity and Athletic Performance in Young Sub-Elite Athletes. Sports (Basel) 2023; 11:sports11030071. [PMID: 36976957 PMCID: PMC10051721 DOI: 10.3390/sports11030071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Oral pathologies can cause athletic underperformance. The aim of this study was to determine the effect of malocclusion on maximal aerobic capacity in young athletes with the same anthropometric data, diet, training mode, and intensity from the same athletics training center. Sub-elite track and field athletes (middle-distance runners) with malocclusion (experimental group (EG); n = 37; 21 girls; age: 15.1 ± 1.5 years) and without malocclusion (control group (CG); n = 13; 5 girls; age: 14.7 ± 1.9 years) volunteered to participate in this study. Participants received an oral diagnosis to examine malocclusion, which was defined as an overlapping of teeth that resulted in impaired contact between the teeth of the mandible and the teeth of the upper jaw. Maximal aerobic capacity was assessed using the VAMEVAL test (calculated MAS and estimated VO2max). The test consisted of baseline values that included the following parameters: maximum aerobic speed (MAS), maximal oxygen uptake (VO2max), heart rate frequency, systolic (SAP) and diastolic arterial pressure (DAP), blood lactate concentration (LBP), and post-exercise blood lactate assessment (LAP) after the performance of the VAMEVAL test. There were no statistically significant differences between the two study groups related to either anthropometric data (age: EG = 15.1 ± 1.5 vs. CC = 14.7 ± 1.9 years (p = 0.46); BMI: EG = 19.25 ± 1.9 vs. CC = 19.42 ± 1.7 kg/m2 (p = 0.76)) or for the following physical fitness parameters and biomarkers: MAS: EG = 15.5 (14.5-16.5) vs. CG = 15.5 (15-17) km/h (p = 0.47); VO2max: EG = 54.2 (52.5-58.6) vs. CG = 54.2 (53.4-59.5) mL/kg/min (p = 0.62) (IQR (Q1-Q3)); heart rate before the physical test: EG = 77.1 ± 9.9 vs. CG = 74.3 ± 14.0 bpm (p = 0.43); SAP: EG = 106.6 ± 13.4 vs. CG = 106.2 ± 14.8 mmHg (p = 0.91); DAP: EG = 66.7 ± 9.1 vs. CG = 63.9 ± 10.2 mmHg (p = 0.36); LBP: EG = 1.5 ± 0.4 vs. CG = 1.3 ± 0.4 mmol/L (p = 0.12); and LAP: EG = 4.5 ± 2.36 vs. CG = 4.06 ± 3.04 mmol/L (p = 0.60). Our study suggests that dental malocclusion does not impede maximal aerobic capacity and the athletic performance of young track and field athletes.
Collapse
Affiliation(s)
- El Mokhtar El Ouali
- Laboratory of Biology and Health, Department of Biology, Ibn Tofail University of Kenitra, Kénitra 14000, Morocco
| | - Hassane Zouhal
- Movement, Sport, Health and Sciences Laboratory (M2S), UFR-STAPS, University of Rennes 2-ENS Cachan, Av. Charles Tillon, 35044 Rennes, France
- Institut International des Sciences du Sport (2IS), 35850 Irodouer, France
| | - Loubna Bahije
- Department of Dentofacial Orthopedics, Faculty of Dental Medicine, Mohammed 5 University of Rabat, Rabat 10000, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory, Faculty of Medicine and Pharmacy, Mohamed 5 Rabat University, Rabat 10000, Morocco
| | - Bahae Benamar
- BENAMAR Medical Analysis Laboratory, Rabat 10000, Morocco
| | - Jihan Kartibou
- Ministry of National Education and Teaching and Sports, Rabat 10000, Morocco
| | - Ayoub Saeidi
- Department of Physical Education and Sport Sciences, Faculty of Humanities and Social Sciences, University of Kurdistan, Sanandaj 66177-15175, Iran
| | - Ismail Laher
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sanae El Harane
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Urs Granacher
- Department of Sport and Sport Science, Exercise and Human Movement Science, University of Freiburg, 79102 Freiburg, Germany
| | - Abdelhalem Mesfioui
- Laboratory of Biology and Health, Department of Biology, Ibn Tofail University of Kenitra, Kénitra 14000, Morocco
| |
Collapse
|
11
|
Erjan A, Asha W, Alhussaini M, Elayyan M, Alshorbaji A, Ibrahimi A, Amarin R, Sarhan N, Awabdeh T, Obeidat M, Abulaban D, Alsughayer M, Almousa A. 1P Clinical characteristics and treatment outcomes for adult medulloblastoma: A tertiary cancer center experience. ESMO Open 2023. [DOI: 10.1016/j.esmoop.2023.101013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
|
12
|
Haddoumi GEL, Mansouri M, Bendani H, Chemao-Elfihri MW, Kourou J, Abbou H, Belyamani L, Kandoussi I, Ibrahimi A. Selective Non-toxics Inhibitors Targeting DHFR for Tuberculosis and Cancer Therapy: Pharmacophore Generation and Molecular Dynamics Simulation. Bioinform Biol Insights 2023; 17:11779322231171778. [PMID: 37180813 PMCID: PMC10170603 DOI: 10.1177/11779322231171778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/07/2023] [Indexed: 05/16/2023] Open
Abstract
Dihydrofolate reductase (DHFR) is a crucial enzyme that catalyzes the conversion of folic acid. Its reserved properties and significance in both human (h-DHFR) and mycobacterium (mt-DHFR) make it a challenging target for developing drugs against cancer and bacterial infections. Although methotrexate (MTX) is commonly used for cancer therapy and bacterial infections, it has a toxic profile. In this study, we aimed to identify selective and non-toxic inhibitors against h-DHFR and mt-DHFR using an in silico approach. From a data set of 8 412 inhibitors, 11 compounds passed the toxicity and drug-likeness tests, and their interaction with h-DHFR and mt-DHFR was studied by performing molecular docking. To evaluate the inhibitory activity of the compounds against mt-DHFR, five known reference ligands and the natural ligand (dihydrofolate) were used to generate a pharmacophoric map. Two potential selective inhibitors for mt-DHFR and h-DHFR were selected for further investigation using molecular dynamics for 100 ns. As a result, BDBM18226 was identified as the best compound selective for mt-DHFR, non-toxic, with five features listed in the map, with a binding energy of -9.6 kcal/mol. BDBM50145798 was identified as a non-toxic selective compound with a better affinity than MTX for h-DHFR. Molecular dynamics of the two best ligands suggest that they provide more stable, compact, and hydrogen bond interactions with the protein. Our findings could significantly expand the chemical space for new mt-DHFR inhibitors and provide a non-toxic alternative toward h-DHFR for the respective treatment of tuberculosis and cancer therapy.
Collapse
Affiliation(s)
- Ghyzlane EL Haddoumi
- Biotechnology lab (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Centre Mohammed VI for Research and Innovation (CM6), Rabat, Morocco
| | - Mariam Mansouri
- Biotechnology lab (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Centre Mohammed VI for Research and Innovation (CM6), Rabat, Morocco
| | - Houda Bendani
- Biotechnology lab (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Centre Mohammed VI for Research and Innovation (CM6), Rabat, Morocco
| | - Mohammed Walid Chemao-Elfihri
- Biotechnology lab (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Centre Mohammed VI for Research and Innovation (CM6), Rabat, Morocco
| | - Jouhaina Kourou
- Biotechnology lab (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Centre Mohammed VI for Research and Innovation (CM6), Rabat, Morocco
| | - Hanane Abbou
- Centre Mohammed VI for Research and Innovation (CM6), Rabat, Morocco
- Mohammed VI university of Health Sciences (UM6SS), Casablanca, Morocco
| | - Lahcen Belyamani
- Centre Mohammed VI for Research and Innovation (CM6), Rabat, Morocco
- Mohammed VI university of Health Sciences (UM6SS), Casablanca, Morocco
- Emergency Department, Military Hospital Mohammed V, Rabat, Morocco
| | - Ilham Kandoussi
- Biotechnology lab (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Centre Mohammed VI for Research and Innovation (CM6), Rabat, Morocco
- Ilham Kandoussi, Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco.
| | - Azeddine Ibrahimi
- Biotechnology lab (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
- Centre Mohammed VI for Research and Innovation (CM6), Rabat, Morocco
- Mohammed VI university of Health Sciences (UM6SS), Casablanca, Morocco
| |
Collapse
|
13
|
EL Haddoumi G, Mansouri M, Bendani H, Bouricha EM, Kandoussi I, Belyamani L, Ibrahimi A. Facing Antitubercular Resistance: Identification of Potential Direct Inhibitors Targeting InhA Enzyme and Generation of 3D-pharmacophore Model by in silico Approach. Adv Appl Bioinform Chem 2023; 16:49-59. [PMID: 37143606 PMCID: PMC10153438 DOI: 10.2147/aabc.s394535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 01/21/2023] [Indexed: 05/06/2023] Open
Abstract
Purpose The enoyl-acyl carrier protein reductase (InhA) is one of the important key enzymes employed in mycolic acids biosynthesis pathway and an important component of mycobacterial cell walls. This enzyme has also been identified as major target of isoniazid drug, except that isoniazid needs to be activated first by the catalase peroxidase (KatG) protein to form the isonicotinoyl-NAD (INH-NAD) adduct that inhibits the action of InhA enzyme. However, this activation becomes more difficult and unreachable with the problem of mutation-related resistance caused mainly by acquired mutations in KatG and InhA protein. Our main interest in this study is to identify direct InhA inhibitors using computer-aided drug design. Methods Computer-aided drug design was used to solve this problem by applying three different approaches including mutation impact modelling, virtual screening and 3D-pharmacophore search. Results A total of 15 mutations were collected from the literature, then a 3D model was generated for each of them and their impact was predicted. Of the 15 mutations, 10 were found to be deleterious and have a direct effect on flexibility, stability and SASA of the protein. In virtual screening, from 1,000 similar INH-NAD analogues obtained by the similarity search method, 823 compounds passed toxicity filter and drug likeness rules, which were then docked to the wild-type of InhA protein. Subsequently, 34 compounds with binding energy score better than that of INH-NAD were selected and docked against the 10 generated mutated models of InhA. Only three leads showed a lower binding affinity better than the reference. The 3D-pharmacophore model approach was used to identify the common features between those three compounds by generating a pharmacophoric map. Conclusion The result of this study may pave the way to develop more potent mutant-specific inhibitors to overcome this resistance.
Collapse
Affiliation(s)
- Ghyzlane EL Haddoumi
- Biotechnology Lab (MedBiotech), Rabat Medical and Pharmacy School, University Mohammed V, Rabat, Morocco
- Centre Mohammed VI for Research & Innovation (CM6), Rabat, Morocco
| | - Mariam Mansouri
- Biotechnology Lab (MedBiotech), Rabat Medical and Pharmacy School, University Mohammed V, Rabat, Morocco
- Centre Mohammed VI for Research & Innovation (CM6), Rabat, Morocco
| | - Houda Bendani
- Biotechnology Lab (MedBiotech), Rabat Medical and Pharmacy School, University Mohammed V, Rabat, Morocco
- Centre Mohammed VI for Research & Innovation (CM6), Rabat, Morocco
| | - El Mehdi Bouricha
- Biotechnology Lab (MedBiotech), Rabat Medical and Pharmacy School, University Mohammed V, Rabat, Morocco
- Centre Mohammed VI for Research & Innovation (CM6), Rabat, Morocco
| | - Ilham Kandoussi
- Biotechnology Lab (MedBiotech), Rabat Medical and Pharmacy School, University Mohammed V, Rabat, Morocco
- Centre Mohammed VI for Research & Innovation (CM6), Rabat, Morocco
| | - Lahcen Belyamani
- Centre Mohammed VI for Research & Innovation (CM6), Rabat, Morocco
- Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
- Emergency Department, Military Hospital Mohammed V, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Rabat Medical and Pharmacy School, University Mohammed V, Rabat, Morocco
- Centre Mohammed VI for Research & Innovation (CM6), Rabat, Morocco
- Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
- Correspondence: Azeddine Ibrahimi, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco, Tel +212660240131, Email
| |
Collapse
|
14
|
El Fakihi S, El Allam A, Tahoune H, Najimi N, Kadi C, Ibrahimi A, Bourkadi JE, Seghrouchni F. Functional characterization of small and large alveolar macrophages in sarcoidosis and idiopathic pulmonary fibrosis compared with non-fibrosis interstitial lung diseases. Hum Antibodies 2023; 31:59-69. [PMID: 37574726 DOI: 10.3233/hab-230005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
BACKGROUND Sarcoidosis is a granulomatous disease that mostly affects the lungs. Advanced tissue injury caused by this disease can progress to pulmonary fibrosis with similar characteristics shared with idiopathic pulmonary fibrosis (IPF). The initial presentations of both sarcoidosis and IPF may be shared with other interstitial lung diseases (ILDs). Two populations of macrophages have been described in the alveolar space: small alveolar macrophages (AMs) and large alveolar macrophages. Despite their protective function, these cells may also play a role in the initiation and maintenance of inflammation leading to fibrosis. OBJECTIVE The aim of this study was the functional characterization of small and large AM subpopulations in sarcoidosis and IPF as a pathology with respectively mild and advanced tissue injury causing fibrosis, in comparison with non-fibrosis ILDs. METHODS Activation and adhesion surface markers as well as functions of small and large AMs isolated from bronchoalveolar lavage (BAL) were assessed by Flow Cytometry within patients with confirmed sarcoidosis (n= 14), IPF (n= 6), and non-fibrosis ILDs (n= 9). RESULTS Our results showed that small AMs are immunologically more active, which may be important for airway inflammation. They are also proportionally more abundant in IPF, and therefore they may be more involved in a fibrosis process associated with the down-regulation of HLA-DR, LeuCAM, and CD62L expression. In Sarcoidosis, the inflammatory process appears to be associated with up-regulation of CD38 expression and oxidative burst activity. CONCLUSION A relevant potential of the activation and adhesion markers as well as oxidative burst activity expressed on small and large AMs, in the perspective of differential diagnosis of sarcoidosis and IPF.
Collapse
Affiliation(s)
- Sara El Fakihi
- , Rabat, Morocco
- Medical Biotechnology Laboratory, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Aicha El Allam
- , Rabat, Morocco
- Department of Immunology, School of Medicine, Yale University, New Haven, CT, USA
| | - Hicham Tahoune
- , Rabat, Morocco
- Department of Microbiology, CHU Mohammed VI, Tangier, Morocco
| | - Nouhaila Najimi
- , Rabat, Morocco
- Laboratory of Human Pathologies, Department of Biology, Faculty of Sciences, University Mohammed V, Rabat, Morocco
| | - Chaimae Kadi
- , Rabat, Morocco
- Department of Biology, Faculty of Sciences, University Abdelmalek Essaadi, Tetouan, Morocco
| | - Azeddine Ibrahimi
- , Rabat, Morocco
- Medical Biotechnology Laboratory, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Jamal-Eddine Bourkadi
- Pneumo-Phtisiology Department, Moulay Youssef Hospital, Rabat, Morocco
- Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | | |
Collapse
|
15
|
Mansouri M, El Haddoumi G, Bendani H, Boumajdi N, Hakmi M, Abbou H, Bouricha EM, Elgharbaoui B, Kartti S, El Jaoudi R, Belyamani L, Kandoussi I, Ibrahimi A, El Hafidi N. In Silico Analyses of All STAT3 Missense Variants Leading to Explore Divergent AD-HIES Clinical Phenotypes. Evol Bioinform Online 2023; 19:11769343231169374. [PMID: 37123531 PMCID: PMC10134169 DOI: 10.1177/11769343231169374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/20/2023] [Indexed: 05/02/2023] Open
Abstract
Autosomal dominant hyper-IgE syndrome (AD-HIES) is linked to dominant negative mutations of the STAT3 protein whose molecular basis for dysfunction is unclear and presenting with a variety of clinical manifestations with only supportive treatment. To establish the relationship between the impact of STAT3 mutations in different domains and the severity of the clinical manifestations, 105 STAT3 mutations were analyzed for their impact on protein stability, flexibility, function, and binding affinity using in Silico approaches. Our results showed that 73% of the studied mutations have an impact on the physicochemical properties of the protein, altering the stability, flexibility and function to varying degrees. In particular, mutations affecting the DNA binding domain (DBD) and the Src Homology 2 (SH2) have a significant impact on the protein structure and disrupt its interaction either with DNA or other STAT3 to form a heterodomain complex, leading to severe clinical phenotypes. Collectively, this study suggests that there is a close relationship between the domain involving the mutation, the degree of variation in the properties of the protein and the degree of loss of function ranging from partial loss to complete loss, explaining the variability of clinical manifestations between mild and severe.
Collapse
Affiliation(s)
- Mariam Mansouri
- Biotechnology lab (MedBiotech),
Bioinova Research Center, Medical and Pharmacy School, Mohammed V University in
Rabat, Morocco
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
| | - Ghyzlane El Haddoumi
- Biotechnology lab (MedBiotech),
Bioinova Research Center, Medical and Pharmacy School, Mohammed V University in
Rabat, Morocco
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
| | - Houda Bendani
- Biotechnology lab (MedBiotech),
Bioinova Research Center, Medical and Pharmacy School, Mohammed V University in
Rabat, Morocco
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
| | - Nasma Boumajdi
- Biotechnology lab (MedBiotech),
Bioinova Research Center, Medical and Pharmacy School, Mohammed V University in
Rabat, Morocco
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
| | - Mohammed Hakmi
- Biotechnology lab (MedBiotech),
Bioinova Research Center, Medical and Pharmacy School, Mohammed V University in
Rabat, Morocco
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
| | - Hanane Abbou
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
- Mohammed VI University of Health
Sciences (UM6SS), Casablanca, Morocco
| | - El Mehdi Bouricha
- Biotechnology lab (MedBiotech),
Bioinova Research Center, Medical and Pharmacy School, Mohammed V University in
Rabat, Morocco
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
| | - Boutaina Elgharbaoui
- Biotechnology lab (MedBiotech),
Bioinova Research Center, Medical and Pharmacy School, Mohammed V University in
Rabat, Morocco
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
| | - Souad Kartti
- Biotechnology lab (MedBiotech),
Bioinova Research Center, Medical and Pharmacy School, Mohammed V University in
Rabat, Morocco
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
| | - Rachid El Jaoudi
- Biotechnology lab (MedBiotech),
Bioinova Research Center, Medical and Pharmacy School, Mohammed V University in
Rabat, Morocco
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
- Pharmacology and Toxicology Department,
Faculty of Medicine and Pharmacy, University Mohamed V, Rabat, Morocco
| | - Lahcen Belyamani
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
- Mohammed VI University of Health
Sciences (UM6SS), Casablanca, Morocco
- Emergency Department, Military Hospital
Mohammed V, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Ilham Kandoussi
- Biotechnology lab (MedBiotech),
Bioinova Research Center, Medical and Pharmacy School, Mohammed V University in
Rabat, Morocco
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology lab (MedBiotech),
Bioinova Research Center, Medical and Pharmacy School, Mohammed V University in
Rabat, Morocco
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
- Mohammed VI University of Health
Sciences (UM6SS), Casablanca, Morocco
| | - Naima El Hafidi
- Biotechnology lab (MedBiotech),
Bioinova Research Center, Medical and Pharmacy School, Mohammed V University in
Rabat, Morocco
- Centre Mohammed VI of Research and
Innovation (CM6), Rabat, Morocco
- Division of Pediatric immunoallergology
and Infectious Diseases, Children University Hospital, Ibn Sina University Hospital,
Rabat, Morocco
- Pr. Naima El Hafidi, Biotechnology lab
(MedBiotech), Bioinova Research Center, Medical & Pharmacy School, Mohammed
V university in Rabat, Imp. Souissi, Rabat 10100, Morocco.
| |
Collapse
|
16
|
Touissi Y, Hjiej G, Hajjioui A, Ibrahimi A, Fourtassi M. Does developing multiple-choice Questions Improve Medical Students' Learning? A Systematic Review. Med Educ Online 2022; 27:2005505. [PMID: 34969352 PMCID: PMC8725700 DOI: 10.1080/10872981.2021.2005505] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Practicing Multiple-choice questions is a popular learning method among medical students. While MCQs are commonly used in exams, creating them might provide another opportunity for students to boost their learning. Yet, the effectiveness of student-generated multiple-choice questions in medical education has been questioned. This study aims to verify the effects of student-generated MCQs on medical learning either in terms of students' perceptions or their performance and behavior, as well as define the circumstances that would make this activity more useful to the students. Articles were identified by searching four databases MEDLINE, SCOPUS, Web of Science, and ERIC, as well as scanning references. The titles and abstracts were selected based on a pre-established eligibility criterion, and the methodological quality of articles included was assessed using the MERSQI scoring system. Eight hundred and eighty-four papers were identified. Eleven papers were retained after abstract and title screening, and 6 articles were recovered from cross-referencing, making it 17 articles in the end. The mean MERSQI score was 10.42. Most studies showed a positive impact of developing MCQs on medical students' learning in terms of both perception and performance. Few articles in the literature examined the influence of student-generated MCQs on medical students learning. Amid some concerns about time and needed effort, writing multiple-choice questions as a learning method appears to be a useful process for improving medical students' learning.
Collapse
Affiliation(s)
- Youness Touissi
- Faculty of Medicine and Pharmacy of Rabat, Mohammed V University, Souissi, Rabat, Morocco
| | - Ghita Hjiej
- Faculty of Medicine and Pharmacy of Oujda, Mohammed Premier University, Oujda, Morocco
| | - Abderrazak Hajjioui
- Laboratory of Neurosciences, Faculty of Medicine and Pharmacy of Fes, Sidi Mohammed Ben Abdallah University, Fez, Morocco
| | - Azeddine Ibrahimi
- Faculty of Medicine and Pharmacy of Rabat, Mohammed V University, Souissi, Rabat, Morocco
- Laboratory of Biotechnology, Mohammed V University, Souissi, Rabat, Morocco
| | - Maryam Fourtassi
- Faculty of Medicine of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
| |
Collapse
|
17
|
Laamarti M, Chemao-Elfihri MW, Essabbar A, Manni A, Kartti S, Alouane T, Temsamani L, Eljamali JE, Sbabou L, Ouadghiri M, Filali-Maltouf A, Belyamani L, Ibrahimi A. Genomic analysis of two Bacillus safensis isolated from Merzouga desert reveals desert adaptive and potential plant growth-promoting traits. Funct Integr Genomics 2022; 22:1173-1187. [PMID: 36175602 DOI: 10.1007/s10142-022-00905-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/04/2022]
Abstract
Deserts represent extreme environments for microorganisms, and conditions such as high soil salinity, nutrient deficiency, and increased levels of UV radiation make desert soil communities of high biotechnological potential. In this study, we isolated, sequenced, and assembled the genomes of Bacillus safensis strains BcP62 and Bcs93, to which we performed comparative genome analyses. Using the DDH and ANI of both strains with the available B. safensis genomes, we identified three potential subspecies within this group. Intra-species core genome phylogenetic analysis did not result in clustering genomes by niche type, with some exceptions. This study also revealed that the genomes of the analyzed strains possessed plant growth-promoting characteristics, most of which were conserved in all B. safensis strains. Furthermore, we highlight the genetic features of B. safensis BcP62 and Bcs93 related to survival in the Merzouga desert in Morocco. These strains could be potentially used in agriculture as PGPB in extreme environments, given their high tolerability to unfavorable conditions.
Collapse
Affiliation(s)
- Meriem Laamarti
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Mohammed Walid Chemao-Elfihri
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelmounim Essabbar
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Amina Manni
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Souad Kartti
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarek Alouane
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Loubna Temsamani
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Jamal-Eddine Eljamali
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Laila Sbabou
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco.,Université Mohamned VI des Sciences de la Santé (UM6SS), Casablanca, Morocco
| | - Mouna Ouadghiri
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelkarim Filali-Maltouf
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Université Mohamned VI des Sciences de la Santé (UM6SS), Casablanca, Morocco.,Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco. .,Université Mohamned VI des Sciences de la Santé (UM6SS), Casablanca, Morocco.
| |
Collapse
|
18
|
El Mazouri S, Bendani H, Boumajdi N, Aanniz T, Kandoussi I, Amzazi S, Belyamani L, Ibrahimi A, Ouadghiri M. Phylogeography and genomic analysis of SARS-CoV-2 delta variant in Morocco. J Infect Dev Ctries 2022; 16:1258-1268. [PMID: 36099368 DOI: 10.3855/jidc.16513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/09/2022] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION Since the COVID-19 pandemic began in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved with many variants of concern emerging across the world. METHODOLOGY In order to monitor the evolution of these variants in Morocco, we analyzed a total of 2130 genomes of the delta variant circulating around the world. We also included 164 Moroccan delta variant sequences in our analysis. RESULTS Our findings suggest at least four introductions from multiple international sources and a rise of a dominant delta sub-lineage AY.33 in Morocco. Moreover, we report three mutations in the N-terminal domain of the S protein specific to the Moroccan AY.33 isolates, T29A, T250I and T299I. The effect of these mutations on the secondary structure and the dynamic behavior of the S protein N-terminal domain was further determined. CONCLUSIONS We conclude that these mutations might have functional consequences on the S protein of SARS-CoV-2.
Collapse
Affiliation(s)
- Safae El Mazouri
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Houda Bendani
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Nasma Boumajdi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarik Aanniz
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Ilham Kandoussi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Mouna Ouadghiri
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco.
| |
Collapse
|
19
|
Bouricha EM, Hakmi M, Kartti S, Zouaidia F, Ibrahimi A. Mechanistic evidence from classical molecular dynamics and metadynamics revealed the mechanism of resistance to 4-hydroxy tamoxifen in estrogen receptor alpha Y537S mutant. Molecular Simulation 2022. [DOI: 10.1080/08927022.2022.2097283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- El Mehdi Bouricha
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Souad Kartti
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Fouad Zouaidia
- Department of pathology, Ibn Sina University Hospital Center, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| |
Collapse
|
20
|
Hakmi M, Bouricha EM, El Harti J, Amzazi S, Belyamani L, Khanfri JE, Ibrahimi A. Computational modeling and druggability assessment of Aggregatibacter actinomycetemcomitans leukotoxin. Comput Methods Programs Biomed 2022; 222:106952. [PMID: 35724475 DOI: 10.1016/j.cmpb.2022.106952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/30/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
The leukotoxin (LtxA) of Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) is a protein exotoxin belonging to the repeat-in-toxin family (RTX). Numerous studies have demonstrated that LtxA may play a critical role in the pathogenicity of A. actinomycetemcomitans since hyper-leukotoxic strains have been associated with severe disease. Accordingly, considerable effort has been made to elucidate the mechanisms by which LtxA interacts with host cells and induce their death. However, these attempts have been hampered by the unavailability of a tertiary structure of the toxin, which limits the understanding of its molecular properties and mechanisms. In this paper, we used homology and template free modeling algorithms to build the complete tertiary model of LtxA at atomic level in its calcium-bound Holo-state. The resulting model was refined by energy minimization, validated by Molprobity and ProSA tools, and subsequently subjected to a cumulative 600ns of all-atom classical molecular dynamics simulation to evaluate its structural aspects. The druggability of the proposed model was assessed using Fpocket and FTMap tools, resulting in the identification of four putative cavities and fifteen binding hotspots that could be targeted by rational drug design tools to find new ligands to inhibit LtxA activity.
Collapse
Affiliation(s)
- Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - El Mehdi Bouricha
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Jaouad El Harti
- Therapeutic Chemistry Laboratory, Medical Biotechnology Laboratory (MedBiotech), Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Said Amzazi
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Jamal Eddine Khanfri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco.
| |
Collapse
|
21
|
Ziani I, Ibrahimi A, Elsayegh H, Abouqal R, Nouini Y, Bouziane A. Facteurs pronostiques histologiques et biologiques de récidive et de progression des tumeurs de vessie non infiltrant le muscle vésical. Rev Epidemiol Sante Publique 2022. [DOI: 10.1016/j.respe.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
22
|
Guerrab W, Akachar J, Jemli ME, Abudunia AM, Ouaabou R, Alaoui K, Ibrahimi A, Ramli Y. Synthesis, molecular docking, ADMET evaluation and in vitro cytotoxic activity evaluation on RD and L20B cell lines of 3-substituted 5,5-diphenylimidazolidine-2,4-dione derivatives. J Biomol Struct Dyn 2022:1-9. [DOI: 10.1080/07391102.2022.2069865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Walid Guerrab
- Laboratory of Medicinal Chemistry, Drug Sciences Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Jihane Akachar
- Biotechnology Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University, Morocco
| | - Meryem El Jemli
- Laboratory of Pharmacology and Toxicology, Faculty of Medicine and Pharmacy, Mohammed V University, Morocco
| | - Abdul-Malik Abudunia
- Biotechnology Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University, Morocco
| | - Rachida Ouaabou
- LICVEDDE/ERIDDECV (Research Team of Innovation and Sustainable Development & Expertise in Green Chemistry), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh, Morocco
| | - Katim Alaoui
- Laboratory of Pharmacology and Toxicology, Faculty of Medicine and Pharmacy, Mohammed V University, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University, Morocco
| | - Youssef Ramli
- Laboratory of Medicinal Chemistry, Drug Sciences Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| |
Collapse
|
23
|
El Agouri H, Azizi M, El Attar H, El Khannoussi M, Ibrahimi A, Kabbaj R, Kadiri H, BekarSabein S, EchCharif S, Mounjid C, El Khannoussi B. Assessment of deep learning algorithms to predict histopathological diagnosis of breast cancer: first Moroccan prospective study on a private dataset. BMC Res Notes 2022; 15:66. [PMID: 35183227 PMCID: PMC8857730 DOI: 10.1186/s13104-022-05936-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 01/29/2022] [Indexed: 11/18/2022] Open
Abstract
Objective Breast cancer is a critical public health issue and a leading cause of cancer-related deaths among women worldwide. Its early diagnosis and detection can effectively help in increasing the chances of survival rate. For this reason, the diagnosis and classification of breast cancer using Deep learning algorithms have attracted a lot of attention. Therefore, our study aimed to design a computational approach based on deep convolutional neural networks for an efficient classification of breast cancer histopathological images by using our own created dataset. We collected overall 328 digital slides, from 116 of surgical breast specimens diagnosed with invasive breast carcinoma of non-specific type, and referred to the histopathology department of the National Institute of Oncology in Rabat, Morocco. We used two models of deep neural network architectures in order to accurately classify the images into one of three categories: normal tissue-benign lesions, in situ carcinoma or invasive carcinoma. Results Both Resnet50 and Xception models achieved comparable results, with a small advantage to Xception extracted features. We reported high degrees of overall correct classification accuracy (88%), and sensitivity (95%) for detection of carcinoma cases, which is important for diagnostic pathology workflow in order to assist pathologists for diagnosing breast cancer with precision. The results of the present study showed that the designed classification model has a good generalization performance in predicting diagnosis of breast cancer, in spite of the limited size of the data. To our knowledge, this approach can be highly compared with other common methods in the automated analysis of breast cancer images reported in literature.
Collapse
Affiliation(s)
- H El Agouri
- Pathology Department, Oncology National Institute, Faculty of Medicine and Pharmacy, Mohammed V University, 10100, Rabat, Morocco.
| | - M Azizi
- Datapathology, 20000, Casablanca, Morocco
| | - H El Attar
- Anatomic Pathology Laboratory Ennassr, 24000, El Jadida, Morocco
| | | | - A Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, 10100, Rabat, Morocco
| | - R Kabbaj
- Pathology Department, Oncology National Institute, Faculty of Medicine and Pharmacy, Mohammed V University, 10100, Rabat, Morocco
| | - H Kadiri
- Pathology Department, Oncology National Institute, Faculty of Medicine and Pharmacy, Mohammed V University, 10100, Rabat, Morocco
| | - S BekarSabein
- Pathology Department, Oncology National Institute, Faculty of Medicine and Pharmacy, Mohammed V University, 10100, Rabat, Morocco
| | - S EchCharif
- Pathology Department, Oncology National Institute, Faculty of Medicine and Pharmacy, Mohammed V University, 10100, Rabat, Morocco
| | - C Mounjid
- Pathology Department, Oncology National Institute, Faculty of Sciences, Mohammed V University, 10100, Rabat, Morocco
| | - B El Khannoussi
- Pathology Department, Oncology National Institute, Faculty of Medicine and Pharmacy, Mohammed V University, 10100, Rabat, Morocco
| |
Collapse
|
24
|
Chkirate K, Akachar J, Hni B, Hökelek T, Anouar EH, Talbaoui A, Mague JT, Sebbar NK, Ibrahimi A, Essassi EM. Synthesis, spectroscopic characterization, crystal structure, DFT, ESI-MS studies, molecular docking and in vitro antibacterial activity of 1,5-benzodiazepin-2-one derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
25
|
Essabbar A, Kartti S, Alouane T, Hakmi M, Belyamani L, Ibrahimi A. IDbSV: An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution. Front Med (Lausanne) 2021; 8:765249. [PMID: 34966754 PMCID: PMC8710592 DOI: 10.3389/fmed.2021.765249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Ending COVID-19 pandemic requires a collaborative understanding of SARS-CoV-2 and COVID-19 mechanisms. Yet, the evolving nature of coronaviruses results in a continuous emergence of new variants of the virus. Central to this is the need for a continuous monitoring system able to detect potentially harmful variants of the virus in real-time. In this manuscript, we present the International Database of SARS-CoV-2 Variations (IDbSV), the result of ongoing efforts in curating, analyzing, and sharing comprehensive interpretation of SARS-CoV-2's genetic variations and variants. Through user-friendly interactive data visualizations, we aim to provide a novel surveillance tool to the scientific and public health communities. The database is regularly updated with new records through a 4-step workflow (1—Quality control of curated sequences, 2—Call of variations, 3—Functional annotation, and 4—Metadata association). To the best of our knowledge, IDbSV provides access to the largest repository of SARS-CoV-2 variations and the largest analysis of SARS-CoV-2 genomes with over 60 thousand annotated variations curated from the 1,808,613 genomes alongside their functional annotations, first known appearance, and associated genetic lineages, enabling a robust interpretation tool for SARS-CoV-2 variations to help understanding SARS-CoV-2 dynamics across the world.
Collapse
Affiliation(s)
- Abdelmounim Essabbar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Souad Kartti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Tarek Alouane
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat, Morocco
| |
Collapse
|
26
|
Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, Martin DP, Rasmussen DA, Zekri ARN, Sangare AK, Ouedraogo AS, Sesay AK, Priscilla A, Kemi AS, Olubusuyi AM, Oluwapelumi AOO, Hammami A, Amuri AA, Sayed A, Ouma AEO, Elargoubi A, Ajayi NA, Victoria AF, Kazeem A, George A, Trotter AJ, Yahaya AA, Keita AK, Diallo A, Kone A, Souissi A, Chtourou A, Gutierrez AV, Page AJ, Vinze A, Iranzadeh A, Lambisia A, Ismail A, Rosemary A, Sylverken A, Femi A, Ibrahimi A, Marycelin B, Oderinde BS, Bolajoko B, Dhaala B, Herring BL, Njanpop-Lafourcade BM, Kleinhans B, McInnis B, Tegomoh B, Brook C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Peyrefitte C, Daubenberger C, Morang’a CM, Nokes DJ, Amoako DG, Bugembe DL, Park D, Baker D, Doolabh D, Ssemwanga D, Tshiabuila D, Bassirou D, Amuzu DSY, Goedhals D, Omuoyo DO, Maruapula D, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Shumba E, El Fahime E, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Leendertz F, Ajili F, Enoch FO, Wasfi F, Abdelmoula F, Mosha FS, Takawira FT, Derrar F, Bouzid F, Onikepe F, Adeola F, Muyembe FM, Tanser F, Dratibi FA, Mbunsu GK, Thilliez G, Kay GL, Githinji G, van Zyl G, Awandare GA, Schubert G, Maphalala GP, Ranaivoson HC, Lemriss H, Anise H, Abe H, Karray HH, Nansumba H, Elgahzaly HA, Gumbo H, Smeti I, Ayed IB, Odia I, Ben Boubaker IB, Gaaloul I, Gazy I, Mudau I, Ssewanyana I, Konstantinus I, Lekana-Douk JB, Makangara JCC, Tamfum JJM, Heraud JM, Shaffer JG, Giandhari J, Li J, Yasuda J, Mends JQ, Kiconco J, Morobe JM, Gyapong JO, Okolie JC, Kayiwa JT, Edwards JA, Gyamfi J, Farah J, Nakaseegu J, Ngoi JM, Namulondo J, Andeko JC, Lutwama JJ, O’Grady J, Siddle K, Adeyemi KT, Tumedi KA, Said KM, Hae-Young K, Duedu KO, Belyamani L, Fki-Berrajah L, Singh L, Martins LDO, Tyers L, Ramuth M, Mastouri M, Aouni M, el Hefnawi M, Matsheka MI, Kebabonye M, Diop M, Turki M, Paye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina M, Nwando M, Owusu M, Wiley MR, Youtchou MT, Ayekaba MO, Abouelhoda M, Seadawy MG, Khalifa MK, Sekhele M, Ouadghiri M, Diagne MM, Mwenda M, Allam M, Phan MVT, Abid N, Touil N, Rujeni N, Kharrat N, Ismael N, Dia N, Mabunda N, Hsiao NY, Silochi NB, Nsenga N, Gumede N, Mulder N, Ndodo N, Razanajatovo NH, Iguosadolo N, Judith O, Kingsley OC, Sylvanus O, Peter O, Femi O, Idowu O, Testimony O, Chukwuma OE, Ogah OE, Onwuamah CK, Cyril O, Faye O, Tomori O, Ondoa P, Combe P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Dussart P, Bester PA, Mbala PK, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Carr RAA, El Kabbaj S, Gargouri S, Masmoudi S, Sankhe S, Lawal SB, Kassim S, Trabelsi S, Metha S, Kammoun S, Lemriss S, Agwa SHA, Calvignac-Spencer S, Schaffner SF, Doumbia S, Mandanda SM, Aryeetey S, Ahmed SS, Elhamoumi S, Andriamandimby S, Tope S, Lekana-Douki S, Prosolek S, Ouangraoua S, Mundeke SA, Rudder S, Panji S, Pillay S, Engelbrecht S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Aanniz T, Mohale T, Le-Viet T, Schindler T, Anyaneji UJ, Chinedu U, Ramphal U, Jessica U, George U, Fonseca V, Enouf V, Gorova V, Roshdy WH, Ampofo WK, Preiser W, Choga WT, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Sall AA, Rebai A, von Gottberg A, Kouriba B, Williamson C, Bridges DJ, Chikwe I, Bhiman JN, Mine M, Cotten M, Moyo S, Gaseitsiwe S, Saasa N, Sabeti PC, Kaleebu P, Tebeje YK, Tessema SK, Happi C, Nkengasong J, de Oliveira T. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science 2021; 374:423-431. [PMID: 34672751 PMCID: PMC7613315 DOI: 10.1126/science.abj4336] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/03/2021] [Indexed: 01/05/2023]
Abstract
The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.
Collapse
Affiliation(s)
- Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diego Cuadros
- Department of Geography and GIS, University of Cincinnati, Cincinnati, OH, USA
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - David A. Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Abdel-Rahman N. Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Abdoul K. Sangare
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Abdoul-Salam Ouedraogo
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | - Abechi Priscilla
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Adedotun-Sulaiman Kemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Adeyemi O. O. Oluwapelumi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Adnène Hammami
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Adrienne A. Amuri
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Ahmad Sayed
- Genomics Research Program, Children’s Cancer Hospital, Cairo, Egypt
| | - Ahmed E. O. Ouma
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Aida Elargoubi
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Nnennaya A. Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ajogbasile F. Victoria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Akano Kazeem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Ali A. Yahaya
- World Health Organization, Africa Region, Brazzaville Congo
| | - Alpha K. Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Montpellier University/IRD/INSERM, Montpellier, France
| | - Amadou Diallo
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Kone
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amel Chtourou
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | | | - Anika Vinze
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Arash Iranzadeh
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arnold Lambisia
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Audu Rosemary
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ayoade Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Baba Marycelin
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bamidele S. Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bankole Bolajoko
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | | | - Bronwyn Kleinhans
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Bronwyn McInnis
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Bryan Tegomoh
- The Biotechnology Center of the University of Yaoundé I, Cameroon and CDC Foundation, Yaounde, Cameroon
| | - Cara Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal G. Akoua-Koffi
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | - Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | | | | | - Collins M. Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - D. James Nokes
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Danny Park
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | | | - Deelan Doolabh
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Deogratius Ssemwanga
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diarra Bassirou
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Dominic S. Y. Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Dominique Goedhals
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | | | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | | | - Eddy K. Lusamaki
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edgar Simulundu
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | - Edith N. Ngabana
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edwin Shumba
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Elmostafa El Fahime
- Functional Genomic Platform/National Centre for Scientific and Technical Research (CNRST), Rabat, Morocco
| | - Emmanuel Lokilo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
| | | | - Eromon Philomena
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Etilé A. Anoh
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | | | - Faida Ajili
- Research Unit of Autoimmune Diseases UR17DN02, Military Hospital of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Fakayode O. Enoch
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
| | - Fares Wasfi
- Laboratory of Clinical Virology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Fatma Abdelmoula
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | | | | | - Fawzi Derrar
- National Influenza Centre, Viral Respiratory Laboratory, Algiers, Algeria
| | - Feriel Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Folarin Onikepe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Fowotade Adeola
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Francisca M. Muyembe
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Frank Tanser
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | | | - Gabriel K. Mbunsu
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | - George Githinji
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Gugu P. Maphalala
- Institution and Department, Ministry Of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
| | | | - Hajar Lemriss
- Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco
| | - Happi Anise
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hela H. Karray
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | - Hesham A. Elgahzaly
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Ibtihel Smeti
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ikhlas B. Ayed
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Ilhem Boutiba Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, 1006 Tunis, Tunisia
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Imed Gaaloul
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Inbal Gazy
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Innocent Mudau
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Jean B. Lekana-Douk
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | - Jean-Claude C. Makangara
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Jacques M. Tamfum
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Michel Heraud
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jingjing Li
- Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Joana Q. Mends
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | - John M. Morobe
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - John O. Gyapong
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Johnson C. Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John T. Kayiwa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Johnathan A. Edwards
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jones Gyamfi
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | | | - Joyce M. Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Julia C. Andeko
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | - Kayode T. Adeyemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Kefentse A. Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
| | - Khadija M. Said
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Kim Hae-Young
- New York University Grossman School of Medicine, New York City, NY, USA
| | - Kwabena O. Duedu
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Lahcen Belyamani
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Lamia Fki-Berrajah
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Lynn Tyers
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Magalutcheemee Ramuth
- Virology/Molecular Biology Department, Central Health Laboratory, Ministry of Health and Wellness, Mauritius
| | - Maha Mastouri
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Mahjoub Aouni
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Mahmoud el Hefnawi
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo Egypt
| | | | | | - Mamadou Diop
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Manel Turki
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Marietou Paye
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | | | - Matoke-Muhia Damaris
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Maureen W. Mburu
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Maximillian Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Institute, Dar-es-Salaam, Tanzania
| | - Mba Nwando
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Michael Owusu
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Mirabeau T. Youtchou
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
| | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Mohamed G. Seadawy
- Biological Prevention Department, Main Chemical Laboratories, Egypt Army, Cairo, Egypt
| | | | - Mooko Sekhele
- National Reference Laboratory Lesotho, Maseru, Lesotho
| | - Mouna Ouadghiri
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | | | | | - Mushal Allam
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - My V. T. Phan
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
| | - Nadia Touil
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Najla Kharrat
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Nalia Ismael
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nedio Mabunda
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Nei-yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Ngoy Nsenga
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicksy Gumede
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | | | | | - Nosamiefan Iguosadolo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Oguzie Judith
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ojide C. Kingsley
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | - Oladiji Femi
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olawoye Idowu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Olumade Testimony
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Omoruyi E. Chukwuma
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Onwe E. Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Chika K. Onwuamah
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | | | - Paul E. Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Paulo Arnaldo
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Peter K. Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Phillip A. Bester
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | - Placide K. Mbala
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Reuben Ayivor-Djanie
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Richard Njouom
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
| | - Richard O. Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Rosina A. A. Carr
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Saâd El Kabbaj
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Saba Gargouri
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Salako B. Lawal
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Samar Kassim
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Sameh Trabelsi
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
| | - Samar Metha
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Sami Kammoun
- CHU Hedi Chaker Sfax, Service de Pneumologie, Tunis, Tunisia
| | - Sanaâ Lemriss
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Sara H. A. Agwa
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | | | | | - Seydou Doumbia
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Sheila M. Mandanda
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | - Sobajo Tope
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Sonia Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Soumeya Ouangraoua
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
| | - Steve A. Mundeke
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Susan Nabadda
- Central Public Health Laboratories (CPHL), Kampala, Uganda
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Tarik Aanniz
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugwu Chinedu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
| | - Uwanibe Jessica
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Uwem George
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | - Vivianne Gorova
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
| | | | - William K. Ampofo
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yvan Butera
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Bourema Kouriba
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | - Carolyn Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | | | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Matthew Cotten
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ngonda Saasa
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | | | - Yenew K. Tebeje
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John Nkengasong
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| |
Collapse
|
27
|
Ramzan M, Philippe C, Belyantseva IA, Nakano Y, Fenollar-Ferrer C, Tona R, Yousaf R, Basheer R, Imtiaz A, Faridi R, Munir Z, Idrees H, Salman M, Nambot S, Vitobello A, Kartti S, Zarrik O, Witmer PD, Sobreria N, Ibrahimi A, Banfi B, Moutton S, Friedman TB, Naz S. Variants of human CLDN9 cause mild to profound hearing loss. Hum Mutat 2021; 42:1321-1335. [PMID: 34265170 DOI: 10.1002/humu.24260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 05/18/2021] [Accepted: 07/13/2021] [Indexed: 02/05/2023]
Abstract
Hereditary deafness is clinically and genetically heterogeneous. We investigated deafness segregating as a recessive trait in two families. Audiological examinations revealed an asymmetric mild to profound hearing loss with childhood or adolescent onset. Exome sequencing of probands identified a homozygous c.475G>A;p.(Glu159Lys) variant of CLDN9 (NM_020982.4) in one family and a homozygous c.370_372dupATC;p.(Ile124dup) CLDN9 variant in an affected individual of a second family. Claudin 9 (CLDN9) is an integral membrane protein and constituent of epithelial bicellular tight junctions (TJs) that form semipermeable, paracellular barriers between inner ear perilymphatic and endolymphatic compartments. Computational structural modeling predicts that substitution of a lysine for glutamic acid p.(Glu159Lys) alters one of two cis-interactions between CLDN9 protomers. The p.(Ile124dup) variant is predicted to locally misfold CLDN9 and mCherry tagged p.(Ile124dup) CLDN9 is not targeted to the HeLa cell membrane. In situ hybridization shows that mouse Cldn9 expression increases from embryonic to postnatal development and persists in adult inner ears coinciding with prominent CLDN9 immunoreactivity in TJs of epithelia outlining the scala media. Together with the Cldn9 deaf mouse and a homozygous frameshift of CLDN9 previously associated with deafness, the two bi-allelic variants of CLDN9 described here point to CLDN9 as a bona fide human deafness gene.
Collapse
Affiliation(s)
- Memoona Ramzan
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam campus, Lahore, Pakistan.,Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Christophe Philippe
- UF Innovation en Diagnostic Genomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France.,INSERM UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, Dijon, France
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Yoko Nakano
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, USA.,Inflammation Program, University of Iowa, Iowa City, Iowa, USA
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA.,Laboratory of Molecular & Cellular Neurobiology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Risa Tona
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Rizwan Yousaf
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Rasheeda Basheer
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam campus, Lahore, Pakistan
| | - Ayesha Imtiaz
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Zunaira Munir
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam campus, Lahore, Pakistan
| | - Hafiza Idrees
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam campus, Lahore, Pakistan
| | - Midhat Salman
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam campus, Lahore, Pakistan
| | - Sophie Nambot
- INSERM UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, Dijon, France.,Department of Medical Genetics, Reference Center for Developmental Anomalies, Dijon University Hospital, Dijon, France
| | - Antonio Vitobello
- UF Innovation en Diagnostic Genomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France.,INSERM UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, Dijon, France
| | - Souad Kartti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Oumaima Zarrik
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - P Dane Witmer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Johns Hopkins Genomics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nara Sobreria
- Johns Hopkins Genomics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Botond Banfi
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, USA.,Inflammation Program, University of Iowa, Iowa City, Iowa, USA.,Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Sebastien Moutton
- INSERM UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, Dijon, France.,Department of Medical Genetics, Reference Center for Developmental Anomalies, Dijon University Hospital, Dijon, France
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam campus, Lahore, Pakistan
| |
Collapse
|
28
|
Ziani I, Lahlou L, Ibrahimi A, El Sayegh H, Benslimane L, Nouini Y. Étude de survie dans les tumeurs de vessie infiltrant le muscle vésical chez une population marocaine en 2020. Rev Epidemiol Sante Publique 2021. [DOI: 10.1016/j.respe.2021.04.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
|
29
|
Elhourch S, Arrouchi H, Mekkaoui N, Allou Y, Ghrifi F, Allam L, Elhafidi N, Belyamani L, Ibrahimi A, Elomri N, Eljaoudi R. Significant Association of Polymorphisms in the TCF7L2 Gene with a Higher Risk of Type 2 Diabetes in a Moroccan Population. J Pers Med 2021; 11:jpm11060461. [PMID: 34073870 PMCID: PMC8225140 DOI: 10.3390/jpm11060461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/06/2022] Open
Abstract
Background and aims: Several studies have shown that genetic polymorphisms of the transcription factor 7-like 2 (TCF7L2) are highly associated with the development of type 2 diabetes mellitus (T2DM) and its associated complications in several populations. The aim of our study was to investigate the association of the rs7903146 (C/T) and rs12255372 (G/T) polymorphism in the TCF7L2 gene with the risk of developing T2DM in the Moroccan population. Material and methods: A total of 150 T2DM patients and 100 healthy controls were recruited for various anthropometric, biochemical and genetic parameters. Genotyping was performed by using Real Time-PCR. The frequency of genotypes, alleles, anthropometric measures, glycemia, glycated hemoglobin (HbA1c) were evaluated in patients and control, while lipid profile was available only for T2DM group. Results: Glycemia, HbA1c and body mass index (BMI) were significantly higher in T2DM group than control. Analysis of the distribution of the TCF7L2 rs7903146 genotype and allele revealed that the TT genotype was more frequent in T2DM group (24.0%) than in healthy controls (5%) (OR = 4.08, 95% confidence interval (CI = 1.95–11.80, p < 0.0001). The T allele was more frequent in diabetic patients (45.2%) than healthy control (34.5%) and it was associated with high risk of diabetes (OR = 2.13, 95% CI = 1.12–7.31, p = 0.005). The same results were found regarding rs12255372, TT genotype frequencies were 18,7% and 6.0% in T2DM and control group, respectively (OR = 3.11, 95% CI = 1.33–7.24, p = 0.004). The T allele was over-presented in diabetics compared to controls (45.3% and 38.0%, respectively) and increases the risk of T2DM (OR = 2.01, 95% CI = 1.04–3.10, p = 0.01). However, there was no significant difference between the three genotypes of rs7903146 and rs12255372 regarding age, BMI, glycemia, HbA1c and lipid profile. Conclusion: The present study confirmed a significant association of the TCF7L2 gene (rs7903146 (C/T) and rs12255372 (G/T) polymorphisms with a higher risk to T2DM in the Moroccan population. No significant difference in respect to anthropometric and metabolic parameters between different genotypes.
Collapse
Affiliation(s)
- Sarah Elhourch
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, 10000 Rabat, Morocco; (S.E.); (H.A.); (Y.A.); (F.G.); (L.A.); (N.E.); (A.I.)
| | - Housna Arrouchi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, 10000 Rabat, Morocco; (S.E.); (H.A.); (Y.A.); (F.G.); (L.A.); (N.E.); (A.I.)
| | - Nour Mekkaoui
- Clinical Research and Epidemiology Biostatistics Laboratory, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, 10000 Rabat, Morocco;
| | - Younes Allou
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, 10000 Rabat, Morocco; (S.E.); (H.A.); (Y.A.); (F.G.); (L.A.); (N.E.); (A.I.)
| | - Fatima Ghrifi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, 10000 Rabat, Morocco; (S.E.); (H.A.); (Y.A.); (F.G.); (L.A.); (N.E.); (A.I.)
| | - Loubna Allam
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, 10000 Rabat, Morocco; (S.E.); (H.A.); (Y.A.); (F.G.); (L.A.); (N.E.); (A.I.)
| | - Naima Elhafidi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, 10000 Rabat, Morocco; (S.E.); (H.A.); (Y.A.); (F.G.); (L.A.); (N.E.); (A.I.)
- Immuno-Allergology Unit Children’s Hospital, 10000 Rabat, Morocco
| | - Lahcen Belyamani
- Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, 10000 Rabat, Morocco; (L.B.); (N.E.)
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, 10000 Rabat, Morocco; (S.E.); (H.A.); (Y.A.); (F.G.); (L.A.); (N.E.); (A.I.)
| | - Naoual Elomri
- Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, 10000 Rabat, Morocco; (L.B.); (N.E.)
| | - Rachid Eljaoudi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, 10000 Rabat, Morocco; (S.E.); (H.A.); (Y.A.); (F.G.); (L.A.); (N.E.); (A.I.)
- Correspondence:
| |
Collapse
|
30
|
Guerrab W, El Jemli M, Akachar J, Demirtaş G, Mague JT, Taoufik J, Ibrahimi A, Ansar M, Alaoui K, Ramli Y. Design, synthesis, structural and molecular characterization, toxicity, psychotropic activity and molecular docking evaluation of a novel phenytoin derivative: 3-decyl-5,5-diphenylimidazolidine-2,4-dione. J Biomol Struct Dyn 2021; 40:8765-8782. [PMID: 33970810 DOI: 10.1080/07391102.2021.1922096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The hydantoin scaffold is of substantial importance and it is commonly used in drug discovery. Herein, we report the synthesis of a novel phenytoine (a hydantoin derivative) with high yield by the reaction of phenytoin with 1-bromodecyl agent. Namely, 3-decyl-5,5- diphenylimidazolidine-2,4-dione (3DDID). The optimized geometry of the compound was calculated using density functional theory (DFT) method by B3LYP with 6-311++G(d,p) basis set. For this calculation, the X-ray data were used as initial values. Molecular electrostatic potential (MEP) surface and Frontier molecular orbitals (FOMs) were prepared for the compound. The crystal structure of the title compound contains intermolecular N-H···O, C-H···O hydrogen bonds and weak C-H···π interactions. Hirshfeld surface analysis and 2D fingerprint plots of the molecule aid comparison of intermolecular interactions and these analysis reveals that two close contacts are associated with intermolecular hydrogen bonds. The psychotropic activity evaluation of the synthesized compound was further explored using hole bored test for exploratory behaviors, dark//light box test for anxiolytic activity and Rota-road, traction, chimney testes were used to assess the myrelaxant effect. In addition, molecular modeling study was also conducted to rationalize the potential as neurotherapeutic drugs of our synthesized compound by predicting their binding modes, binding affinities and optimal orientation at the active site of the GABA-A receptor and Na+ channel. Finally, in silico ADMET predictions was also examined. HighlightsSynthesis, structural, and molecular characterization of a novel phenytoin derivative.DFT, XRD, and the Hirshfeld surface analysis of crystal structure was studied.Acute toxicity and psychotropic activity evaluation of 3-decyl-5,5 diphenylimidazolidine-2,4-dione (3DDID).Molecular modeling studies have been conducted to rationalize the obtained data and to determine the probable binding mode.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Walid Guerrab
- Laboratory of Medicinal Chemistry, Drug Sciences Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Meryem El Jemli
- Laboratory of Pharmacology and Toxicology, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Jihane Akachar
- Laboratoire of Biotechnologie, Faculté de Médecine et de Pharmacie de rabat, Université Mohamed V, Rabat, Morocco
| | - Güneş Demirtaş
- Faculty of Arts and Sciences, Department of Physics, Ondokuz Mayıs University, Samsun, Turkey
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Jamal Taoufik
- Laboratory of Medicinal Chemistry, Drug Sciences Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Azeddine Ibrahimi
- Laboratoire of Biotechnologie, Faculté de Médecine et de Pharmacie de rabat, Université Mohamed V, Rabat, Morocco
| | - M'Hammed Ansar
- Laboratory of Medicinal Chemistry, Drug Sciences Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Katim Alaoui
- Laboratory of Pharmacology and Toxicology, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Youssef Ramli
- Laboratory of Medicinal Chemistry, Drug Sciences Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| |
Collapse
|
31
|
Ouadghiri M, Aanniz T, Essabbar A, Seffar M, Kabbaj H, El Amin G, Zouaki A, Amzazi S, Belyamani L, Ibrahimi A. Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. Microbiol Resour Announc 2021; 10:e00240-21. [PMID: 33888505 PMCID: PMC8063648 DOI: 10.1128/mra.00240-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/30/2021] [Indexed: 11/21/2022] Open
Abstract
Here, we report the near-complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring the N501Y mutation assigned to the B.1.1.7 lineage. The sample was collected from a nasopharyngeal swab of a female patient from Temara, Morocco, and the sequencing was done using Ion S5 technology.
Collapse
Affiliation(s)
- Mouna Ouadghiri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarik Aanniz
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelomunim Essabbar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Myriam Seffar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Hakima Kabbaj
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Ghizlane El Amin
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Amal Zouaki
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| |
Collapse
|
32
|
Bouricha EM, Hakmi M, Akachar J, Zouaidia F, Ibrahimi A. In-silico identification of potential inhibitors targeting the DNA binding domain of estrogen receptor α for the treatment of hormone therapy-resistant breast cancer. J Biomol Struct Dyn 2021; 40:5203-5210. [PMID: 33402049 DOI: 10.1080/07391102.2020.1869094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Estrogen receptor α (ERα) plays a critical role in breast cancer (BC) development. The standard therapeutic strategies for ERα- positive (ERα+) BC consist of impairing ERα signalling pathway by either estrogen competitors blocking its interaction with the ligand binding domain (LBD) or agents inhibiting the production of estrogen. These strategies are limited by many factors that lead to constitutive activation of ERα and consequently, resistance to treatment. Targeting the DNA binding domain (DBD) of ERα instead of its LBD with small-molecule inhibitors could be an alternative to impair ERα's signalling pathway. For this purpose, we conducted a structure based virtual screening of DrugBank against the crystal structure of ERα-DBD (PDB ID: 1HCQ) using the Glide module in standard precision (SP) and extra precision (XP) mode of docking. Molecules with XP Gscore less than -8 kcal/mol were selected and visually inspected to keep only the reasonable docking poses. Subsequently, these molecules were clustered using structural interaction fingerprints analysis and the complexes of the top ranked molecules of each cluster based on XP Gscore were subjected to 200 ns molecular dynamics simulations followed by MM-GBSA binding free energy calculation for the last 100 ns of each complex. In this study, we identified three molecules from DrugBank namely DB03450, DB02593 and DB08001 showing significant stability and strong interaction with the key amino acids during MD simulation suggesting a potential inhibition of the target. These molecules could be used as promising lead compounds to impair the ERα signalisation in hormone therapy-resistant breast cancer.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- El Mehdi Bouricha
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Jihane Akachar
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Fouad Zouaidia
- Department of pathology, Ibn Sina University Hospital Center, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| |
Collapse
|
33
|
Rezzouk B, Bouattar T, Belkadi B, Razine R, Bayahia R, Ouzeddoun N, Benamar L, Rhou H, Bouihat N, Ibrahimi A, Seffar M, Kabbaj H. Characteristics and Outcomes of Cytomegalovirus Infection in Seropositive Kidney Transplant Recipients in the Era of Antiviral Prophylaxis with Valacyclovir: A Single-Center Study in Morocco. TRRM 2021. [DOI: 10.2147/trrm.s278655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
|
34
|
Sarah EH, El Omri N, Ibrahimi A, El Jaoudi R. Metabolic and genetic studies of glimepiride and metformin and their association with type 2 diabetes. Gene Reports 2020. [DOI: 10.1016/j.genrep.2020.100787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
35
|
Akachar J, Bouricha EM, Hakmi M, Belyamani L, El Jaoudi R, Ibrahimi A. Identifying epitopes for cluster of differentiation and design of new peptides inhibitors against human SARS-CoV-2 spike RBD by an in-silico approach. Heliyon 2020; 6:e05739. [PMID: 33364503 PMCID: PMC7753134 DOI: 10.1016/j.heliyon.2020.e05739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/27/2020] [Accepted: 12/11/2020] [Indexed: 12/23/2022] Open
Abstract
The coronavirus disease 19 (COVID-19) is a highly contagious and rapidly spreading infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some cases, the disease can be fatal which resulted in more than one million deaths worldwide according the WHO. Currently, there is no effective vaccine or treatment for COVID-19, however many small-molecule inhibitors have shown potent antiviral activity against SARS-CoV-2 and some of them are now under clinical trials. Despite their promising activities, the development of these small molecules for the clinical use can be limited by many factors like the off-target effect, the poor stability, and the low bioavailability. The clusters of differentiation CD147, CD209, CD299 have been identified as essential entry co-receptors for SARS-CoV-2 species specificity to humans, although the underlying mechanisms are yet to be fully elucidated. In this paper, protein-protein docking was utilized for identifying the critical epitopes in CD147, CD209 and CD299 which are involved in the binding with SARS-CoV-2 Spike receptor binding domain (RBD). The results of binding free energies showed a high affinity of SARS-CoV-2 RBD to CD299 receptor which was used as a reference to derive hypothetical peptide sequences with specific binding activities to SARS-CoV-2 RBD. Molecular docking and molecular dynamics simulations of the newly designed peptides showed favorable binding features and stability with SARS-CoV-2 RBD and therefore can be further considered as potential candidates in future anti-SARS CoV-2 drug discovery studies.
Collapse
Affiliation(s)
- Jihane Akachar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - El Mehdi Bouricha
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Rachid El Jaoudi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| |
Collapse
|
36
|
Laamarti M, Alouane T, Kartti S, Chemao-Elfihri MW, Hakmi M, Essabbar A, Laamarti M, Hlali H, Bendani H, Boumajdi N, Benhrif O, Allam L, El Hafidi N, El Jaoudi R, Allali I, Marchoudi N, Fekkak J, Benrahma H, Nejjari C, Amzazi S, Belyamani L, Ibrahimi A. Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. PLoS One 2020; 15:e0240345. [PMID: 33170902 PMCID: PMC7654798 DOI: 10.1371/journal.pone.0240345] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/24/2020] [Indexed: 12/17/2022] Open
Abstract
In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variants sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 68 recurrent mutations, including ten hotspot non-synonymous mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed that certain genotypes are specific to geographic locations. We also identified co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets. We have also created an inclusive unified database (http://covid-19.medbiotech.ma) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.
Collapse
Affiliation(s)
- Meriem Laamarti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Tarek Alouane
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Souad Kartti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - M. W. Chemao-Elfihri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Abdelomunim Essabbar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Mohamed Laamarti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Haitam Hlali
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Houda Bendani
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Nassma Boumajdi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Oussama Benhrif
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Loubna Allam
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Naima El Hafidi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Rachid El Jaoudi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Imane Allali
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | | | - Jamal Fekkak
- Anoual Laboratory of Radio-Immuno Analysis, Casablanca, Morocco
| | - Houda Benrahma
- Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Chakib Nejjari
- International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Saaid Amzazi
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| |
Collapse
|
37
|
Bendahou MA, Ibrahimi A, Boutarbouch M. Bioinformatics Analysis of Differentially Expressed Genes and miRNAs in Low-Grade Gliomas. Cancer Inform 2020; 19:1176935120969692. [PMID: 33223819 PMCID: PMC7649870 DOI: 10.1177/1176935120969692] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/01/2020] [Indexed: 12/28/2022] Open
Abstract
Low-grade glioma is the most common type of primary intracranial tumor. In the last 3 years, new observations of molecular precursors in adults with gliomas have led to a modification in the histopathologic classification of these brain tumors. Among the biomarkers that have been highlighted, we have the micro RNAs (miRNAs) which play a crucial role in the regulation of gene expression and the long noncoding RNAs (lncRNAs) controlling various cellular and metabolic pathways. In our study, large-scale data on sequenced RNA and miRNAs from 516 patients were obtained from the Cancer Genome Atlas database by the TCGAbiolinks package. We identified the differential expression of miRNAs and genes using the Limma package and then we used the ClusterProfiler package for annotations of the biological pathways of the expressed genes, the survival package to estimate the survival analysis, and the GDCRNATools package to determine miRNAs-genes and miRNAs-lncRNAs interactions. We obtained a significant correlation between the miRNAs identified and the overall survival of the patients (log-rank P < .05) and we have theoretically proposed a novel network of miRNAs involved in low-grade gliomas, specifically astrocytomas and oligodendrogliomas, which combine both genes and lncRNAs.
Collapse
Affiliation(s)
- Mohammed Amine Bendahou
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University in Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University in Rabat, Morocco
| | - Mahjouba Boutarbouch
- Department of Neurosurgery, Hospital of Specialties, CHU Ibn Sina, Rabat, Medical and Pharmacy School, Mohammed V University in Rabat, Morocco
| |
Collapse
|
38
|
Bouricha EM, Hakmi M, Akachar J, Belyamani L, Ibrahimi A. In silico analysis of ACE2 orthologues to predict animal host range with high susceptibility to SARS-CoV-2. 3 Biotech 2020; 10:483. [PMID: 33101829 PMCID: PMC7577366 DOI: 10.1007/s13205-020-02471-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/07/2020] [Indexed: 11/01/2022] Open
Abstract
SARS-CoV-2, which causes severe pneumonia epidemics, probably originated from Chinese horseshoe bats, but the intermediate and host range is still unknown. ACE2 is the entry receptor for SARS-CoV-2. The binding capacity of SARS-CoV-2 spike protein to ACE2 is the critical determinant of viral host range and cross-species infection. Here, we used an in silico approach to predict the potential animals range with high susceptibility to SARS-CoV-2 by modelling and studying the Spike-ACE2 interaction of 22 domestic and wild animals. Our results showed that all studied animals are potentially susceptible to SARS-CoV-2 infection with a slight difference in the binding affinity and stability of their ACE2-RBD complexes. Furthermore, we identified a specific substitution of tyrosine to histidine at position 41 in ACE2 that likely reduces the affinity to SARS-CoV-2 in horses and greater horseshoe bats. These results may help to provide important insights into SARS-CoV-2 host range which will make it possible to control the spread of the virus and identify animal models that could be used for screening antiviral drugs or vaccine candidates against SARS-CoV-2.
Collapse
Affiliation(s)
- El Mehdi Bouricha
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical and Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical and Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Jihane Akachar
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical and Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical and Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| |
Collapse
|
39
|
Ziani I, Boualaloui I, Bouziane A, Ibrahimi A, El Sayegh H, Benslimane L, Nouini Y. La lymphocytopénie pré-traitement peut-elle être un facteur prédictif de l’échec de l’immunothérapie intravésicale par BCG dans les tumeurs de vessie non infiltrantes ? Prog Urol 2020. [DOI: 10.1016/j.purol.2020.07.168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
40
|
Allam L, Arrouchi H, Ghrifi F, El Khazraji A, Kandoussi I, Bendahou MA, El Amri H, El Absi M, Ibrahimi A. AKT1 Polymorphism (rs10138227) and Risk of Colorectal Cancer in Moroccan Population: A Case Control Study. Asian Pac J Cancer Prev 2020; 21:3165-3170. [PMID: 33247671 PMCID: PMC8033122 DOI: 10.31557/apjcp.2020.21.11.3165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND LMTK3 and AKT1 each have a role in carcinogenesis and tumor progression. The analysis of single nucleotide polymorphisms of AKT1 and LMTK3 could lead to more complete and accurate risk estimates for colorectal cancer. AIM We evaluated the association between single nucleotide polymorphisms (SNPs) of AKT1 and LMTK3 and the risk of colorectal cancer in a case-control study in Moroccan population. METHODS Genomic DNA from 70 colorectal cancer patients and 50 healthy control subjects was extracted from whole blood. Genotyping was performed by direct sequencing after polymerase chain reactions for the 7 SNPs (AKT1rs1130214G/T, AKT1rs10138227C/T, AKT1rs3730358C/T, AKT1rs1000559097G/A, AKT1rs2494737A/T, LMTK3rs8108419G/A, and LMTK3rs9989661A/G.). Study subjects provided detailed information during the collection. All P values come from bilateral tests. RESULTS In the logistic regression analysis, a significantly high risk of colorectal cancer was associated with TC/TT genotypes of rs10138227 with adjusted odds ratio [OR] equal to 2.82 and 95% confidence interval [CI] of 1.15 to 6.91. CONCLUSION Our results suggest that the SNP AKT1rs10138227 could affect susceptibility to CRC, probably by modulating the transcriptional activity of AKT1. However, larger independent studies are needed to validate our results.
Collapse
Affiliation(s)
- Loubna Allam
- Laboratoire De Biotechnologie (MedBiotech), Faculté De Medecine Et De Pharmacie De Rabat, Université Mohamed V De Rabat, Rabat, Maroc, Morocco.,Instituts Des Analyses Génétique De La Gendarmerie Royale De Rabat, Maroc, Morocco
| | - Housna Arrouchi
- Laboratoire De Biotechnologie (MedBiotech), Faculté De Medecine Et De Pharmacie De Rabat, Université Mohamed V De Rabat, Rabat, Maroc, Morocco
| | - Fatima Ghrifi
- Laboratoire De Biotechnologie (MedBiotech), Faculté De Medecine Et De Pharmacie De Rabat, Université Mohamed V De Rabat, Rabat, Maroc, Morocco
| | - Abdelhak El Khazraji
- Laboratoire De Biotechnologie (MedBiotech), Faculté De Medecine Et De Pharmacie De Rabat, Université Mohamed V De Rabat, Rabat, Maroc, Morocco
| | - Ilham Kandoussi
- Laboratoire De Biotechnologie (MedBiotech), Faculté De Medecine Et De Pharmacie De Rabat, Université Mohamed V De Rabat, Rabat, Maroc, Morocco
| | - Mohammed Amine Bendahou
- Biotechnology Laboratory (Medbiotech), Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morroco
| | - Hamid El Amri
- Instituts Des Analyses Génétique De La Gendarmerie Royale De Rabat, Maroc, Morocco
| | - Mohamed El Absi
- Faculté De Medecine Et De Pharmacie De Rabat, Université Mohamed V Rabat, Rabaat Maroc, Morocco
| | - Azeddine Ibrahimi
- Laboratoire De Biotechnologie (MedBiotech), Faculté De Medecine Et De Pharmacie De Rabat, Université Mohamed V De Rabat, Rabat, Maroc, Morocco
| |
Collapse
|
41
|
Allam L, Ghrifi F, Mohammed H, El Hafidi N, El Jaoudi R, El Harti J, Lmimouni B, Belyamani L, Ibrahimi A. Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules. Bioinform Biol Insights 2020; 14:1177932220965505. [PMID: 33149560 PMCID: PMC7585878 DOI: 10.1177/1177932220965505] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/19/2020] [Indexed: 12/28/2022] Open
Abstract
The global burden of infections and the rapid spread of viral diseases show the need for new approaches in the prevention and development of effective therapies. To this end, we aimed to explore novel inhibitor compounds that can stop replication or decrease the viral load of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which there is currently no approved treatment. Besides using the angiotensin-converting enzyme (ACE2) receptor as a main gate, the CoV-2 can bind to the glucose-regulating protein 78 (GRP78) receptor to get into the cells to start an infection. Here, we report potential inhibitors comprising small molecules and peptides that could interfere with the interaction of SARS-CoV-2 and its target cells by blocking the recognition of the GRP78 cellular receptor by the viral Spike protein. These inhibitors were discovered through an approach of in silico screening of available databases of bioactive peptides and polyphenolic compounds and the analysis of their docking modes. This process led to the selection of 9 compounds with optimal binding affinities to the target sites. The peptides (satpdb18674, satpdb18446, satpdb12488, satpdb14438, and satpdb28899) act on regions III and IV of the viral Spike protein and on its binding sites in GRP78. However, 4 polyphenols such as epigallocatechin gallate (EGCG), homoeriodictyol, isorhamnetin, and curcumin interact, in addition to the Spike protein and its binding sites in GRP78, with the ATPase domain of GRP78. Our work demonstrates that there are at least 2 approaches to block the spread of SARS-CoV-2 by preventing its fusion with the host cells via GRP78.
Collapse
Affiliation(s)
- Loubna Allam
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Fatima Ghrifi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Hakmi Mohammed
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Naima El Hafidi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Rachid El Jaoudi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Jaouad El Harti
- Therapeutic Chemistry Laboratory, Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Badreddine Lmimouni
- Parasitology and Mycology Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| |
Collapse
|
42
|
Alouane T, Laamarti M, Essabbar A, Hakmi M, Bouricha EM, Chemao-Elfihri MW, Kartti S, Boumajdi N, Bendani H, Laamarti R, Ghrifi F, Allam L, Aanniz T, Ouadghiri M, El Hafidi N, El Jaoudi R, Benrahma H, Attar JE, Mentag R, Sbabou L, Nejjari C, Amzazi S, Belyamani L, Ibrahimi A. Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the "Confined Virus"? Pathogens 2020; 9:E829. [PMID: 33050463 PMCID: PMC7600297 DOI: 10.3390/pathogens9100829] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from 24 December 2019, to 13 May 2020, according to the GISAID database. Our analysis revealed the presence of 3206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (>10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein, and one in each of three proteins: Spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the receptor-binding domain (RBD) of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with intra-genomic divergence of SARS-CoV-2 could indicate that unlike the influenza virus or HIV viruses, SARS-CoV-2 has a low mutation rate which makes the development of an effective global vaccine very likely.
Collapse
Affiliation(s)
- Tarek Alouane
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Meriem Laamarti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Abdelomunim Essabbar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - El Mehdi Bouricha
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - M. W. Chemao-Elfihri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Souad Kartti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Nasma Boumajdi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Houda Bendani
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Rokia Laamarti
- Medical Biotechnology Center, Moroccan Foundation for Science, Innovation & Research (MAScIR), Rabat 10100, Morocco;
| | - Fatima Ghrifi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Loubna Allam
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Tarik Aanniz
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Mouna Ouadghiri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Naima El Hafidi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Rachid El Jaoudi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Houda Benrahma
- Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca 82403, Morocco;
| | - Jalil El Attar
- Riad Laboratory, City Center Hay Riad, Rabat 10112, Morocco;
| | - Rachid Mentag
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat 10101, Morocco;
| | - Laila Sbabou
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco;
| | - Chakib Nejjari
- International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca 82403, Morocco;
| | - Saaid Amzazi
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco;
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10112, Morocco;
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| |
Collapse
|
43
|
Kartti S, Bouihat N, El Hajjami N, Ouadghiri M, Aanniz T, Elouennass M, Belyamani L, Ibrahimi A, Benaouda A. Draft Genome Sequences of Six Moroccan Helicobacter pylori Isolates Belonging to the hspWAfrica Group. Microbiol Resour Announc 2020; 9:e00714-20. [PMID: 33033122 PMCID: PMC7545276 DOI: 10.1128/mra.00714-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/10/2020] [Indexed: 11/20/2022] Open
Abstract
Helicobacter pylori affects up to 50% of people worldwide. Here, we present the draft genome sequences of six H. pylori strains isolated from Moroccan patients with different gastric diseases. Multilocus sequence typing analysis showed that all of the H. pylori isolates belonged to the hspWAfrica group.
Collapse
Affiliation(s)
- Souad Kartti
- Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Najat Bouihat
- Microbiology Laboratory, Cheick-Zaid University Hospital, Abulcasis University of Health Sciences, Rabat, Morocco
| | - Nargisse El Hajjami
- Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Mouna Ouadghiri
- Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarik Aanniz
- Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Mostafa Elouennass
- Bacteriology Laboratory, Military Instruction Hospital Mohammed V, Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Instruction Hospital Mohammed V, Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Amina Benaouda
- Microbiology Laboratory, Cheick-Zaid University Hospital, Abulcasis University of Health Sciences, Rabat, Morocco
| |
Collapse
|
44
|
Hakmi M, Bouricha ELM, Akachar J, Lmimouni B, El Harti J, Belyamani L, Ibrahimi A. In silico exploration of small-molecule α-helix mimetics as inhibitors of SARS-COV-2 attachment to ACE2. J Biomol Struct Dyn 2020; 40:1546-1557. [PMID: 33023417 DOI: 10.1080/07391102.2020.1830175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The novel coronavirus, SARS-CoV-2, has infected more than 10 million people and caused more than 502,539 deaths worldwide as of June 2020. The explosive spread of the virus and the rapid increase in the number of cases require the immediate development of effective therapies and vaccines as well as accurate diagnosis tools. The pathogenesis of the disease is triggered by the entry of SARS-CoV-2 via its spike protein into ACE2-bearing host cells, particularly pneumocytes, resulting in overactivation of the immune system, which attacks the infected cells and damages the lung tissue. The interaction of the SARS-CoV-2 receptor binding domain (RBD) with host cells is primarily mediated by the N-terminal helix of ACE2; thus, inhibition of the spike-ACE2 interaction may be a promising therapeutic strategy for blocking the virus entry into host cells. In this paper, we used an in-silico approach to explore small-molecule α-helix mimetics as inhibitors that may disrupt the attachment of SARS-CoV-2 to ACE2. First, the RBD-ACE2 interface in the 6M0J structure was studied by the MM-GBSA decomposition module of the HawkDock server, which led to the identification of two critical target regions in the RBD. Next, two virtual screening experiments of 7236 α-helix mimetics from ASINEX were conducted on the above regions using the iDock tool, which resulted in 10 candidates with favorable binding affinities. Finally, the stability of RBD complexes with the top-two ranked compounds was further validated by 100 ns of molecular dynamics simulations.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - E L Mehdi Bouricha
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Jihane Akachar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Badreddine Lmimouni
- Laboratory of medical parasitology and mycology, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Bioinova Research Center, Rabat, Morocco
| | - Jaouad El Harti
- Therapeutic Chemistry Laboratory, Medical Biotechnology Laboratory (MedBiotech), Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Bioinova Research Center, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Rabat, Morocco
| |
Collapse
|
45
|
Crooks L, Cooper-Knock J, Heath PR, Bouhouche A, Elfahime M, Azzouz M, Bakri Y, Adnaoui M, Ibrahimi A, Amzazi S, Tazi-Ahnini R. Identification of single nucleotide variants in the Moroccan population by whole-genome sequencing. BMC Genet 2020; 21:111. [PMID: 32957965 PMCID: PMC7507649 DOI: 10.1186/s12863-020-00917-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 09/08/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Large-scale human sequencing projects have described around a hundred-million single nucleotide variants (SNVs). These studies have predominately involved individuals with European ancestry despite the fact that genetic diversity is expected to be highest in Africa where Homo sapiens evolved and has maintained a large population for the longest time. The African Genome Variation Project examined several African populations but these were all located south of the Sahara. Morocco is on the northwest coast of Africa and mostly lies north of the Sahara, which makes it very attractive for studying genetic diversity. The ancestry of present-day Moroccans is unknown and may be substantially different from Africans found South of the Sahara desert, Recent genomic data of Taforalt individuals in Eastern Morocco revealed 15,000-year-old modern humans and suggested that North African individuals may be genetically distinct from previously studied African populations. RESULTS We present SNVs discovered by whole genome sequencing (WGS) of three Moroccans. From a total of 5.9 million SNVs detected, over 200,000 were not identified by 1000G and were not in the extensive gnomAD database. We summarise the SNVs by genomic position, type of sequence gene context and effect on proteins encoded by the sequence. Analysis of the overall genomic information of the Moroccan individuals to individuals from 1000G supports the Moroccan population being distinct from both sub-Saharan African and European populations. CONCLUSIONS We conclude that Moroccan samples are genetically distinct and lie in the middle of the previously observed cline between populations of European and African ancestry. WGS of Moroccan individuals can identify a large number of novel SNVs and aid in functional characterisation of the genome.
Collapse
Affiliation(s)
- Lucy Crooks
- Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Howard Street, Sheffield,, S1 1WB, UK
| | - Johnathan Cooper-Knock
- Neuroscience (SITraN), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Paul R Heath
- Neuroscience (SITraN), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Ahmed Bouhouche
- Neurology and Neurogenetics, Genomic of Human Pathlogies Center, Medical School and Pharmacy, Mohammed-V University, Rabat, Morocco
| | | | - Mimoun Azzouz
- Neuroscience (SITraN), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Youssef Bakri
- Laboratory of human pathologies Biology BioPatH-Faculty of science-Center of human pathologies Genomics, GenoPatH- Faculty of Medicine- Mohammed V University in Rabat, Rabat, Morocco
| | - Mohammed Adnaoui
- Medical School and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Lab (MedBiotech), Medical School and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of human pathologies Biology BioPatH-Faculty of science-Center of human pathologies Genomics, GenoPatH- Faculty of Medicine- Mohammed V University in Rabat, Rabat, Morocco
| | - Rachid Tazi-Ahnini
- Medical School and Pharmacy, Mohammed V University, Rabat, Morocco.
- Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, S10 2RX, UK.
| |
Collapse
|
46
|
Ziani I, Ibrahimi A, Lahlou L, De Sousa P, Saint F, sayegh HE, Benslimane L, Nouini Y. Facteurs pronostiques de micro-métastase ganglionnaire des tumeurs de vessie infiltrant le muscle chez une population marocaine en 2019. Rev Epidemiol Sante Publique 2020. [DOI: 10.1016/j.respe.2020.03.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
47
|
Laamarti M, Chemao-Elfihri MW, Kartti S, Laamarti R, Allam L, Ouadghiri M, Smyej I, Rahoui J, Benrahma H, Diawara I, Alouane T, Essabbar A, Siah S, Karra M, El Hafidi N, El Jaoudi R, Sbabou L, Nejjari C, Amzazi S, Mentag R, Belyamani L, Ibrahimi A. Genome Sequences of Six SARS-CoV-2 Strains Isolated in Morocco, Obtained Using Oxford Nanopore MinION Technology. Microbiol Resour Announc 2020; 9:e00767-20. [PMID: 32763945 PMCID: PMC7409862 DOI: 10.1128/mra.00767-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/17/2020] [Indexed: 01/07/2023] Open
Abstract
Here, we report the draft genome sequences of six severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains. SARS-CoV-2 is responsible for the COVID-19 pandemic, which started at the end of 2019 in Wuhan, China. The isolates were obtained from nasopharyngeal swabs from Moroccan patients with COVID-19. Mutation analysis revealed the presence of the spike D614G mutation in all six genomes, which is widely present in several genomes around the world.
Collapse
Affiliation(s)
- Meriem Laamarti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - M W Chemao-Elfihri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Souad Kartti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Rokia Laamarti
- Medical Biotechnology Center, Moroccan Foundation for Science, Innovation & Research (MAScIR), Rabat, Morocco
| | - Loubna Allam
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Mouna Ouadghiri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Imane Smyej
- National Reference Laboratory, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Jalila Rahoui
- National Reference Laboratory, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Houda Benrahma
- National Reference Laboratory, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Idrissa Diawara
- National Reference Laboratory, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Tarek Alouane
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Abdelomunim Essabbar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Samir Siah
- Department of Burns, Mohammed V Military Teaching Hospital/Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Mohammed Karra
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Naima El Hafidi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Rachid El Jaoudi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Laila Sbabou
- Research Center of Plants and Microbial Biotechnologies, Biodiversity and Environment, Microbiology and Molecular Biology Team, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Chakib Nejjari
- International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Saaid Amzazi
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Rachid Mentag
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| |
Collapse
|
48
|
Hakmi M, Bouricha EM, Kandoussi I, Harti JE, Ibrahimi A. Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis. Bioinformation 2020; 16:301-306. [PMID: 32773989 PMCID: PMC7392094 DOI: 10.6026/97320630016301] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 12/31/2022] Open
Abstract
The new SARS-CoV-2 coronavirus is the causative agent of the COVID-19 pandemic outbreak that affected more than 190 countries worldwide with more than 292,000 confirmed cases and over
12,700 deaths. There is at the moment no vaccine or effective treatment for this disease which constitutes a serious global health problem. It is of interest to use a structure based virtual
screening approach for the identification of potential inhibitors of the main protease of SARS-CoV-2 (Mpro) from antiviral drugs used to treat other viral disease such as human immunodeficiency
virus (HIV) and hepatitis C virus (HCV) infections. The crystallographic structure with PDB ID: 6LU7 of Mpro in complex with the inhibitor N3 was used as a model in the virtual screening
of 33 protease inhibitors collected from the ChEMBL chemical database. Molecular docking analysis was performed using the standard AutoDock vina protocol followed by ranking and selection
of compounds based on their binding affinity. We report 10 candidates with optimal binding features to the active site of the protease for further consideration as potential drugs to treat
patients infected with the emerging COVID-19 disease.
Collapse
Affiliation(s)
- Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical and Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - El Mehdi Bouricha
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical and Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Ilham Kandoussi
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical and Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Jaouad El Harti
- Therapeutic Chemistry Laboratory, Medical Biotechnology Laboratory (MedBiotech), Rabat Medical and Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Rabat Medical and Pharmacy School, Mohammed Vth University in Rabat, Morocco
| |
Collapse
|
49
|
Bendahou MA, Arrouchi H, Lakhlili W, Allam L, Aanniz T, Cherradi N, Ibrahimi A, Boutarbouch M. Computational Analysis of IDH1, IDH2, and TP53 Mutations in Low-Grade Gliomas Including Oligodendrogliomas and Astrocytomas. Cancer Inform 2020; 19:1176935120915839. [PMID: 32313423 PMCID: PMC7160765 DOI: 10.1177/1176935120915839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/09/2020] [Indexed: 12/18/2022] Open
Abstract
Introduction: The emergence of new omics approaches, such as genomic algorithms to identify
tumor mutations and molecular modeling tools to predict the
three-dimensional structure of proteins, has facilitated the understanding
of the dynamic mechanisms involved in the pathogenesis of low-grade gliomas
including oligodendrogliomas and astrocytomas. Methods: In this study, we targeted known mutations involved in low-grade gliomas,
starting with the sequencing of genomic regions encompassing exon 4 of
isocitrate dehydrogenase 1 (IDH1) and isocitrate
dehydrogenase 2 (IDH2) and the four exons (5-6 and 7-8) of
TP53 from 32 samples, followed by computational
analysis to study the impact of these mutations on the structure and
function of 3 proteins IDH1, IDH2, and
p53. Results: We obtain a mutation that has an effect on the catalytic site of the protein
IDH1 as R132H and on the catalytic site of the protein
IDH2 as R172M. Other mutations at p53
have been identified as K305N, which is a pathogenic mutation; R175 H, which
is a benign mutation; and R158G, which disrupts the structural conformation
of the tumor suppressor protein. Conclusion: In low-grade gliomas, mutations in IDH1, IDH2, and
TP53 may be the key to tumor progression because they
have an effect on the function of the protein such as mutations R132H in
IDH1 and R172M in IDH2, which change
the function of the enzyme alpha-ketoglutarate, or R158G in
TP53, which affects the structure of the generated
protein, thus their importance in understanding gliomagenesis and for more
accurate diagnosis complementary to the anatomical pathology tests.
Collapse
Affiliation(s)
- Mohammed Amine Bendahou
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Housna Arrouchi
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Wiame Lakhlili
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Loubna Allam
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Tarik Aanniz
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Nadia Cherradi
- Department of Pathological Anatomy, Hospital of Specialties, CHU Ibn Sina, Rabat, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Mahjouba Boutarbouch
- Department of Neurosurgery, Hospital of Specialties, CHU Ibn Sina, Rabat, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| |
Collapse
|
50
|
Ziani I, Ibrahimi A, El Sayegh H, Benslimane L, Nouini Y. Le rapport neutrophiles/lymphocytes peut-il être utilisé pour prédire la récidive et la progression des tumeurs de la vessie non infiltrant le muscle ? Prog Urol 2019. [DOI: 10.1016/j.purol.2019.08.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|