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Rahiyab M, Khan I, Ali SS, Hussain Z, Ali S, Iqbal A. Computational profiling of molecular biomarkers in congenital disorders of glycosylation Type-I and binding analysis of Ginkgolide A with P4HB. Comput Biol Med 2025; 190:110042. [PMID: 40117797 DOI: 10.1016/j.compbiomed.2025.110042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Revised: 03/14/2025] [Accepted: 03/16/2025] [Indexed: 03/23/2025]
Abstract
AIMS Congenital disorders of glycosylation (CDG) comprise a diverse group of genetic diseases characterized by aberrant glycosylation that leads to severe multi-systematic effects. Despite advancements in understanding the underlying molecular mechanisms, curative options remain limited. This study employed computational methods to identify key molecular biomarkers for CDG-I and examine the pharmacological effects of Ginkgolide A (GA), a potent bioactive natural compound. METHODS We analyzed the GSE8440 microarray dataset to discover differentially expressed genes (DEGs) in patients compared to healthy individuals with CDG-I utilizing GEO2R. Functional enrichments, including gene ontologies (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses, were conducted to contextualize the biological mechanisms and molecular signatures involved in CDG-I (Congenital Disorders of Glycosylation Type-1). The protein-protein interaction (PPI) network for DEGs was constructed using the STRING database, and the central hub genes within the PPI network were identified using Cytohubba. Furthermore, the 3D structure of the top hub gene (P4HB) was predicted by using the Robetta server. The CASTp was employed to evaluate the active sites. Molecular docking of P4HB with GA was carried out to investigate the binding affinity using the PyRx tool, and the stability of the docked complex was validated through MD simulation. The pharmacokinetics, toxicity, and bioactivity score of GA were comprehensively assessed using SwissADME, ProTox-II, and Molinspiration. RESULTS Our findings indicated 247 significant DEGs, including 146 up-regulated and 101 down-regulated genes. GO and KEGG pathway analyses confirmed that the up-regulated and hub genes were strongly associated with protein folding, glycoprotein processing in the endoplasmic reticulum, and endoplasmic reticulum stress (ER) pathways. P4HB emerged as the top hub gene in CDG-I, playing a significant role in protein folding and ER stress. The 3D structure of P4HB was refined and validated, achieving 95.8 % residues in the most favored region of the Ramachandran plot, with an overall quality of 92.97 %. The CASTp server predicted the largest active site with an area of 2243.660 Å2 and a volume of 3236.584 Å3. Molecular docking revealed that GA has a strong binding affinity with P4HB (-8.9 kcal/mol). The ADME (Absorption, Distribution, Metabolism, Excretion) and toxicity assessments confirmed promising drug-like characteristics, excellent bioavailability, and minimal toxicity risk. CONCLUSION This study emphasizes GA as a potential treatment possibility option to alleviated CDG-I pathology by targeting protein misfolding and ER stress, which are fundamental aspects of the disease. Additionally, our findings indicate that P4HB is a critical molecular target in CDG-I. These results pave the way for future preclinical and clinical investigations aimed at advancing the targeted and tailored treatments for CDG.
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Affiliation(s)
- Muhammad Rahiyab
- Center for Biotechnology and Microbiology, University of Swat, KPK, Pakistan
| | - Ishaq Khan
- Center for Biotechnology and Microbiology, University of Swat, KPK, Pakistan
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, KPK, Pakistan
| | - Zahid Hussain
- Center for Biotechnology and Microbiology, University of Swat, KPK, Pakistan
| | - Shahid Ali
- Center for Biotechnology and Microbiology, University of Swat, KPK, Pakistan
| | - Arshad Iqbal
- Center for Biotechnology and Microbiology, University of Swat, KPK, Pakistan.
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E U, T M, A V G, D P. A comprehensive survey of drug-target interaction analysis in allopathy and siddha medicine. Artif Intell Med 2024; 157:102986. [PMID: 39326289 DOI: 10.1016/j.artmed.2024.102986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 08/13/2024] [Accepted: 09/18/2024] [Indexed: 09/28/2024]
Abstract
Effective drug delivery is the cornerstone of modern healthcare, ensuring therapeutic compounds reach their intended targets efficiently. This paper explores the potential of personalized and holistic healthcare, driven by the synergy between traditional and allopathic medicine systems, with a specific focus on the vast reservoir of medicinal compounds found in plants rooted in the historical legacy of traditional medicine. Motivated by the desire to unlock the therapeutic potential of medicinal plants and bridge the gap between traditional and allopathic medicine, this survey delves into in-silico computational approaches for studying Drug-Target Interactions (DTI) within the contexts of allopathy and siddha medicine. The contributions of this survey are multifaceted: it offers a comprehensive overview of in-silico methods for DTI analysis in both systems, identifies common challenges in DTI studies, provides insights into future directions to advance DTI analysis, and includes a comparative analysis of DTI in allopathy and siddha medicine. The findings of this survey highlight the pivotal role of in-silico computational approaches in advancing drug research and development in both allopathy and siddha medicine, emphasizing the importance of integrating these methods to drive the future of personalized healthcare.
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Affiliation(s)
- Uma E
- Department of Information Science and Technology, College of Engineering Guindy, Chennai, India.
| | - Mala T
- Department of Information Science and Technology, College of Engineering Guindy, Chennai, India
| | - Geetha A V
- Department of Information Science and Technology, College of Engineering Guindy, Chennai, India
| | - Priyanka D
- Department of Information Science and Technology, College of Engineering Guindy, Chennai, India
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Boukandou Mounanga MM, Mezui A, Mewono L, Mogangué JB, Aboughe Angone S. Medicinal plants used in Gabon for prophylaxis and treatment against COVID-19-related symptoms: an ethnobotanical survey. Front Pharmacol 2024; 15:1393636. [PMID: 39035990 PMCID: PMC11258373 DOI: 10.3389/fphar.2024.1393636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/04/2024] [Indexed: 07/23/2024] Open
Abstract
Background: Gabon faced COVID-19 with more than 49,000 individuals tested positive and 307 recorded fatalities since the first reported case in 2020. A popular hypothesis is that the low rate of cases and deaths in the country was attributed to the use of medicinal plants in prevention and treatment. This study aimed to document the plants used for remedial and preventive therapies by the Gabonese population during the COVID-19 pandemic and to pinpoint specific potential plant species that merit further investigation. Methods: An ethnobotanical survey involving 97 participants was conducted in Libreville. Traditional healers and medicinal plant vendors were interviewed orally using a semi-structured questionnaire sheet, while the general population responded to an online questionnaire format. Various quantitative indexes were calculated from the collected data and included the relative frequency of citation (RFC), use value (UV), informant consensus factor (ICF), relative importance (RI), and popular therapeutic use value (POPUT). One-way ANOVA and independent samples t-test were used for statistical analyses. p-values ≤0.05 were considered significant. Results: The survey identified 63 plant species belonging to 35 families. Prevalent symptoms treated included fever (18%), cough (16%), fatigue (13%), and cold (12%). The demographic data highlighted that 52.58% of male subjects (p > 0.94) aged 31-44 years were enrolled in the survey, of which 48.45% (p < 0.0001) and 74.73% (p < 0.99) of informants had university-level education. In addition, the results indicated that a total of 66% of the informants used medicinal plants for prophylaxis (34%), for both prevention and treatment (26%), exclusively for treatment (3%), and only for prevention (3%) while suffering from COVID-19, against 34% of the participants who did not use plants for prevention or treatment. Annickia chlorantha, Citrus sp., Alstonia congensis, Zingiber officinale, and Carica papaya emerged as the most commonly cited plants with the highest RFC (0.15-0.26), UV (0.47-0.75), and RI (35.72-45.46) values. Most of these plants were used either individually or in combination with others. Conclusion: The survey reinforces the use of traditional medicine as a method to alleviate COVID-19 symptoms, thereby advocating for the utilization of medicinal plants in managing coronavirus infections.
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Affiliation(s)
- Marlaine Michel Boukandou Mounanga
- Institut de Pharmacopée et de Médecine Traditionnelle (IPHAMETRA), Centre National de la Recherche Scientifique et Technologique (CENAREST), Libreville, Gabon
| | - Annais Mezui
- Centre Hospitalier Universitaire Mère- Enfant, Fondation Jeanne EBORI, Libreville, Gabon
| | - Ludovic Mewono
- Groupe de Recherche en Immunologie 2, Microbiologie appliquée, Hygiène et Physiologie, Département des Sciences de la Vie et de la Terre-Ecole Normale Supérieure, Libreville, Gabon
| | - Jean Bertrand Mogangué
- Institut de Pharmacopée et de Médecine Traditionnelle (IPHAMETRA), Centre National de la Recherche Scientifique et Technologique (CENAREST), Libreville, Gabon
| | - Sophie Aboughe Angone
- Institut de Pharmacopée et de Médecine Traditionnelle (IPHAMETRA), Centre National de la Recherche Scientifique et Technologique (CENAREST), Libreville, Gabon
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Tilkat E, Jahan I, Hoşer A, Kaplan A, Özdemir O, Onay A. Anatolian medicinal plants as potential antiviral agents: bridging traditional knowledge and modern science in the fight against COVID-19 and related viral infections. Turk J Biol 2024; 48:218-241. [PMID: 39296335 PMCID: PMC11407354 DOI: 10.55730/1300-0152.2699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 08/23/2024] [Accepted: 06/26/2024] [Indexed: 09/21/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was the cause of the coronavirus 2019 (COVID-19), commonly known as the coronavirus pandemic. Since December 2020, COVID-19 vaccines have been extensively administered in numerous countries. In addition to new antiviral medications, the treatment regimen encompasses symptom management. Despite sustained research efforts, the outbreak remains uncontrolled, with affected patients still lacking proper treatment. This review is a valuable asset for researchers and practitioners aiming to delve into the yet unexplored potential of Anatolian flora in the fight against COVID-19 and other viral infections. Numerous medicinal plants in Anatolia, such as thyme, sage, cannabis, oregano, licorice root, and Origanum sp., contain bioactive compounds with proven antiviral properties that have been used in the region for centuries. The rich legacy of traditional Anatolian medicine (TAM), has significantly influenced modern medicine; thus, the profusion of medicinal plants native to Anatolia holds promise for antiviral drug development, making this review essential for researchers and practitioners.
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Affiliation(s)
- Engin Tilkat
- Department of Biology, Faculty of Science and Literature, Batman University, Batman, Turkiye
| | - Israt Jahan
- Department of Health Care Services, Vocational School of Health Services, Mardin Artuklu University, Mardin, Turkiye
| | - Ayşe Hoşer
- Department of Biology, Faculty of Science and Literature, Batman University, Batman, Turkiye
| | - Alevcan Kaplan
- Department of Crop and Animal Production, Sason Vocational School, Batman University, Batman, Turkiye
| | - Oğuzhan Özdemir
- Department of Veterinary Science, Technical Sciences Vocational School, Batman University, Batman, Turkiye
| | - Ahmet Onay
- Department of Biology, Faculty of Science, Dicle University, Diyarbakır, Turkiye
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Ushasree MV, Jia Q, Do SG, Lee EY. New opportunities and perspectives on biosynthesis and bioactivities of secondary metabolites from Aloe vera. Biotechnol Adv 2024; 72:108325. [PMID: 38395206 DOI: 10.1016/j.biotechadv.2024.108325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/10/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
Historically, the genus Aloe has been an indispensable part of both traditional and modern medicine. Decades of intensive research have unveiled the major bioactive secondary metabolites of this plant. Recent pandemic outbreaks have revitalized curiosity in aloe metabolites, as they have proven pharmacokinetic profiles and repurposable chemical space. However, the structural complexity of these metabolites has hindered scientific advances in the chemical synthesis of these compounds. Multi-omics research interventions have transformed aloe research by providing insights into the biosynthesis of many of these compounds, for example, aloesone, aloenin, noreugenin, aloin, saponins, and carotenoids. Here, we summarize the biological activities of major aloe secondary metabolites with a focus on their mechanism of action. We also highlight the recent advances in decoding the aloe metabolite biosynthetic pathways and enzymatic machinery linked with these pathways. Proof-of-concept studies on in vitro, whole-cell, and microbial synthesis of aloe compounds have also been briefed. Research initiatives on the structural modification of various aloe metabolites to expand their chemical space and activity are detailed. Further, the technological limitations, patent status, and prospects of aloe secondary metabolites in biomedicine have been discussed.
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Affiliation(s)
- Mrudulakumari Vasudevan Ushasree
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Qi Jia
- Unigen, Inc., 2121 South street suite 400 Tacoma, Washington 98405, USA
| | - Seon Gil Do
- Naturetech, Inc., 29-8, Yongjeong-gil, Chopyeong-myeon, Jincheon-gun, Chungcheongbuk-do 27858, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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Dávila-Rangel IE, Charles-Rodríguez AV, López-Romero JC, Flores-López ML. Plants from Arid and Semi-Arid Zones of Mexico Used to Treat Respiratory Diseases: A Review. PLANTS (BASEL, SWITZERLAND) 2024; 13:792. [PMID: 38592789 PMCID: PMC10974781 DOI: 10.3390/plants13060792] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
Medicinal plants have been a traditional remedy for numerous ailments for centuries. However, their usage is limited due to a lack of evidence-based studies elucidating their mechanisms of action. In some countries, they are still considered the first treatment due to their low cost, accessibility, and minor adverse effects. Mexico is in second place, after China, in inventoried plants for medicinal use. It has around 4000 species of medicinal plants; however, pharmacological studies have only been carried out in 5% of its entirety. The species of the Mexican arid zones, particularly in semi-desert areas, exhibit outstanding characteristics, as their adverse growing conditions (e.g., low rainfall and high temperatures) prompt these plants to produce interesting metabolites with diverse biological activities. This review explores medicinal plants belonging to the arid and semi-arid zones of Mexico, focusing on those that have stood out for their bioactive potential, such as Jatropha dioica, Turnera diffusa, Larrea tridentata, Opuntia ficus-indica, Flourensia cernua, Fouquieria splendes, and Prosopis glandulosa. Their extraction conditions, bioactive compounds, mechanisms of action, and biological efficacy are presented, with emphasis on their role in the treatment of respiratory diseases. Additionally, current research, novel applications, and perspectives concerning medicinal plants from these zones are also discussed.
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Affiliation(s)
| | - Ana V. Charles-Rodríguez
- Departamento de Ciencia y Tecnología de Alimentos, Universidad Autónoma Agraria Antonio Narro, Saltillo 25315, Mexico
| | - Julio C. López-Romero
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Caborca 83600, Mexico;
| | - María L. Flores-López
- Universidad Interserrana del Estado de Puebla Ahuactlán, Ahuacatlán 73330, Mexico;
- Centro de Investigación e Innovación Científica y Tecnológica, Universidad Autónoma de Coahuila, Saltillo 25070, Mexico
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Oliveira APS, Lima DR, Bezerra LL, Monteiro NKV, Loiola OD, Silva MGV. Virtual screening of flavonoids from Chamaecrista genus: ADME and pharmacokinetic properties, interactions of flavonoid-DNA complex by molecular docking and molecular dynamics. J Biomol Struct Dyn 2023; 41:7677-7685. [PMID: 36120963 DOI: 10.1080/07391102.2022.2124455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
This research aimed to conduct an in silico study of compounds, mainly flavonoids, that are found in several plants, including the species of the Chamaecrista genus. The ADME properties, the drug-likeness score and properties of Lipinski and Veber rules of the molecules were determined using online databases. Based on the predicted properties, four flavonoids, apigenin, fisetin, luteolin and ononin were selected for molecular docking and dynamic simulations to study their interactions with DNA (PDB ID: 1BNA). The molecular docking showed that ononin has a high affinity for B-DNA, exhibiting a ΔG value of -9.3 kcal mol-1, compared with the other flavonoids. The molecular dynamic simulations of the flavonoid-DNA complexes showed that the flavonoids interacted with DNA by hydrogen bonding, hydrophobic interaction and π-stacking. The flavonoid ononin showed the best interaction energy value of -291.3490 kJ mol-1, compared with the other flavonoids.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ana Paula S Oliveira
- Department of Organic and Inorganic Chemistry, Federal University of Ceará, Fortaleza, Brazil
| | - Daniele R Lima
- Department of Physico-chemical and Analytic Chemistry, Federal University of Ceará, Fortaleza, Brazil
| | - Lucas L Bezerra
- Department of Physico-chemical and Analytic Chemistry, Federal University of Ceará, Fortaleza, Brazil
| | - Norberto K V Monteiro
- Department of Physico-chemical and Analytic Chemistry, Federal University of Ceará, Fortaleza, Brazil
| | - Otília D Loiola
- Department of Organic and Inorganic Chemistry, Federal University of Ceará, Fortaleza, Brazil
| | - Maria Goretti V Silva
- Department of Organic and Inorganic Chemistry, Federal University of Ceará, Fortaleza, Brazil
- Department of Physico-chemical and Analytic Chemistry, Federal University of Ceará, Fortaleza, Brazil
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Rafiq A, Jabeen T, Aslam S, Ahmad M, Ashfaq UA, Mohsin NUA, Zaki MEA, Al-Hussain SA. A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products. Molecules 2023; 28:4860. [PMID: 37375415 PMCID: PMC10305344 DOI: 10.3390/molecules28124860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The ongoing COVID-19 pandemic has resulted in a global panic because of its continual evolution and recurring spikes. This serious malignancy is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the outbreak, millions of people have been affected from December 2019 till now, which has led to a great surge in finding treatments. Despite trying to handle the pandemic with the repurposing of some drugs, such as chloroquine, hydroxychloroquine, remdesivir, lopinavir, ivermectin, etc., against COVID-19, the SARS-CoV-2 virus continues its out-of-control spread. There is a dire need to identify a new regimen of natural products to combat the deadly viral disease. This article deals with the literature reports to date of natural products showing inhibitory activity towards SARS-CoV-2 through different approaches, such as in vivo, in vitro, and in silico studies. Natural compounds targeting the proteins of SARS-CoV-2-the main protease (Mpro), papain-like protease (PLpro), spike proteins, RNA-dependent RNA polymerase (RdRp), endoribonuclease, exoribonuclease, helicase, nucleocapsid, methyltransferase, adeno diphosphate (ADP) phosphatase, other nonstructural proteins, and envelope proteins-were extracted mainly from plants, and some were isolated from bacteria, algae, fungi, and a few marine organisms.
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Affiliation(s)
- Ayesha Rafiq
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Tooba Jabeen
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Sana Aslam
- Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Noor ul Amin Mohsin
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Magdi E. A. Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Sami A. Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
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Rabaan AA, Halwani MA, Aljeldah M, Al Shammari BR, Garout M, Aldali J, Alawfi A, Alshengeti A, Alsulaiman AM, Alsayyah A. Exploration of potent antiviral phytomedicines from Lauraceae family plants against SARS-CoV-2 RNA-dependent RNA polymerase. J Biomol Struct Dyn 2023; 41:15085-15105. [PMID: 36883874 DOI: 10.1080/07391102.2023.2186720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
RNA-dependent RNA polymerase, also known as RdRp, is a possible therapeutic target that could be used to suppress the proliferation of RNA viruses such as SARS-CoV-2. This protein has two major functional sites (a) catalytic and (b) substrate entry, which regulate the natural substrate entry and its corresponding interaction with the protein. In this study, a computational drug design pipeline was applied to investigate potential inhibitors against SARS-CoV-2 RdRp from Lauraceae plants, and five top hits were selected based on the docked score (< -7 kcal/mol). The docking study suggested that the Glochidioboside had a minimum binding score of -7.8 kcal/mol. This compound showed total five hydrogen bonds while two of them were with catalytic residues Asp618 and Asp760. However, another compound, Sitogluside showed a binding score of -7.3 kcal/mol with four hydrogen bonds targeting three functional residues (Arg555, Ser759, and Asp760). Later, 100 ns explicit solvent molecular dynamics (MD) simulation was performed to evaluate the stability of the protein-ligand docked system. These compounds translocated their positions from the catalytic site to the substrate entry site, as observed in the MD simulation trajectory. However, translocation did not affect the binding strength of these compounds, and they retained the strong binding affinity (ΔG < -11.5 kcal/mol), estimated using the MM/GBSA method. In general, the findings of this study indicated the potential therapeutic compounds that may be used targeting SARS-CoV-2 RdRp. However, these compounds still need to be validated by experimentation in order to determine their inhibitory function.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Al Baha, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Basim R Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Jehad Aldali
- Pathology Organization, Imam Mohammed Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah, Saudi Arabia
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah, Saudi Arabia
| | | | - Ahmed Alsayyah
- Department of Pathology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Ahmed SI, Jamil S, Ismatullah H, Hussain R, Bibi S, Khandaker MU, Naveed A, Idris AM, Emran TB. A comprehensive perspective of traditional Arabic or Islamic medicinal plants as an adjuvant therapy against COVID-19. Saudi J Biol Sci 2023; 30:103561. [PMID: 36684115 PMCID: PMC9838045 DOI: 10.1016/j.sjbs.2023.103561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/09/2022] [Accepted: 01/08/2023] [Indexed: 01/15/2023] Open
Abstract
COVID-19 is a pulmonary disease caused by SARS-CoV-2. More than 200 million individuals are infected by this globally. Pyrexia, coughing, shortness of breath, headaches, diarrhoea, sore throats, and body aches are among the typical symptoms of COVID-19. The virus enters into the host body by interacting with the ACE2 receptor. Despite many SARS-CoV-2 vaccines manufactured by distinct strategies but any evidence-based particular medication to combat COVID-19 is not available yet. However, further research is required to determine the safety and effectiveness profile of the present therapeutic approaches. In this study, we provide a summary of Traditional Arabic or Islamic medicinal (TAIM) plants' historical use and their present role as adjuvant therapy for COVID-19. Herein, six medicinal plants Aloe barbadensis Miller, Olea europaea, Trigonella foenum-graecum, Nigella sativa, Cassia angustifolia, and Ficus carica have been studied based upon their pharmacological activities against viral infections. These plants include phytochemicals that have antiviral, immunomodulatory, antiasthmatic, antipyretic, and antitussive properties. These bioactive substances could be employed to control symptoms and enhance the development of a possible COVID-19 medicinal synthesis. To determine whether or if these TAIMs may be used as adjuvant therapy and are appropriate, a detailed evaluation is advised.
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Affiliation(s)
- Shabina Ishtiaq Ahmed
- Department of Plant Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000, Islamabad, Pakistan
- The Standard College for Girls, 3/530 Paris Road, Sialkot Pakistan
| | - Sehrish Jamil
- The Standard College for Girls, 3/530 Paris Road, Sialkot Pakistan
| | - Humaira Ismatullah
- School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Rashid Hussain
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China
| | - Mayeen Uddin Khandaker
- Center for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Selangor, Malaysia
| | - Aisha Naveed
- Caribbean Medical University, Willemastad, Curacao-Caribbean Island, Curaçao
| | - Abubakr M. Idris
- Department of Chemistry, College of Science, King Khalid University, Abha 62529, Saudi Arabia
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 62529, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
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Rahman MM, Shohag S, Islam MR, Akhter S, Mim SA, Sharma R, Rauf A. An Insight into COVID-19 and Traditional Herbs: Bangladesh Perspective. Med Chem 2023; 19:361-383. [PMID: 36043762 DOI: 10.2174/1573406418666220829144746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/07/2022] [Accepted: 07/14/2022] [Indexed: 11/22/2022]
Abstract
SARS-CoV-2 was first discovered in Wuhan in late 2019 and has since spread over the world, resulting in the present epidemic. Because targeted therapeutics are unavailable, scientists have the opportunity to discover new drugs or vaccines to counter COVID-19, and therefore a number of synthetic bioactive compounds are now being tested in clinical studies. Due to its broad therapeutic spectrum and low adverse effects, medicinal herbs have been used as traditional healing medication in those countries for ages. Due to a lack of synthetic bioactive antiviral medications, pharmaceutical and alternative therapies have been developed using a variety of herbal compositions. Due to the widespread availability of herbal and dietary products worldwide, people frequently use them. Notably, the majority of Bangladeshi people continue to use a variety of natural plants and herbs to treat various types of diseases. This review article discusses how previous research has shown that some herbs in Bangladesh have immunomodulatory and antiviral effects and how their active ingredients have been gathered. Even though FDA-approved medications and vaccines are available for the treatment of COVID-19, the purpose is to encourage the use of herbal medicine as immunomodulators and vaccine adjuvants for the treatment of COVID-19 prevention.
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Affiliation(s)
- Md Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Sheikh Shohag
- Department of Genetic Engineering and Biotechnology, Faculty of Earth and Ocean Science, Bangabandhu Sheikh Mujibur Rahman Maritime University, Mirpur 12, Dhaka 1216, Bangladesh
| | - Md Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Shomaya Akhter
- Department of Genetic Engineering and Biotechnology, Faculty of Earth and Ocean Science, Bangabandhu Sheikh Mujibur Rahman Maritime University, Mirpur 12, Dhaka 1216, Bangladesh
| | - Sadia Afsana Mim
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Rohit Sharma
- Faculty of Ayurveda,Department of Rasa Shastra & Bhaishajya Kalpana, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar 23561, Khyber Pakhtunkhwa, Pakistan
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12
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LC-MS Based Phytochemical Profiling towards the Identification of Antioxidant Markers in Some Endemic Aloe Species from Mascarene Islands. Antioxidants (Basel) 2022; 12:antiox12010050. [PMID: 36670912 PMCID: PMC9854647 DOI: 10.3390/antiox12010050] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Aloe plant species have been used for centuries in traditional medicine and are reported to be an important source of natural products. However, despite the large number of species within the Aloe genus, only a few have been investigated chemotaxonomically. A Molecular Network approach was used to highlight the different chemical classes characterizing the leaves of five Aloe species: Aloe macra, Aloe vera, Aloe tormentorii, Aloe ferox, and Aloe purpurea. Aloe macra, A. tormentorii, and A. purpurea are endemic from the Mascarene Islands comprising Reunion, Mauritius, and Rodrigues. UHPLC-MS/MS analysis followed by a dereplication process allowed the characterization of 93 metabolites. The newly developed MolNotator algorithm was usedfor molecular networking and allowed a better exploration of the Aloe metabolome chemodiversity. The five species appeared rich in polyphenols (anthracene derivatives, flavonoids, phenolic acids). Therefore, the total phenolic content and antioxidant activity of the five species were evaluated, and a DPPH-On-Line-HPLC assay was used to determine the metabolites responsible for the radical scavenging activity. The use of computational tools allowed a better description of the comparative phytochemical profiling of five Aloe species, which showed differences in their metabolite composition, both qualitative and quantitative. Moreover, the molecular network approach combined with the On-Line-HPLC assay allowed the identification of 9 metabolites responsible for the antioxidant activity. Two of them, aloeresin A and coumaroylaloesin, could be the principal metabolites responsible for the activity. From 374 metabolites calculated by MolNator, 93 could be characterized. Therefore, the Aloe species can be a rich source of new chemical structures that need to be discovered.
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13
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Mitra SS, Ghorai M, Nandy S, Mukherjee N, Kumar M, Radha, Ghosh A, Jha NK, Proćków J, Dey A. Barbaloin: an amazing chemical from the 'wonder plant' with multidimensional pharmacological attributes. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2022; 395:1525-1536. [PMID: 36173445 PMCID: PMC9520999 DOI: 10.1007/s00210-022-02294-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 09/09/2022] [Indexed: 11/26/2022]
Abstract
Aloe vera (L.) Burm.f. is nicknamed the 'Miracle plant' or sometimes as the 'Wonder plant'. It is a plant that has been used since ancient times for the innumerable health benefits associated with it. It is one of the important plants that has its use in conventional medicinal treatments. It is a perennial succulent, drought-tolerant member of the family Asphodelaceae. There are scores of properties associated with the plant that help in curing various forms of human ailments. Extracts and gels obtained from plants have been shown to be wonderful healers of different conditions, mainly various skin problems. Also, this plant is popular in the cosmetics industry. The underlying properties of the plant are now mainly associated with the natural phytochemicals present in the plant. Diverse groups of phytoingredients are found in the plant, including various phenolics, amino acids, sugars, vitamins, and different other organic compounds, too. One of the primary ingredients found in the plant is the aloin molecule. It is an anthraquinone derivative and exists as an isomer of Aloin A and Aloin B. Barbaloin belonging to the first group is a glucoside of the aloe-emodin anthrone molecule. Various types of pharmacological properties exhibited by the plant can be attributed to this chemical. Few significant ones are antioxidant, anti-inflammatory, anti-diabetic, anti-cancer, anti-microbial, and anti-viral, along with their different immunity-boosting actions. Recently, molecular coupling studies have also found the role of these molecules as a potential cure against the ongoing COVID-19 disease. This study comprehensively focuses on the numerous pharmacological actions of the primary compound barbaloin obtained from the Aloe vera plant along with the mechanism of action and the potent application of these natural molecules under various conditions.
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Affiliation(s)
- Shreya Sikdar Mitra
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India
| | - Mimosa Ghorai
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India
| | - Samapika Nandy
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India
| | - Nobendu Mukherjee
- Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, Australia
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research On Cotton Technology, Mumbai, 400019, Maharashtra, India
| | - Radha
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173229, Himachal Pradesh, India
| | - Arabinda Ghosh
- Department of Botany, Gauhati University, 781014, Guwahati, Assam, India
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, 140413, Punjab, India
- Department of Biotechnology, School of Applied & Life Sciences, Uttaranchal University, Dehradun, 248007, Uttarakhand, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631, Wrocław, Poland.
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India.
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14
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Alavi M, Mozafari MR, Ghaemi S, Ashengroph M, Hasanzadeh Davarani F, Mohammadabadi M. Interaction of Epigallocatechin Gallate and Quercetin with Spike Glycoprotein (S-Glycoprotein) of SARS-CoV-2: In Silico Study. Biomedicines 2022; 10:biomedicines10123074. [PMID: 36551830 PMCID: PMC9775955 DOI: 10.3390/biomedicines10123074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/14/2022] [Accepted: 11/19/2022] [Indexed: 12/03/2022] Open
Abstract
Severe acute respiratory syndrome (SARS)-CoV-2 from the family Coronaviridae is the cause of the outbreak of severe pneumonia, known as coronavirus disease 2019 (COVID-19), which was first recognized in 2019. Various potential antiviral drugs have been presented to hinder SARS-CoV-2 or treat COVID-19 disease. Side effects of these drugs are among the main complicated issues for patients. Natural compounds, specifically primary and secondary herbal metabolites, may be considered as alternative options to provide therapeutic activity and reduce cytotoxicity. Phenolic materials such as epigallocatechin gallate (EGCG, polyphenol) and quercetin have shown antibacterial, antifungal, antiviral, anticancer, and anti-inflammatory effects in vitro and in vivo. Therefore, in this study, molecular docking was applied to measure the docking property of epigallocatechin gallate and quercetin towards the transmembrane spike (S) glycoprotein of SARS-CoV-2. Results of the present study showed Vina scores of -9.9 and -8.3 obtained for EGCG and quercetin by CB-Dock. In the case of EGCG, four hydrogen bonds of OG1, OD2, O3, and O13 atoms interacted with the Threonine (THR778) and Aspartic acid (ASP867) amino acids of the spike glycoprotein (6VSB). According to these results, epigallocatechin gallate and quercetin can be considered potent therapeutic compounds for addressing viral diseases.
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Affiliation(s)
- Mehran Alavi
- Department of Biological Science, Faculty of Science, University of Kurdistan, Kurdistan 6617715175, Iran
- Nanobiotechnology Department, Faculty of Innovative Science and Technology, Razi University, Kermanshah 6714414971, Iran
- Correspondence: (M.A.); (M.R.M.)
| | - M. R. Mozafari
- Australasian Nanoscience and Nanotechnology Initiative (ANNI), Monash University LPO, Clayton, VIC 3168, Australia
- Correspondence: (M.A.); (M.R.M.)
| | - Saba Ghaemi
- Research Committee of Medical School, Alborz University of Medical Science, Karaj 3149779453, Iran
| | - Morahem Ashengroph
- Department of Biological Science, Faculty of Science, University of Kurdistan, Kurdistan 6617715175, Iran
| | | | - Mohammadreza Mohammadabadi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616913439, Iran
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15
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ŞEN A. Complementary medicines used in ulcerative colitis and unintended interactions with cytochrome P450-dependent drug-metabolizing enzymes. Turk J Med Sci 2022; 52:1425-1447. [PMID: 36422483 PMCID: PMC10395683 DOI: 10.55730/1300-0144.5482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 10/19/2022] [Accepted: 07/28/2022] [Indexed: 11/07/2022] Open
Abstract
Ulcerative colitis (UC) is an idiopathic, chronic inflammatory disease with multiple genetic and a variety of environmental risk factors. Although current drugs significantly aid in controlling the disease, many people have led to the application of complementary therapies due to the common belief that they are natural and safe, as well as due to the consideration of the side effect of current drugs. Curcumin, cannabinoids, wheatgrass, Boswellia, wormwood and Aloe vera are among the most commonly used complementary medicines in UC. However, these treatments may have adverse and toxic effects due to unintended interactions with drugs or drug-metabolizing enzymes such as cytochrome P450s; thus, being ignorant of these interactions might cause deleterious effects with severe consequences. In addition, the lack of complete and controlled long-term studies with the use of these complementary medicines regarding drug metabolism pose additional risk and unsafety. Thus, this review aims to give an overview of the potential interactions of drug-metabolizing enzymes with the complementary botanical medicines used in UC, drawing attention to possible adverse effects.
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Affiliation(s)
- Alaattin ŞEN
- Department of Molecular Biology and Genetics, Faculty of Life and Natural Sciences, Abdullah Gül University, Kayseri,
Turkey
- Department of Biology, Faculty of Arts and Sciences, Pamukkale University, Denizli,
Turkey
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16
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Matondo A, Dendera W, Isamura BK, Ngbolua KTN, Mambo HVS, Muzomwe M, Mudogo V. In silico Drug Repurposing of Anticancer Drug 5-FU and Analogues Against SARS-CoV-2 Main Protease: Molecular Docking, Molecular Dynamics Simulation, Pharmacokinetics and Chemical Reactivity Studies. Adv Appl Bioinform Chem 2022; 15:59-77. [PMID: 35996620 PMCID: PMC9391940 DOI: 10.2147/aabc.s366111] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022] Open
Abstract
Background Since the last COVID-19 outbreak, several approaches have been given a try to quickly tackle this global calamity. One of the well-established strategies is the drug repurposing, which consists in finding new therapeutic uses for approved drugs. Following the same paradigm, we report in the present study, an investigation of the potential inhibitory activity of 5-FU and nineteen of its analogues against the SARS-CoV-2 main protease (3CLpro). Material and Methods Molecular docking calculations were performed to investigate the binding affinity of the ligands within the active site of 3CLpro. The best binding candidates were further considered for molecular dynamics simulations for 100 ns to gain a time-resolved understanding of the behavior of the guest-host complexes. Furthermore, the profile of druggability of the best binding ligands was assessed based on ADMET predictions. Finally, their chemical reactivity was elucidated using different reactivity descriptors, namely the molecular electrostatic potential (MEP), Fukui functions and frontier molecular orbitals. Results and Discussion From the calculations performed, four candidates (compounds 14, 15, 16 and 18) show promising results with respect to the binding affinity to the target protease, 3CLpro, the therapeutic profile of druggability and safety. These compounds are maintained inside the active site of 3CLpro thanks to a variety of noncovalent interactions, especially hydrogen bonds, involving important amino acids such as GLU166, HIS163, GLY143, ASN142, HIS172, CYS145. Molecular dynamics simulations suggest that the four ligands are well trapped within the active site of the protein over a time gap of 100 ns, ligand 18 being the most retained. Conclusion In line with the findings reported herein, we recommend that further in-vitro and in-vivo investigations are carried out to shed light on the possible mechanism of pharmacological action of the proposed ligands.
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Affiliation(s)
- Aristote Matondo
- Department of Chemistry, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Washington Dendera
- Department of Chemistry, Rhodes University, Makhanda, Eastern Cape, South Africa
| | - Bienfait Kabuyaya Isamura
- Department of Chemistry, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.,Department of Chemistry, Rhodes University, Makhanda, Eastern Cape, South Africa.,Research Center for Theoretical Chemistry and Physics in Central Africa, Department of Chemistry, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Koto-Te-Nyiwa Ngbolua
- Department of Biology, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Hilaire V S Mambo
- Department of Chemistry, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Mayaliwa Muzomwe
- Department of Chemistry, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Virima Mudogo
- Department of Chemistry, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
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17
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Shaji D, Suzuki R, Yamamoto S, Orihashi D, Kurita N. Natural inhibitors for severe acute respiratory syndrome coronavirus 2 main protease from Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis: molecular docking and ab initio fragment molecular orbital calculations. Struct Chem 2022; 33:1771-1788. [PMID: 35938063 PMCID: PMC9340690 DOI: 10.1007/s11224-022-02021-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/25/2022] [Indexed: 11/26/2022]
Abstract
The novel coronavirus 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly worldwide, and new drug treatments for COVID-19 are urgently required. To find the potential inhibitors against the main protease (Mpro) of SARS-CoV-2, we investigated the inhibitory potential of naturally occurring compounds from the plants Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis, using molecular docking, classical molecular mechanics optimizations, and ab initio fragment molecular orbital (FMO) calculations. Of the 35 compounds that we simulated, feralolide from Aloe vera exhibited the highest binding affinity against Mpro. Therefore, we proposed novel compounds based on the feralolide and investigated their binding properties to Mpro. The FMO results indicated that the introduction of a hydroxyl group into feralolide significantly enhances its binding affinity to Mpro. These results provide useful information for developing potent Mpro inhibitors.
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Affiliation(s)
- Divya Shaji
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
| | - Ryo Suzuki
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
| | - Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
| | - Daisuke Orihashi
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
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18
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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19
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Chen X, Song X, Li L, Chen Y, Jia R, Zou Y, Wan H, Zhao L, Tang H, Lv C, Zhao X, Yin Z. Resveratrol Inhibits Pseudorabies Virus Replication by Targeting IE180 Protein. Front Microbiol 2022; 13:891978. [PMID: 35722304 PMCID: PMC9203040 DOI: 10.3389/fmicb.2022.891978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Resveratrol is a natural polyphenolic product in red wine and peanuts and has many pharmacological activities in humans. Our previous studies showed that resveratrol has good antiviral activity against the pseudorabies virus (PRV). However, little is known about the antiviral mechanism of resveratrol against PRV. In this study, we found that resveratrol inhibited the nuclear localization of IE180 protein, which is an important step for activating early/late genes transcription. Interestingly, the results show that resveratrol inhibited the activity of IE180 protein by dual-luciferase assay. Furthermore, molecular docking analysis shows that resveratrol could bind to the Thr601, Ser603, and Pro606 of IE180 protein. Point mutation assay confirmed that resveratrol lost its inhibition activity against the mutant IE180 protein. The results demonstrate that resveratrol exerts its antiviral activity against PRV by targeting the Thr601/Ser603/Pro606 sites of IE180 protein and inhibiting the transcriptional activation activity of IE180 protein. This study provides a novel insight into the antiviral mechanism of resveratrol against herpes viruses.
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Affiliation(s)
- Xiangxiu Chen
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xu Song
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lixia Li
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yaqin Chen
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yuanfeng Zou
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Hongping Wan
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhao
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Huaqiao Tang
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Cheng Lv
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinghong Zhao
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhongqiong Yin
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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20
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Bhar A, Jain A, Das S. Natural therapeutics against SARS CoV2: the potentiality and challenges. VEGETOS (BAREILLY, INDIA) 2022; 36:322-331. [PMID: 35729947 PMCID: PMC9198211 DOI: 10.1007/s42535-022-00401-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/24/2022] [Accepted: 04/29/2022] [Indexed: 11/28/2022]
Abstract
The incidence of the COVID-19 pandemic completely reoriented global socio-economic parameters and human civilization have experienced the worst situation in the recent past. The rapid mutation rates in viruses have continuously been creating emerging variants of concerns (VOCs) which devastated different parts of the world with subsequent waves of infection. Although, series of antiviral drugs and vaccines were formulated but cent percent effectiveness of these drugs is still awaited. Many of these drugs have different side effects which necessitate proper trial before release. Plants are the storehouse of antimicrobial metabolites which have also long been utilized as traditional medicines against different viral infections. Although, proper mechanism of action of these traditional medicines are unknown, they may be a potential source of effective anti-COVID drug for future implications. Advanced bioinformatic applications have opened up a new arena in predicting these repurposed drugs as a potential COVID mitigator. The present review summarizes brief accounts of the corona virus with their possible entry mechanism. This study also tries to classify different possible anti COVID-19 plant-derived metabolites based on their probable mode of action. This review will surely provide useful information on repurposed drugs to combat COVID-19 in this critical situation.
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Affiliation(s)
- Anirban Bhar
- Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata, 700118 India
| | - Akansha Jain
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kolkata, West Bengal 700054 India
| | - Sampa Das
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kolkata, West Bengal 700054 India
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21
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Nowak-Perlak M, Bromke MA, Ziółkowski P, Woźniak M. The Comparison of the Efficiency of Emodin and Aloe-Emodin in Photodynamic Therapy. Int J Mol Sci 2022; 23:ijms23116276. [PMID: 35682955 PMCID: PMC9181794 DOI: 10.3390/ijms23116276] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/13/2022] Open
Abstract
Skin cancer (melanoma and non-melanoma) is the most frequent type of malignancy in the Caucasian population. Photodynamic therapy (PDT) as an interesting and unique strategy may potentially boost standard therapeutic approaches. In the present study, the potential of emodin and aloe-emodin as photosensitizers in photodynamic therapy has been investigated. The conducted research presents for the first-time comparison of the phototoxic and anti-cancerous effects of emodin and aloe-emodin on skin cancer cell lines, including SCC-25 representing cutaneous squamous cell carcinoma, MUG-Mel2 representing a melanoma cell line, and normal human keratinocytes HaCaT representing control normal skin cells. To assess the effectiveness of emodin and aloe-emodin as a photosensitizer in PDT on different skin cell lines, we performed MTT assay measuring cytotoxicity of natural compounds, cellular uptake, apoptosis with flow cytometry, and a wound-healing assay. Although emodin and aloe-emodin are isomers and differ only in the position of one hydroxyl group, our phototoxicity and apoptosis detection results show that both substances affect skin cancer cells (SSC-25 squamous cell carcinoma and MUG-Mel2 melanoma) and normal keratinocytes (HaCaT cell line) in other ways. In conclusion, our study provides evidence suggesting that emodin and aloe-emodin mediated PDT exhibits the potential for clinical development as a new effective and safe photosensitizer to treat skin cancer.
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Affiliation(s)
- Martyna Nowak-Perlak
- Department of Clinical and Experimental Pathology, Division of General and Experimental Pathology, Wroclaw Medical University, 50-368 Wroclaw, Poland; (M.N.-P.); (P.Z.)
| | - Mariusz A. Bromke
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, 50-368 Wroclaw, Poland;
| | - Piotr Ziółkowski
- Department of Clinical and Experimental Pathology, Division of General and Experimental Pathology, Wroclaw Medical University, 50-368 Wroclaw, Poland; (M.N.-P.); (P.Z.)
| | - Marta Woźniak
- Department of Clinical and Experimental Pathology, Division of General and Experimental Pathology, Wroclaw Medical University, 50-368 Wroclaw, Poland; (M.N.-P.); (P.Z.)
- Correspondence:
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22
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Prasetyo WE, Purnomo H, Sadrini M, Wibowo FR, Firdaus M, Kusumaningsih T. Identification of potential bioactive natural compounds from Indonesian medicinal plants against 3-chymotrypsin-like protease (3CL pro) of SARS-CoV-2: molecular docking, ADME/T, molecular dynamic simulations, and DFT analysis. J Biomol Struct Dyn 2022:1-18. [DOI: 10.1080/07391102.2022.2068071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Wahyu Eko Prasetyo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Heri Purnomo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Miracle Sadrini
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Fajar Rakhman Wibowo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Maulidan Firdaus
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Triana Kusumaningsih
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
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23
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Sadeghi M, Miroliaei M. Inhibitory effects of selected isoquinoline alkaloids against main protease (M pro) of SARS-CoV-2, in silico study. In Silico Pharmacol 2022; 10:5. [PMID: 35310017 PMCID: PMC8918422 DOI: 10.1007/s40203-022-00122-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 02/22/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global threat. Despite the production of various vaccines and different treatments, finding natural compounds to control COVID-19 is still a challenging task. Isoquinoline alkaloids are naturally occurring compounds known to have some potential antiviral activity. In this study, ten abundant isoquinoline alkaloids with antiviral activity were selected to analyze the preventive effect on COVID-19. A scrutinized evaluation based on Lipinski's rule showed that one out of ten compounds was toxic. Based on molecular docking analysis using Autodock software one of the best molecules with maximum negative binding energy was selected for further analysis. The Gromacs simulation analysis revealed that Coptisine has more action against active site Mpro of COVID-19. Overall, to make a rational design of various preventive analogues that inhibit the COVID-19, associated in vitro and in vivo analyses are needed to confirm this claim.
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Affiliation(s)
- Morteza Sadeghi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mehran Miroliaei
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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24
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Xiao J, Chen S, Chen Y, Su J. The potential health benefits of aloin from genus Aloe. Phytother Res 2022; 36:873-890. [PMID: 35040198 DOI: 10.1002/ptr.7371] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 01/04/2023]
Abstract
The Aloe species is known for its medicinal and cosmetic properties. Aloin is an active ingredient found in the leaves of medicinal plants of the genus Aloe. Aloin has attracted considerable interest for its antiinflammatory, anticancer, antibacterial, and antioxidant activities. However, since its clinical application is restricted by its unclear mechanism of action, a deeper understanding of its pharmacological activity is required. This review provides an overview of current pharmacological and toxicological studies published in English from February 2000 to August 2021. Herein, we summarized the sources and potential health benefits of aloin from a clinical application perspective to guide for further studies on the sources of aloin, aimed at efficiently increasing aloin production. Importantly, the function and mechanism of action of aloin remain unclarified. In future research, it is necessary to develop new approaches for studying the pharmacological molecular mechanisms underlying the activity of this compound against various diseases.
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Affiliation(s)
- Jianbin Xiao
- College of Life Science, Fujian Normal University, Fuzhou, China.,The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, China
| | - Siyuan Chen
- College of Life Science, Fujian Normal University, Fuzhou, China.,The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, China
| | - Youqiang Chen
- College of Life Science, Fujian Normal University, Fuzhou, China.,The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, China
| | - Jingqian Su
- College of Life Science, Fujian Normal University, Fuzhou, China.,Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou, China
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25
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Cetin A, Bursal E, Türkan F. 2-methylindole analogs as cholinesterases and glutathione S-transferase inhibitors: Synthesis, biological evaluation, molecular docking, and pharmacokinetic studies. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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26
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Bachar SC, Mazumder K, Bachar R, Aktar A, Al Mahtab M. A Review of Medicinal Plants with Antiviral Activity Available in Bangladesh and Mechanistic Insight Into Their Bioactive Metabolites on SARS-CoV-2, HIV and HBV. Front Pharmacol 2021; 12:732891. [PMID: 34819855 PMCID: PMC8606584 DOI: 10.3389/fphar.2021.732891] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/22/2021] [Indexed: 12/23/2022] Open
Abstract
Currently, viral infection is the most serious health issue which causing unexpected higher rate of death globally. Many viruses are not yet curable, such as corona virus-2 (SARS-CoV-2), human immunodeficiency virus (HIV), hepatitis virus, human papilloma virus and so others. Furthermore, the toxicities and ineffective responses to resistant strains of synthetic antiviral drugs have reinforced the search of effective and alternative treatment options, such as plant-derived antiviral drug molecules. Therefore, in the present review, an attempt has been taken to summarize the medicinal plants reported for exhibiting antiviral activities available in Bangladesh along with discussing the mechanistic insights into their bioactive components against three most hazardous viruses, namely SARS-CoV-2, HIV, and HBV. The review covers 46 medicinal plants with antiviral activity from 25 families. Among the reported 79 bioactive compounds having antiviral activities isolated from these plants, about 37 of them have been reported for significant activities against varieties of viruses. Hesperidin, apigenin, luteolin, seselin, 6-gingerol, humulene epoxide, quercetin, kaempferol, curcumin, and epigallocatechin-3-gallate (EGCG) have been reported to inhibit multiple molecular targets of SARS-CoV-2 viral replication in a number of in silico investigations. Besides, numerous in silico, in vitro, and in vivo bioassays have been demonstrated that EGCG, anolignan-A, and B, ajoene, curcumin, and oleanolic acid exhibit anti-HIV activity while piperine, ursolic acid, oleanolic acid, (+)-cycloolivil-4'-O-β-d-glucopyranoside, quercetin, EGCG, kaempferol, aloin, apigenin, rosmarinic acid, andrographolide, and hesperidin possess anti-HBV activity. Thus, the antiviral medicinal plants and the isolated bioactive compounds may be considered for further advanced investigations with the aim of the development of effective and affordable antiviral drugs.
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Affiliation(s)
- Sitesh C Bachar
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Kishor Mazumder
- Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh.,School of Optometry and Vision Science, UNSW Medicine, University of New South Wales (UNSW), Sydney, NSW, Australia.,School of Biomedical Sciences and Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga, NSW, Australia
| | - Ritesh Bachar
- Department of Pharmacy, School of Science and Engineering, University of Information Technology and Sciences, Dhaka, Bangladesh
| | - Asma Aktar
- Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Mamun Al Mahtab
- Department of Hepatology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
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27
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Targeting autophagy with natural products to prevent SARS-CoV-2 infection. J Tradit Complement Med 2021; 12:55-68. [PMID: 34664025 PMCID: PMC8516241 DOI: 10.1016/j.jtcme.2021.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/27/2021] [Accepted: 10/12/2021] [Indexed: 01/18/2023] Open
Abstract
Autophagy is a catabolic process that maintains internal homeostasis and energy balance through the lysosomal degradation of redundant or damaged cellular components. During virus infection, autophagy is triggered both in parenchymal and in immune cells with different finalistic objectives: in parenchymal cells, the goal is to destroy the virion particle while in macrophages and dendritic cells the goal is to expose virion-derived fragments for priming the lymphocytes and initiate the immune response. However, some viruses have developed a strategy to subvert the autophagy machinery to escape the destructive destiny and instead exploit it for virion assembly and exocytosis. Coronaviruses (like SARS-CoV-2) possess such ability. The autophagy process requires a set of proteins that constitute the core machinery and is controlled by several signaling pathways. Here, we report on natural products capable of interfering with SARS-CoV-2 cellular infection and replication through their action on autophagy. The present study provides support to the use of such natural products as adjuvant therapeutics for the management of COVID-19 pandemic to prevent the virus infection and replication, and so mitigating the progression of the disease.
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28
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Nalimu F, Oloro J, Kahwa I, Ogwang PE. Review on the phytochemistry and toxicological profiles of Aloe vera and Aloe ferox. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021; 7:145. [PMID: 34307697 PMCID: PMC8294304 DOI: 10.1186/s43094-021-00296-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/05/2021] [Indexed: 12/11/2022] Open
Abstract
Background Aloe vera and Aloe ferox have over the years been among the most sought-after Aloe species in the treatment of ailments worldwide. This review provides categorized literature on the phytochemical and scientifically proven toxicological profiles of A. vera and A. ferox to facilitate their exploitation in therapy. Main body of the abstract Original full-text research articles were searched in PubMed, ScienceDirect, Research gate, Google Scholar, and Wiley Online Library using specific phrases. Phenolic acids, flavonoids, tannins, and anthraquinones were the main phytochemical classes present in all the two Aloe species. Most of the phytochemical investigations and toxicity studies have been done on the leaves. Aloe vera and Aloe ferox contain unique phytoconstituents including anthraquinones, flavonoids, tannins, sterols, alkaloids, and volatile oils. Aloe vera hydroalcoholic leaf extract showed a toxic effect on Kabir chicks at the highest doses. The methanolic, aqueous, and supercritical carbon dioxide extracts of A. vera leaf gel were associated with no toxic effects. The aqueous leaf extract of A. ferox is well tolerated for short-term management of ailments but long-term administration may be associated with organ toxicity. Long-term administration of the preparations from A. vera leaves and roots was associated with toxic effects. Short conclusion This review provides beneficial information about the phytochemistry and toxicity of A. vera and A. ferox and their potential in the treatment of COVID-19 which up to date has no definite cure. Clinical trials need to be carried out to clearly understand the toxic effects of these species.
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Affiliation(s)
- Florence Nalimu
- Pharm-Bio Technology and Traditional Medicine Centre of Excellence, Mbarara University of Science and Technology, Mbarara, Uganda.,Department of Pharmaceutical Sciences, Faculty of Medicine, Mbarara University of Science and Technology, P.O. Box 1410, Mbarara, Uganda
| | - Joseph Oloro
- Pharm-Bio Technology and Traditional Medicine Centre of Excellence, Mbarara University of Science and Technology, Mbarara, Uganda.,Department of Pharmacology and Therapeutics, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Ivan Kahwa
- Pharm-Bio Technology and Traditional Medicine Centre of Excellence, Mbarara University of Science and Technology, Mbarara, Uganda.,Department of Pharmacy, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Patrick Engeu Ogwang
- Pharm-Bio Technology and Traditional Medicine Centre of Excellence, Mbarara University of Science and Technology, Mbarara, Uganda.,Department of Pharmacy, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
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29
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Oubahmane M, Hdoufane I, Bjij I, Jerves C, Villemin D, Cherqaoui D. COVID-19: In silico identification of potent α-ketoamide inhibitors targeting the main protease of the SARS-CoV-2. J Mol Struct 2021; 1244:130897. [PMID: 34149065 PMCID: PMC8205609 DOI: 10.1016/j.molstruc.2021.130897] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/23/2022]
Abstract
The COVID-19 has been creating a global crisis, causing countless deaths and unbearable panic. Despite the progress made in the development of the vaccine, there is an urge need for the discovery of antivirals that may better work at different stages of SARS-CoV-2 reproduction. The main protease (Mpro) of the SARS-CoV-2 is a crucial therapeutic target due to its critical function in virus replication. The α-ketoamide derivatives represent an important class of inhibitors against the Mpro of the SARS-CoV. While there is 99% sequence similarity between SARS-CoV and SARS-CoV-2 main proteases, anti-SARS-CoV compounds may have a huge demonstration's prospect of their effectiveness against the SARS-CoV-2. In this study, we applied various computational approaches to investigate the inhibition potency of novel designed α-ketoamide-based compounds. In this regard, a set of 21 α-ketoamides was employed to construct a QSAR model, using the genetic algorithm-multiple linear regression (GA-MLR), as well as a pharmacophore fit model. Based on the GA-MLR model, 713 new designed molecules were reduced to 150 promising hits, which were later subject to the established pharmacophore fit model. Among the 150 compounds, the best selected compounds (3 hits) with greater pharmacophore fit score were further studied via molecular docking, molecular dynamic simulations along with the Absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Our approach revealed that the three hit compounds could serve as potential inhibitors against the SARS-CoV-2 Mpro target.
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Affiliation(s)
- Mehdi Oubahmane
- Department of Chemistry, Faculty of Sciences Semlalia, BP, 2390 Marrakech, Morocco
| | - Ismail Hdoufane
- Department of Chemistry, Faculty of Sciences Semlalia, BP, 2390 Marrakech, Morocco
| | - Imane Bjij
- Department of Chemistry, Faculty of Sciences Semlalia, BP, 2390 Marrakech, Morocco
| | - Carola Jerves
- Departamento de Quimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal.,Facultad de Ciencias Químicas, Universidad de Cuenca, Cuenca, Ecuador
| | - Didier Villemin
- Ecole Nationale Supérieure d'Ingénieurs (ENSICAEN) Laboratoire de Chimie Moléculaire et Thioorganique. UMR 6507 CNRS, INC3M, FR3038, Labex EMC3, Labex SynOrg ENSICAEN & Université de Caen, France
| | - Driss Cherqaoui
- Department of Chemistry, Faculty of Sciences Semlalia, BP, 2390 Marrakech, Morocco
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30
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Cetin A. In silico studies on stilbenolignan analogues as SARS-CoV-2 Mpro inhibitors. Chem Phys Lett 2021; 771:138563. [PMID: 33776065 PMCID: PMC7983322 DOI: 10.1016/j.cplett.2021.138563] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022]
Abstract
COVID-19, a new strain of coronavirus family, was identified at the end of 2019 in China. The COVID-19 virus spread rapidly all over the world. Scientists strive to find virus-specific antivirals for the treatment of COVID-19. The present study reports a molecular docking study of the stilbenolignans and SARS-CoV-2 main protease (SARS-CoV-2 Mpro) inhibitors. The detailed interactions between the stilbenolignan analogues and SARS-CoV-2 Mpro inhibitors were determined as hydrophobic bonds, hydrogen bonds and electronic bonds, inhibition activity, ligand efficiency, bonding type and distance and etc. The binding energies of the stilbenolignan analogues were obtained from the molecular docking of SARS-CoV-2 Mpro. Lehmbachol D, Maackolin, Gnetucleistol, Gnetifolin F, Gnetofuran A and Aiphanol were found to be -7.7, -8.2, -7.3, -8.5, -8.0 and -7.3 kcal/mol, respectively. Osirus, Molinspiration and SwissADME chemoinformatic tools were used to examine ADMET properties, pharmacokinetic parameters and toxicological characteristics of the stilbenolignan analogues. All analogues obey the Lipinski's rule of five. Furthermore, stilbenolignan analogues were studied to predict their binding affinities against SARS-CoV-2 Mpro using molecular modeling and simulation techniques, and the binding free energy calculations of all complexes were calculated using the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) method. With the data presented here it has been observed that these analogues may be a good candidate for SARS-CoV-2 Mpro in vivo studies, so more research can be done on stilbenolignan analogues.
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31
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Abouelela ME, Assaf HK, Abdelhamid RA, Elkhyat ES, Sayed AM, Oszako T, Belbahri L, El Zowalaty AE, Abdelkader MSA. Identification of Potential SARS-CoV-2 Main Protease and Spike Protein Inhibitors from the Genus Aloe: An In Silico Study for Drug Development. Molecules 2021; 26:1767. [PMID: 33801151 PMCID: PMC8004122 DOI: 10.3390/molecules26061767] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/22/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-2) disease is a global rapidly spreading virus showing very high rates of complications and mortality. Till now, there is no effective specific treatment for the disease. Aloe is a rich source of isolated phytoconstituents that have an enormous range of biological activities. Since there are no available experimental techniques to examine these compounds for antiviral activity against SARS-CoV-2, we employed an in silico approach involving molecular docking, dynamics simulation, and binding free energy calculation using SARS-CoV-2 essential proteins as main protease and spike protein to identify lead compounds from Aloe that may help in novel drug discovery. Results retrieved from docking and molecular dynamics simulation suggested a number of promising inhibitors from Aloe. Root mean square deviation (RMSD) and root mean square fluctuation (RMSF) calculations indicated that compounds 132, 134, and 159 were the best scoring compounds against main protease, while compounds 115, 120, and 131 were the best scoring ones against spike glycoprotein. Compounds 120 and 131 were able to achieve significant stability and binding free energies during molecular dynamics simulation. In addition, the highest scoring compounds were investigated for their pharmacokinetic properties and drug-likeness. The Aloe compounds are promising active phytoconstituents for drug development for SARS-CoV-2.
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Affiliation(s)
- Mohamed E. Abouelela
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut-Branch, Assiut 71524, Egypt; (M.E.A.); (H.K.A.); (R.A.A.); (E.S.E.)
| | - Hamdy K. Assaf
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut-Branch, Assiut 71524, Egypt; (M.E.A.); (H.K.A.); (R.A.A.); (E.S.E.)
| | - Reda A. Abdelhamid
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut-Branch, Assiut 71524, Egypt; (M.E.A.); (H.K.A.); (R.A.A.); (E.S.E.)
| | - Ehab S. Elkhyat
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut-Branch, Assiut 71524, Egypt; (M.E.A.); (H.K.A.); (R.A.A.); (E.S.E.)
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt;
| | - Tomasz Oszako
- Department of Forest Protection, Forest Research Institute, 05-090 Sekocin Stary, Poland;
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchatel, 2000 Neuchatel, Switzerland
| | - Ahmed E. El Zowalaty
- Sahlgrenska Center for Cancer Research, Department of Surgery, Institute of Clinical Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
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Olasupo SB, Uzairu A, Shallangwa GA, Uba S. Unveiling novel inhibitors of dopamine transporter via in silico drug design, molecular docking, and bioavailability predictions as potential antischizophrenic agents. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021. [DOI: 10.1186/s43094-021-00198-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The inhibition of dopamine transporter is known to play a significant role in the treatment of schizophrenia-related and other mental disorders. In a continuing from our previous study, computational drug design approach, molecular docking simulation, and pharmacokinetics study were explored for the identification of novel inhibitors dopamine transporter as potential Antischizophrenic agents. Consequently, thirteen (13) new inhibitors of dopamine transporter were designed by selecting the molecule with serial number 39 from our previous study as the template molecule because it exhibits good pharmacological attributes.
Results
Molecular docking simulation results revealed excellent molecular interactions between the protein target (PDB: 4m48) and the ligands (designed inhibitors) with major interactions that involved hydrogen bonding and hydrophobic interactions. Also, some of the designed inhibitors displayed a superior binding affinity range from − 10.0 to − 10.7 kcal/mol compared to the referenced drug (Lumateperone) with a binding affinity of − 9.7 kcal/mol. Computed physicochemical parameters showed that none of the designed inhibitors including the referenced drug violate Lipinski’s rule of five indicating that all the designed inhibitors would be orally bioavailable as potential drug candidates. Similarly, the ADMET/pharmacokinetics evaluations of some designed inhibitors revealed that they possessed good absorption, distribution, metabolism and excretion properties and none of the inhibitors is neither carcinogens nor toxic toward human ether-a-go-go related gene (hERG I) inhibitor or skin sensitization. Likewise, the BOILED-Egg graphics unveils that all the designed inhibitors demonstrate a high probability to be absorbed by the human gastrointestinal tract and could permeate into the brain. Besides, the predicted bioactive parameters suggested that all the selected inhibitors would be active as drug candidates. Furthermore, the synthetic accessibility scores for all the selected inhibitors and referenced drug lied within the easy zone (i.e., between 1–4) with their computed values range from 2.55 to 3.92, this implies that all the selected inhibitors would be very easy to synthesize in the laboratory.
Conclusions
Hence, all the designed inhibitors having shown excellent pharmacokinetics properties and good bioavailabilities attributes with remarkable biochemical interactions could be developed and optimized as novel Antischizophrenic agents after the conclusion of other experimental investigations.
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Berries anthocyanins as potential SARS-CoV–2 inhibitors targeting the viral attachment and replication; molecular docking simulation. EGYPTIAN JOURNAL OF PETROLEUM 2021; 30. [PMCID: PMC7825908 DOI: 10.1016/j.ejpe.2021.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The viral respiratory disease, severe acute respiratory syndrome (SARS), has turned into a global health concern. Till now, there is no drug or vaccine has yet been specifically approved for SARS-CoV-2. One of the urgent solutions against the recent COVID-19 disease is the use of dietary molecules, which can be found abundantly in functional food. In the current study, we have conducted a molecular docking approach for eighteen dietary molecules belong to the subclass of anthocyanins, as potential inhibitors of the main protease and spike glycoprotein of SARS-CoV-2. Both selected targets, playing a vital role in attachment and replication of the virus. The results indicated that cyanidin-3-arabinoside exhibited the lowest binding energy and located onto the pocket through a sufficient number of hydrogen bonds with the main protease virus. However, pelargonidin-3-glucoside and pelargonidin 3-rhamnoside display significant binding energy with the spike glycoprotein of SARS-CoV-2. All compounds mentioned above shown high drug-likeness and fulfils the Lipinski’s rule of five, as well as confer favorable toxicity parameters, in addition to ADME values. Considering the obtained results, regular consumption of berry fruits, which are rich in anthocyanin compounds, should be supportive to inhibit viral infectious by reducing of propagation and pathogenicity of SARS-CoV–2.
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34
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Mahmud S, Uddin MAR, Paul GK, Shimu MSS, Islam S, Rahman E, Islam A, Islam MS, Promi MM, Emran TB, Saleh MA. Virtual screening and molecular dynamics simulation study of plant-derived compounds to identify potential inhibitors of main protease from SARS-CoV-2. Brief Bioinform 2021; 22:bbaa428. [PMID: 33517367 PMCID: PMC7929365 DOI: 10.1093/bib/bbaa428] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/09/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022] Open
Abstract
The new coronavirus (SARS-CoV-2) halts the world economy and caused unbearable medical emergency due to high transmission rate and also no effective vaccine and drugs has been developed which brought the world pandemic situations. The main protease (Mpro) of SARS-CoV-2 may act as an effective target for drug development due to the conservation level. Herein, we have employed a rigorous literature review pipeline to enlist 3063 compounds from more than 200 plants from the Asian region. Therefore, the virtual screening procedure helps us to shortlist the total compounds into 19 based on their better binding energy. Moreover, the Prime MM-GBSA procedure screened the compound dataset further where curcumin, gartanin and robinetin had a score of (−59.439, −52.421 and − 47.544) kcal/mol, respectively. The top three ligands based on binding energy and MM-GBSA scores have most of the binding in the catalytic groove Cys145, His41, Met165, required for the target protein inhibition. The molecular dynamics simulation study confirms the docked complex rigidity and stability by exploring root mean square deviations, root mean square fluctuations, solvent accessible surface area, radius of gyration and hydrogen bond analysis from simulation trajectories. The post-molecular dynamics analysis also confirms the interactions of the curcumin, gartanin and robinetin in the similar binding pockets. Our computational drug designing approach may contribute to the development of drugs against SARS-CoV-2.
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Affiliation(s)
- Shafi Mahmud
- Genetic Engineering and Biotechnology at the University of Rajshahi, Bangladesh
| | - Mohammad Abu Raihan Uddin
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong, Bangladesh
| | - Gobindo Kumar Paul
- Department of Genetic Engineering and Biotechnology at the University of Rajshahi, Bangladesh
| | | | - Saiful Islam
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong, Bangladesh
| | - Ekhtiar Rahman
- Genetic Engineering and Biotechnology at the University of Rajshahi, Bangladesh
| | - Ariful Islam
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Bangladesh
| | - Md Samiul Islam
- Department of Molecular Plant Pathology, Huazhong Agricultural University, Wuhan, China
| | - Maria Meha Promi
- Genetic Engineering and Biotechnology at the University of Rajshahi, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy at the BGC Trust University, Bangladesh
- University of Chittagong, PhD from Graduate School of Medicines, Kanazawa University, Japan
| | - Md Abu Saleh
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Administration Building 1, Rajshahi 6205, Bangladesh
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appeared in 2019 and is the causative agent of the new pandemic viral disease COVID-19. The outbreak of COVID-19 infection is affecting the entire world, thus many researchers and scientists are desperately looking for suitable vaccines and treatment options. Indeed, researches to find potential inhibitors of SARS-CoV-2 are mainly focussed on targeting virus-host interactions or inhibiting viral assembly. Additionally, drugs and other therapeutic agents that modulate broad-spectrum host innate immune responses or interfere with signalling pathways involved in viral replication are important. These drugs may be capable of engaging host receptors or proteases utilised for viral entry or may impact the endocytosis pathway. 3CLpro (3-chymotrypsin-like protease), PLpro (papain-like protease), RdRp (RNA-dependent RNA polymerase), S protein (viral spike glycoprotein), TMPRSS2 (transmembrane protease serine 2), ACE2 (angiotensin-converting enzyme 2), and AT2 (angiotensin AT2 receptor) are important targets. With no approved therapies, this pandemic illustrates the urgent need for safe and broad-spectrum antiviral agents and strategies against SARS-CoV-2 and future pathogenic viruses. In this review, we discussed about the recent trends and important challenges regarding the potential inhibitors, antiviral drugs and nanomaterials screened against SARS-CoV-2.
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Affiliation(s)
| | - Siavash Iravani
- Faculty of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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Alfaro M, Alfaro I, Angel C. Identification of potential inhibitors of SARS-CoV-2 papain-like protease from tropane alkaloids from Schizanthus porrigens: A molecular docking study. Chem Phys Lett 2020; 761:138068. [PMID: 33052144 PMCID: PMC7540197 DOI: 10.1016/j.cplett.2020.138068] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/16/2022]
Abstract
Antivirals against SARS-CoV-2 are needed. The papain-like protease represents an important target for antivirals. We investigated tropane alkaloids from Schizanthus porrigens. By molecular docking and MS simulations we identified two leads. Shizanthine Z has favorable ADME properties and can be considered a lead.
This paper presents identification of potential inhibitors of SARS-CoV-2 papain-like protease from tropane alkaloids from Schizanthus porrigens, using molecular docking method. Binding affinities were compared with those obtained with Lopinavir as a SARS-CoV-2 papain-like protease inhibitor. Overall, our findings indicate that Schizanthine Z binds to the SARS-CoV-2 papain-like protease with relatively high affinity and favorable ADME properties. Therefore, Schizanthine Z may represent an appropriate compound for further evaluation in antiviral assays.
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Affiliation(s)
- Marco Alfaro
- Departamento de Química, Campus Andrés Bello, Facultad de Ciencias, Universidad de La Serena, Colina el Pino S/N, La Serena, Chile.,Instituto de Investigación Multidisciplinario en Ciencia y Tecnología, Universidad de La Serena, Colina el Pino S/N, La Serena, Chile
| | - Ignacio Alfaro
- Departamento de Química, Campus Andrés Bello, Facultad de Ciencias, Universidad de La Serena, Colina el Pino S/N, La Serena, Chile.,Centro de Investigación CENBIOEL, La Serena, Chile
| | - Constanza Angel
- Departamento de Química, Campus Andrés Bello, Facultad de Ciencias, Universidad de La Serena, Colina el Pino S/N, La Serena, Chile.,Centro de Investigación CENBIOEL, La Serena, Chile
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37
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A Computational Study to Identify Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro) from Eucalyptus Active Compounds. COMPUTATION 2020. [DOI: 10.3390/computation8030079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was found to be a severe threat to global public health in late 2019. Nevertheless, no approved medicines have been found to inhibit the virus effectively. Anti-malarial and antiviral medicines have been reported to target the SARS-CoV-2 virus. This paper chose eight natural eucalyptus compounds to study their binding interactions with the SARS-CoV-2 main protease (Mpro) to assess their potential for becoming herbal drugs for the new SARS-CoV-2 infection virus. In-silico methods such as molecular docking, molecular dynamics (MD) simulations, and Molecular Mechanics Poisson Boltzmann Surface Area (MM/PBSA) analysis were used to examine interactions at the atomistic level. The results of molecular docking indicate that Mpro has good binding energy for all compounds studied. Three docked compounds, α-gurjunene, aromadendrene, and allo-aromadendrene, with highest binding energies of −7.34 kcal/mol (−30.75 kJ/mol), −7.23 kcal/mol (−30.25 kJ/mol), and −7.17 kcal/mol (−29.99 kJ/mol) respectively, were simulated with GROningen MAchine for Chemical Simulations (GROMACS) to measure the molecular interactions between Mpro and inhibitors in detail. Our MD simulation results show that α-gurjunene has the strongest binding energy of −20.37 kcal/mol (−85.21 kJ/mol), followed by aromadendrene with −18.99 kcal/mol (−79.45 kJ/mol), and finally allo-aromadendrene with −17.91 kcal/mol (−74.95 kJ/mol). The findings indicate that eucalyptus may be used to inhibit the Mpro enzyme as a drug candidate. This is the first computational analysis that gives an insight into the potential role of structural flexibility during interactions with eucalyptus compounds. It also sheds light on the structural design of new herbal medicinal products against Mpro.
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