1
|
Abudeshesh RM, Aboul-Nasr AM, Khairy HM, Atia MAM, Sabra MA. Differential impacts of interactions between Serendipita indica, Chlorella vulgaris, Ulva lactuca and Padina pavonica on Basil (Ocimum basilicumL.). Plant Physiol Biochem 2024; 206:108218. [PMID: 38029616 DOI: 10.1016/j.plaphy.2023.108218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023]
Abstract
Plant biostimulants (PBs) are used globally to increase crop yield and productivity. PBs such as (Serendipita indica) or algal extracts stimulate and accelerate plant physiological processes. The physiological, ecological, and biochemical effects of (Serendipita indica) or algal extracts individually and in combination on basil plant (Ocimum basilicum L.) were investigated. Macroalgae samples were collected from Abu Qir, Alexandria, Egypt. The growth parameters, chlorophyll index, and biochemical composition of basil were analyzed at 90th day. The (Chlorella vulgaris) + (Serendipita indica) (MI + F) treatment increased chlorophyll index by 61.7% (SPAD) compared to control. (Chlorella vulgaris) had the highest growth hormones, including GA3 at 158.2 ppb, GA4 at 149.1 ppb, GA7 at 142.6 ppb, IAA at 136.6 ppb, and TC at 130.9 ppb, while (Ulva lactuca) had the lowest. The MI + F treatment yielded the highest essential oil and antioxidant values. Treatment with (Chlorella vulgaris) increased S. indica colonization by 66%. In contrast, Ulva lactuca and (Padina Pavonica) inhibited S. indica colonization by 80% and 40%, respectively. (Ulva lactuca) and (Padina Pavonica) inhibited S. indica colonization by 80% and 40%, respectively. Combined treatments had a greater influence on basil performance than the individual treatments. The evidence of synergistic/additive benefits to plants performance due to the interactive effects of (Chlorella vulgaris) and (Serendipita indica) had been studied. Complementary modes of action between (Chlorella vulgaris) and (Serendipita indica), through their components newly emerging properties on basil, may explain observed synergistic effects. This study explores the potential of microbial-algal interactions, particularly (Chlorella vulgaris) and (Serendipita indica), as innovative plant biostimulants. These interactions demonstrate positive effects on basil growth, offering promise for more effective microbial-based formulations to enhance crop productivity and sustainability in agriculture. These novelties will help create a second generation of PBs with integrated and complementary actions.
Collapse
Affiliation(s)
| | - Amal M Aboul-Nasr
- Agricultural Botany Department, (Agricultural Microbiology), Faculty of Agriculture Saba Basha, Alexandria University, Egypt
| | - Hanan M Khairy
- National Institute of Oceanography and Fisheries, NIOF, Egypt
| | - Mohamed A M Atia
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Mayada A Sabra
- Agricultural Botany Department, (Agricultural Microbiology), Faculty of Agriculture Saba Basha, Alexandria University, Egypt
| |
Collapse
|
2
|
Mohamed TA, Abdelmawgoud SM, Hamdy AA, Ibrahim MAA, Elshamy AI, Atia MAM, Kassem HA, Hegazy MEF, Selim NM. A new cembranoid from the Red Sea soft coral Sarcophyton acutum. Nat Prod Res 2024; 38:512-522. [PMID: 36200738 DOI: 10.1080/14786419.2022.2130915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/25/2022] [Indexed: 10/10/2022]
Abstract
The Red Sea soft coral Sarcophyton acutum ethyl acetate extract has afforded one new cembranoid; sarcacutumolid A (1), along with six known metabolites have been isolated from S. acutum for the first time (2-7). Chemical structures were elucidated by employing several spectroscopic analyses. The cytotoxic potential of the isolated compounds was assessed against four human cancer cell lines; hepatocellular (HepG2), cervical (HeLa), breast (MCF-7) and colorectal cancer (Colo-205). Sarcacutumolid A (1) and gorgosterol (7) inhibited colorectal cancer cell proliferation in a concentration-dependent manner with IC50 values of 35.5 and 44.0 μM, respectively.
Collapse
Affiliation(s)
- Tarik A Mohamed
- Chemistry of Medicinal Plants Dept, Chemistry of Medicinal Plants, Dokki, Giza, Egypt
| | - Seba M Abdelmawgoud
- Chemistry of Natural and Microbial Products Department, National Research Centre, Dokki, Giza, Egypt
| | - Abdelhamid A Hamdy
- Chemistry of Natural and Microbial Products Department, National Research Centre, Dokki, Giza, Egypt
| | - Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Abdelsamed I Elshamy
- Department of Natural Compounds Chemistry, National Research Centre, Dokki, Giza, Egypt
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt
| | - Hanaa A Kassem
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | | | - Nabil M Selim
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| |
Collapse
|
3
|
Ibrahim MAA, Abdeljawaad KAA, Jaragh-Alhadad LA, Oraby HF, Atia MAM, Alzahrani OR, Mekhemer GAH, Moustafa MF, Shawky AM, Sidhom PA, Abdelrahman AHM. Potential drug candidates as P-glycoprotein inhibitors to reverse multidrug resistance in cancer: an in silico drug discovery study. J Biomol Struct Dyn 2023; 41:13977-13992. [PMID: 36883864 DOI: 10.1080/07391102.2023.2176360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/29/2023] [Indexed: 03/09/2023]
Abstract
The failure of chemotherapy in the treatment of carcinoma is mainly due to the development of multidrug resistance (MDR), which is largely caused by the overexpression of P-glycoprotein (P-gp/ABCB1/MDR1). Until recently, the 3D structure of the P-gp transporter has not been experimentally resolved, which restricted the discovery of prospective P-gp inhibitors utilizing in silico techniques. In this study, the binding energies of 512 drug candidates in clinical or investigational stages were assessed as potential P-gp inhibitors employing in silico methods. On the basis of the available experimental data, the performance of the AutoDock4.2.6 software to predict the drug-P-gp binding mode was initially validated. Molecular docking and molecular dynamics (MD) simulations combined with molecular mechanics-generalized Born surface area (MM-GBSA) binding energy computations were subsequently conducted to screen the investigated drug candidates. Based on the current results, five promising drug candidates, namely valspodar, dactinomycin, elbasvir, temsirolimus, and sirolimus, showed promising binding energies against P-gp transporter with ΔGbinding values of -126.7, -112.1, -111.9, -102.9, and -101.4 kcal/mol, respectively. The post-MD analyses revealed the energetical and structural stabilities of the identified drug candidates in complex with the P-gp transporter. Furthermore, in order to mimic the physiological conditions, the potent drugs complexed with the P-gp were subjected to 100 ns MD simulations in an explicit membrane-water environment. The pharmacokinetic properties of the identified drugs were predicted and demonstrated good ADMET characteristics. Overall, these results indicated that valspodar, dactinomycin, elbasvir, temsirolimus, and sirolimus hold promise as prospective P-gp inhibitors and warrant further invitro/invivo investigations.
Collapse
Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, South Africa
| | - Khlood A A Abdeljawaad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | | | - Hesham Farouk Oraby
- Deanship of Scientific Research, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt
| | - Othman R Alzahrani
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Mahmoud F Moustafa
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, Saudi Arabia
| | - Peter A Sidhom
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Alaa H M Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| |
Collapse
|
4
|
Abdelmoneim TK, Mohamed MSM, Abdelhamid IA, Wahdan SFM, Atia MAM. Development of rapid and precise approach for quantification of bacterial taxa correlated with soil health. Front Microbiol 2023; 13:1095045. [PMID: 36713193 PMCID: PMC9878287 DOI: 10.3389/fmicb.2022.1095045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/29/2022] [Indexed: 01/14/2023] Open
Abstract
The structure and dynamic of soil bacterial community play a crucial role in soil health and plant productivity. However, there is a gap in studying the un-/or reclaimed soil bacteriome and its impact on future plant performance. The 16S metagenomic analysis is expensive and utilize sophisticated pipelines, making it unfavorable for researchers. Here, we aim to perform (1) in silico and in vitro validation of taxon-specific qPCR primer-panel in the detection of the beneficial soil bacterial community, to ensure its specificity and precision, and (2) multidimensional analysis of three soils/locations in Egypt ('Q', 'B', and 'G' soils) in terms of their physicochemical properties, bacteriome composition, and wheat productivity as a model crop. The in silico results disclosed that almost all tested primers showed high specificity and precision toward the target taxa. Among 17 measured soil properties, the electrical conductivity (EC) value (up to 5 dS/m) of 'Q' soil provided an efficient indicator for soil health among the tested soils. The 16S NGS analysis showed that the soil bacteriome significantly drives future plant performance, especially the abundance of Proteobacteria and Actinobacteria as key indicators. The functional prediction analysis results disclosed a high percentage of N-fixing bacterial taxa in 'Q' soil compared to other soils, which reflects their positive impact on wheat productivity. The taxon-specific qPCR primer-panel results revealed a precise quantification of the targeted taxa compared to the 16S NGS analysis. Moreover, 12 agro-morphological parameters were determined for grown wheat plants, and their results showed a high yield in the 'Q' soil compared to other soils; this could be attributed to the increased abundance of Proteobacteria and Actinobacteria, high enrichment in nutrients (N and K), or increased EC/nutrient availability. Ultimately, the potential use of a taxon-specific qPCR primer-panel as an alternative approach to NGS provides a cheaper, user-friendly setup with high accuracy.
Collapse
Affiliation(s)
- Taghreed Khaled Abdelmoneim
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt,Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt
| | - Mahmoud S. M. Mohamed
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
| | | | | | - Mohamed A. M. Atia
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt,*Correspondence: Mohamed A. M. Atia, ✉
| |
Collapse
|
5
|
Abd Almaksoud HM, El-Hawary SS, Atia MAM, Sayed AM, El-Daly M, Kamel AA, Elimam H, Abdelmohsen UR, Saber FR. Anti-androgenic potential of the fruit extracts of certain Egyptian Sabal species and their genetic variability studies: a metabolomic-molecular modeling approach. Food Funct 2022; 13:7813-7830. [PMID: 35766799 DOI: 10.1039/d1fo03930j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This work aimed to evaluate the anti-androgenic activity of S. blackburniana Glazebrook, S. causiarum (O. F. Cook) Becc, and S. palmetto (Walter) Lodd. Ex Schult fruit extracts in rats using Hershberger assay. Furthermore, to annotate secondary metabolites using LC-HRMS technique, to investigate underlying mechanisms responsible for 5-α-reductase inhibitory activity in silico and to compare cytotoxic effects in vitro against human prostatic stromal myofibroblast (WPMY-1) and human benign prostatic hyperplasia (BPH-1) cell lines using MTT, 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (spectrophotometrically). The results showed significant anti-androgenic implications with varying degrees, markedly decreased sex organ weights, reduction in testosterone and increase in LH and FSH serum levels. Genetic diversity study ensured the correct genotype and revealed outperformance of SCoT compared with CBDP markers to interpret polymorphism among selected species. S. blackburniana exhibited selective cytotoxic activity against BPH-1 compared to finasteride. Molecular docking of 59 dereplicated metabolites belonging to various chemical classes revealed that helasaoussazine, pinoresinol and tetra-O-caffeoylquinic acid are the top inhibitors of 5-α-reductase-2. Our study provides an insight into the anti-androgenic activity of selected species of Egyptian Sabal supported by docking study for the first time, demonstrates safety toward liver and kidney and highlights a new potential therapeutic candidate for anti-androgenic related disease such as benign prostatic hyperplasia.
Collapse
Affiliation(s)
| | - Seham S El-Hawary
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt.
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
| | - Mahmoud El-Daly
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, Minia University, El-Minia 61519, Egypt
| | - Amr Abdallah Kamel
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, Minia University, El-Minia 61519, Egypt
| | - Hanan Elimam
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt.,Department of Biochemistry, Faculty of Pharmacy, Sinai University, Kantara, Egypt
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt. .,Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, 61111 New Minia City, Minia, Egypt
| | - Fatema R Saber
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt.
| |
Collapse
|
6
|
Nasrallah AK, Atia MAM, Abd El-Maksoud RM, Kord MA, Fouad AS. Salt Priming as a Smart Approach to Mitigate Salt Stress in Faba Bean (Vicia faba L.). Plants 2022; 11:plants11121610. [PMID: 35736763 PMCID: PMC9228577 DOI: 10.3390/plants11121610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 01/24/2023]
Abstract
The present investigation aims to highlight the role of salt priming in mitigating salt stress on faba bean. In the absence of priming, the results reflected an increase in H2O2 generation and lipid peroxidation in plants subjected to 200 mM salt shock for one week, accompanied by a decline in growth, photosynthetic pigments, and yield. As a defense, the shocked plants showed enhancements in ascorbate peroxidase (APX), catalase (CAT), glutathione reductase (GR), peroxidase (POX), and superoxide dismutase (SOD) activities. Additionally, the salt shock plants revealed a significant increase in phenolics and proline content, as well as an increase in the expression levels of glutathione (GSH) metabolism-related genes (the L-ascorbate peroxidase (L-APX) gene, the spermidine synthase (SPS) gene, the leucyl aminopeptidase (LAP) gene, the aminopeptidase N (AP-N) gene, and the ribonucleo-side-diphosphate reductase subunit M1 (RDS-M) gene). On the other hand, priming with increasing concentrations of NaCl (50–150 mM) exhibited little significant reduction in some growth- and yield-related traits. However, it maintained a permanent alert of plant defense that enhanced the expression of GSH-related genes, proline accumulation, and antioxidant enzymes, establishing a solid defensive front line ameliorating osmotic and oxidative consequences of salt shock and its injurious effect on growth and yield.
Collapse
Affiliation(s)
- Amira K. Nasrallah
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (A.K.N.); (M.A.K.)
| | - Mohamed A. M. Atia
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt
- Correspondence: (M.A.M.A.); (A.S.F.); Tel.: +20-1000164922 (M.A.M.A.); +20-1203770992 (A.S.F.)
| | - Reem M. Abd El-Maksoud
- Nucleic Acid & Protein Chemistry Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Maimona A. Kord
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (A.K.N.); (M.A.K.)
| | - Ahmed S. Fouad
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (A.K.N.); (M.A.K.)
- Correspondence: (M.A.M.A.); (A.S.F.); Tel.: +20-1000164922 (M.A.M.A.); +20-1203770992 (A.S.F.)
| |
Collapse
|
7
|
Mohamed TA, Ali SK, Elshamy AI, Saleh IA, Ibrahim MAA, Atia MAM, Alshammari SO, Mohamed AEHH, Hussien TA, Hamed AR, Saedi HRE, Abdel-Azim NS, Shams KA, Efferth T, Saker M, Paré PW, Hegazy MEF. Plant cell cultures: An enzymatic tool for polyphenolic and flavonoid transformations. Phytomedicine 2022; 100:154019. [PMID: 35325826 DOI: 10.1016/j.phymed.2022.154019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/26/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND In the pharmaceutical sector, tissue culture techniques for large-scale production of natural chemicals can be a less expensive alternative to large-scale synthesis. Although recent biotransformation research have used plant cell cultures to target a wide range of bioactive compounds, more compiled information and synopses are needed to better understand metabolic pathways and improve biotransformation efficiencies. PURPOSE This report reviews the biochemical transformation of phenolic natural products by plant cell cultures in order to identify potential novel biotechnological approaches for ensuring more homogeneous and stable phenolic production year-round under controlled environmental conditions. METHODS Articles on the use of plant cell culture for polyphenolic and flavonoid transformations (1988 - 2021) were retrieved from SciFinder, PubMed, Scopus, and Web of Science through electronic and manual search in English. Following that, the authors chose the required papers based on the criteria they defined. The following keywords were used for the online search: biotransformation, Plant cell cultures, flavonoids, phenolics, and pharmaceutical products. RESULTS The initial search found a total of 96 articles. However, only 70 of them were selected as they met the inclusion criteria defined by the authors. The analysis of these studies revealed that plant tissue culture is applicable for the large-scale production of plant secondary metabolites including the phenolics, which have high therapeutic value. CONCLUSION Plant tissue cultures could be employed as an efficient technique for producing secondary metabolites including phenolics. Phenolics possess a wide range of therapeutic benefits, as anti-oxidant, anti-cancer, and anti-inflammatory properties. Callus culture, suspension cultures, transformation, and other procedures have been used to improve the synthesis of phenolics. Their production on a large scale is now achievable. More breakthroughs will lead to newer insights and, without a doubt, to a new era of phenolics-based pharmacological agents for the treatment of a variety of infectious and degenerative disorders.
Collapse
Affiliation(s)
- Tarik A Mohamed
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Sherin K Ali
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Abdelsamed I Elshamy
- Natural Compounds Chemistry Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Ibrahim A Saleh
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Shifaa O Alshammari
- Department of Biology, College of Science, University of Hafr Al Batin, Hafar Al Batin, Saudi Arabia
| | | | - Taha A Hussien
- Pharmacognosy Department, Faculty of Pharmacy, Sphinx University, New Assiut City, Assiut 10, Egypt
| | - Ahmed R Hamed
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Hesham R El Saedi
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm S-10691, Sweden; nternational Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China; Department of Chemistry, Faculty of Science, El-Menoufia University, Shebin El-Kom 32512, Egypt
| | - Nahla S Abdel-Azim
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Khaled A Shams
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, Mainz 55128, Germany.
| | - Mahmoud Saker
- Genetic Engineering and Biotech. Division, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Paul W Paré
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Mohamed-Elamir F Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt.
| |
Collapse
|
8
|
Ibrahim MAA, Abdelrahman AHM, Badr EAA, Almansour NM, Alzahrani OR, Ahmed MN, Soliman MES, Naeem MA, Shawky AM, Sidhom PA, Mekhemer GAH, Atia MAM. Naturally occurring plant-based anticancerous candidates as prospective ABCG2 inhibitors: an in silico drug discovery study. Mol Divers 2022; 26:3255-3277. [DOI: 10.1007/s11030-022-10389-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023]
Abstract
Abstract
ATP-binding cassette transporter G2 (ABCG2) is an efflux transporter related to the clinical multidrug resistance (MDR) phenomenon. Identifying ABCG2 inhibitors could help discover extraordinary curative strategies for carcinoma remediation. Hitherto, there is no medication drug inhibiting ABCG2 transporter, notwithstanding that a considerable number of drugs have been submitted to clinical-trial and investigational phases. In the search for unprecedented chemical compounds that could inhibit the ABCG2 transporter, an in silico screening was conducted on the Naturally Occurring Plant-based Anticancer Compound-Activity-Target (NPACT) database containing 1574 compounds. Inhibitor-ABCG2 binding affinities were estimated based on molecular docking and molecular minimization (MM) calculations and compared to a co-crystallized inhibitor (BWQ) acting as a reference inhibitor. Molecular dynamics (MD) simulations pursued by molecular mechanics-generalized Born surface area (MM-GBSA) binding energy estimations were further executed for compounds with MM-GBSA//MM binding energies lower than BWQ (calc. − 60.5 kcal/mol). NPACT00968 and NPACT01545 demonstrated auspicious inhibitory activities according to binding affinities (ΔGbinding) over the 100 ns MD simulations that were nearly one and a half folds compared to BWQ (− 100.4, − 94.7, and − 62.9 kcal/mol, respectively). Throughout the 100 ns MD simulations, structural and energetical analyses unveiled outstanding stability of the ABCG2 transporter when bound with NPACT00968 and NPACT01545. In silico calculations hold a promise for those two inhibitors as drug candidates of ABCG2 transporter and emphasize that further in vitro and in vivo experiments are guaranteed.
Graphical abstract
Collapse
|
9
|
Awad M, Ibrahim EDS, Osman EI, Elmenofy WH, Mahmoud AWM, Atia MAM, Moustafa MAM. Nano-insecticides against the black cutworm Agrotis ipsilon (Lepidoptera: Noctuidae): Toxicity, development, enzyme activity, and DNA mutagenicity. PLoS One 2022; 17:e0254285. [PMID: 35113879 PMCID: PMC8812990 DOI: 10.1371/journal.pone.0254285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/18/2022] [Indexed: 01/08/2023] Open
Abstract
Frequent applications of synthetic insecticides might cause environmental pollution due to the high residue. In addition, increasing insecticide resistance in many insect pests requires novel pest control methods. Nanotechnology could be a promising field of modern agriculture, and is receiving considerable attention in the development of novel nano-agrochemicals, such as nanoinsectticides and nanofertilizers. This study assessed the effects of the lethal and sublethal concentrations of chlorantraniliprole, thiocyclam, and their nano-forms on the development, reproductive activity, oxidative stress enzyme activity, and DNA changes in the black cutworm, Agrotis ipsilon, at the molecular level. The results revealed that A. ipsilon larvae were more susceptible to the nano-forms than the regular forms of both nano chlorine and sulfur within the chlorantraniliprole and thiocyclam insecticides, respectively, with higher toxicities than the regular forms (ca. 3.86, and ca.2.06-fold, respectively). Significant differences in biological parameters, including developmental time and reproductive activity (fecundity and hatchability percent) were also observed. Correspondingly, increases in oxidative stress enzyme activities were observed, as were mutagenic effects on the genomic DNA of A. ipsilon after application of the LC50 of the nano-forms of both insecticides compared to the control. These promising results could represent a crucial step toward developing efficient nanoinsecticides for sustainable control of A. ipsilon.
Collapse
Affiliation(s)
- Mona Awad
- Faculty of Agriculture, Department of Economic Entomology and Pesticides, Cairo University, Giza, Egypt
| | - El-Desoky S. Ibrahim
- Faculty of Agriculture, Department of Economic Entomology and Pesticides, Cairo University, Giza, Egypt
| | - Engy I. Osman
- Faculty of Agriculture, Department of Genetics, Cairo University, Giza, Egypt
| | - Wael H. Elmenofy
- Agricultural Genetic Engineering Research Institute, ARC, Giza, Egypt
| | - Abdel Wahab M. Mahmoud
- Faculty of Agriculture, Plant Physiology Section, Botany Department, Cairo University, Giza, Egypt
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- * E-mail: (MAMM); (MAMA)
| | - Moataz A. M. Moustafa
- Faculty of Agriculture, Department of Economic Entomology and Pesticides, Cairo University, Giza, Egypt
- * E-mail: (MAMM); (MAMA)
| |
Collapse
|
10
|
Mokhtar MM, El Allali A, Hegazy MEF, Atia MAM. PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes. Sci Rep 2021; 11:21300. [PMID: 34716373 PMCID: PMC8556342 DOI: 10.1038/s41598-021-00504-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/06/2021] [Indexed: 11/12/2022] Open
Abstract
Over the past decade, the problem of finding an efficient gene-targeting marker set or signature for plant trait characterization has remained challenging. Many databases focusing on pathway mining have been released with one major deficiency, as they lack to develop marker sets that target only genes controlling a specific pathway or certain biological process. Herein, we present the PlantPathMarks database (PPMdb) as a comprehensive, web-based, user-friendly, and interactive hub for pathway-based markers in plant genomes. Based on our newly developed pathway gene set mining approach, two novel pathway-based marker systems called pathway gene-targeted markers (PGTMs) and pathway microsatellite-targeted markers (PMTMs) were developed as a novel class of annotation-based markers. In the PPMdb database, 2,690,742 pathway-based markers reflecting 9,894 marker panels were developed across 82 plant genomes. The markers include 691,555 PGTMs and 1,999,187 PMTMs. Across these genomes, 165,378 enzyme-coding genes were mapped against 126 KEGG reference pathway maps. PPMdb is furnished with three interactive visualization tools (Map Browse, JBrowse and Species Comparison) to visualize, map, and compare the developed markers over their KEGG reference pathway maps. All the stored marker panels can be freely downloaded. PPMdb promises to create a radical shift in the paradigm of the area of molecular marker research. The use of PPMdb as a mega-tool represents an impediment for non-bioinformatician plant scientists and breeders. PPMdb is freely available at http://ppmdb.easyomics.org.
Collapse
Affiliation(s)
- Morad M Mokhtar
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco.
| | | | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, 12619, Egypt.
| |
Collapse
|
11
|
Elkelish A, El-Mogy MM, Niedbała G, Piekutowska M, Atia MAM, Hamada MMA, Shahin M, Mukherjee S, El-Yazied AA, Shebl M, Jahan MS, Osman A, El-Gawad HGA, Ashour H, Farag R, Selim S, Ibrahim MFM. Roles of Exogenous α-Lipoic Acid and Cysteine in Mitigation of Drought Stress and Restoration of Grain Quality in Wheat. Plants (Basel) 2021; 10:plants10112318. [PMID: 34834681 PMCID: PMC8619972 DOI: 10.3390/plants10112318] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 05/13/2023]
Abstract
Cysteine (Cys) and α-lipoic acid (ALA) are naturally occurring antioxidants (sulfur-containing compounds) that can protect plants against a wide spectrum of environmental stresses. However, up to now, there are no conclusive data on their integrative roles in mitigation of drought stress in wheat plants. Here, we studied the influence of ALA at 0.02 mM (grain dipping pre-cultivation treatment) and Cys (25 and 50 ppm as a foliar application) under well watered and deficit irrigation (100% and 70% of recommended dose). The results showed that deficit irrigation markedly caused obvious cellular oxidative damage as indicated by elevating the malondialdehyde (MDA) and hydrogen peroxide content (H2O2). Moreover, water stressed plants exhibited multiple changes in physiological metabolism, which affected the quantitative and qualitative variables of grain yield. The enzymatic antioxidants, including superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT) and peroxidase (POX) were improved by Cys application. SOD and APX had the same response when treated with ALA, but CAT and POX did not. Moreover, both studied molecules stimulated chlorophyll (Chl) and osmolytes' biosynthesis. In contrast, the Chl a/b ratio was decreased, while flavonoids were not affected by either of the examined molecules. Interestingly, all above-mentioned changes were associated with an improvement in the scavenging capacity of reactive oxygen species (ROS), leaf relative water content (RWC), grain number, total grain yield, weight of 1000 kernels, gluten index, falling number, and alveographic parameters (P, W, and P/L values). Furthermore, heatmap plot analysis revealed several significant correlations between different studied parameters, which may explore the importance of applied Cys and ALA as effective compounds in wheat cultivation under water deficit conditions.
Collapse
Affiliation(s)
- Amr Elkelish
- Botany Department, Faculty of Science, Suez Canal University Ismailia, Ismailia 41522, Egypt;
| | - Mohamed M. El-Mogy
- Vegetable Crops Department, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
- Correspondence: (M.M.E.-M); (M.F.M.I.); Tel.: +20-1068027607 (M.M.E.-M); +20-1123403173 (M.F.M.I.)
| | - Gniewko Niedbała
- Department of Biosystems Engineering, Faculty of Environmental and Mechanical Engineering, Poznań University of Life Sciences, Wojska Polskiego 50, 60-627 Poznań, Poland;
| | - Magdalena Piekutowska
- Department of Geoecology and Geoinformation, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, Partyzantów 27, 76-200 Słupsk, Poland;
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Maha M. A. Hamada
- Department of Agronomy, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (M.M.A.H.); (M.S.)
| | - Mostafa Shahin
- Department of Agronomy, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (M.M.A.H.); (M.S.)
| | - Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, Kalyani 742213, India;
| | - Ahmed Abou El-Yazied
- Department of Horticulture, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (A.A.E.-Y.); (H.G.A.E.-G.)
| | - Mohamed Shebl
- Food Science Department, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt;
| | - Mohammad Shah Jahan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
- Department of Horticulture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
| | - Ali Osman
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt;
| | - Hany G. Abd El-Gawad
- Department of Horticulture, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (A.A.E.-Y.); (H.G.A.E.-G.)
| | - Hatem Ashour
- Department of Agricultural Botany, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (H.A.); (R.F.)
| | - Reham Farag
- Department of Agricultural Botany, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (H.A.); (R.F.)
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia;
| | - Mohamed F. M. Ibrahim
- Department of Agricultural Botany, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt; (H.A.); (R.F.)
- Correspondence: (M.M.E.-M); (M.F.M.I.); Tel.: +20-1068027607 (M.M.E.-M); +20-1123403173 (M.F.M.I.)
| |
Collapse
|
12
|
Nazir S, El-Sherif AA, Abdel-Ghani NT, Ibrahim MAA, Hegazy MEF, Atia MAM. Lepidium sativum Secondary Metabolites (Essential Oils): In Vitro and In Silico Studies on Human Hepatocellular Carcinoma Cell Lines. Plants (Basel) 2021; 10:plants10091863. [PMID: 34579396 PMCID: PMC8470406 DOI: 10.3390/plants10091863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/03/2021] [Accepted: 09/05/2021] [Indexed: 01/04/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver cancer and the greatest cause of cancer-related death in the world. Garden cress (Lepidium sativum) seeds have been proven to possess extraordinary antioxidant, anti-inflammatory, hypothermic, and analgesic properties. In this study, in vitro cytotoxic efficiency evaluation of L. sativum fractions was performed against two hepatocellular carcinoma cell lines (HuH-7 and HEPG-2), and the expression of some apoptotic genes was explored. In addition, the chemical composition of a potent extract of L. sativum was analyzed using gas chromatography coupled with mass spectrometry. Then, molecular docking analysis was implemented to identify the potential targets of the L. sativum components’ most potent extract. Overall, the n-hexane extract was the most potent against the two HCC cell lines. Moreover, these cytotoxicity levels were supported by the significant downregulation of EGFR and BCL2 gene expression levels and the upregulation of SMAD3, BAX, and P53 expression levels in both HuH-7 and HEPG2 cell lines. Regarding L. sativum’s chemical composition, GC–MS analysis of the n-hexane extract led to the identification of thirty compounds, including, mainly, hydrocarbons and terpenoids, as well as other volatile compounds. Furthermore, the binding affinities and interactions of the n-hexane fraction’s major metabolites were predicted against EGFR and BCL2 molecular targets using the molecular docking technique. These findings reveal the potential use of L. Sativum in the management of HCC.
Collapse
Affiliation(s)
- Shaimaa Nazir
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.N.); (N.T.A.-G.)
| | - Ahmed A. El-Sherif
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.N.); (N.T.A.-G.)
- Correspondence: (A.A.E.-S.); (M.-E.F.H.); (M.A.M.A.); Tel.: +20-10-6016-0168 (A.A.E.-S.); +20-33-371-635 (M.-E.F.H.); +20-10-0016-4922 (M.A.M.A.)
| | - Nour T. Abdel-Ghani
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.N.); (N.T.A.-G.)
| | - Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt;
| | - Mohamed-Elamir F. Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre, Giza 12622, Egypt
- Correspondence: (A.A.E.-S.); (M.-E.F.H.); (M.A.M.A.); Tel.: +20-10-6016-0168 (A.A.E.-S.); +20-33-371-635 (M.-E.F.H.); +20-10-0016-4922 (M.A.M.A.)
| | - Mohamed A. M. Atia
- Molecular Genetic and Genome Mapping Laboratory, Genome Mapping Department, Agriculture Genetic Engineering Research Institute (AGERI), Agriculture Research Centre (ARC), Giza 12619, Egypt
- Correspondence: (A.A.E.-S.); (M.-E.F.H.); (M.A.M.A.); Tel.: +20-10-6016-0168 (A.A.E.-S.); +20-33-371-635 (M.-E.F.H.); +20-10-0016-4922 (M.A.M.A.)
| |
Collapse
|
13
|
Ibrahim MAA, Badr EAA, Abdelrahman AHM, Almansour NM, Mekhemer GAH, Shawky AM, Moustafa MF, Atia MAM. In Silico Targeting Human Multidrug Transporter ABCG2 in Breast Cancer: Database Screening, Molecular Docking, and Molecular Dynamics Study. Mol Inform 2021; 41:e2060039. [PMID: 34491628 DOI: 10.1002/minf.202060039] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/25/2021] [Indexed: 12/24/2022]
Abstract
ABCG2 is a substantial member of the ABC transporter superfamily that plays a significant role in multidrug resistance in cancer. Until recently, the 3D structure of ABCG2 has not been resolved, which resulted in the limitation of developing potential ABCG2 inhibitors using structure-based drug discovery. Herein, eMolecules, ChEMBL, and ChEBI databases, containing >25 million compounds, were virtually screened against the ABCG2 transporter in homodimer form. Performance of AutoDock4.2.6 software to predict inhibitor-ABCG2 binding mode and affinity were validated on the basis of available experimental data. The explored databases were filtered based on docking scores. The most potent hits with binding affinities higher than that of experimental bound ligand (MZ29) were then selected and subjected to molecular mechanics minimization, followed by binding energy calculation using molecular mechanics-generalized Born surface area (MM-GBSA) approach. Furthermore, molecular dynamics simulations for 50 ns, followed by MM-GBSA binding energy calculations, were performed for the promising compounds, unveiling eight potential inhibitors with binding affinities <-55.8 kcal/mol. Structural and energetic analyses demonstrated the stability of the eight identified inhibitors over the 50 ns MD simulation. This research sheds light on the potentiality of the identified ABCG2 inhibitors as a therapeutic approach to overcome multidrug resistance cancer therapy.
Collapse
Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Esraa A A Badr
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Alaa H M Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Nahlah Makki Almansour
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin, 1803, Saudi Arabia
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Mahmoud F Moustafa
- Department of Biology, College of Science, King Khalid University, Abha, 9004, Saudi Arabia.,Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena, Egypt
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, 12619, Egypt
| |
Collapse
|
14
|
Mohamed TA, Elshamy AI, Ibrahim MAA, Atia MAM, Ahmed RF, Ali SK, Mahdy KA, Alshammari SO, Al-Abd AM, Moustafa MF, Farrag ARH, Hegazy MEF. Gastroprotection against Rat Ulcers by Nephthea Sterol Derivative. Biomolecules 2021; 11:1247. [PMID: 34439913 PMCID: PMC8393318 DOI: 10.3390/biom11081247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 12/23/2022] Open
Abstract
Different species belonging to the genus Nephthea (Acyonaceae) are a rich resource for bioactive secondary metabolites. The literature reveals that the gastroprotective effects of marine secondary metabolites have not been comprehensively studied in vivo. Hence, the present investigation aimed to examine and determine the anti-ulcer activity of 4α,24-dimethyl-5α-cholest-8β,18-dihydroxy,22E-en-3β-ol (ST-1) isolated from samples of a Nephthea species. This in vivo study was supported by in silico molecular docking and protein-protein interaction techniques. Oral administration of ST-1 reduced rat stomach ulcers with a concurrent increase in gastric mucosa. Molecular docking calculations against the H+/K+-ATPase transporter showed a higher binding affinity of ST-1, with a docking score value of -9.9 kcal/mol and a pKi value of 59.7 nM, compared to ranitidine (a commercial proton pump inhibitor, which gave values of -6.2 kcal/mol and 27.9 µM, respectively). The combined PEA-reactome analysis results revealed promising evidence of ST-1 potency as an anti-ulcer compound through significant modulation of the gene set controlling the PI3K signaling pathway, which subsequently plays a crucial role in signaling regarding epithelialization and tissue regeneration, tissue repairing and tissue remodeling. These results indicate a probable protective role for ST-1 against ethanol-induced gastric ulcers.
Collapse
Affiliation(s)
- Tarik A. Mohamed
- National Research Centre, Chemistry of Medicinal Plants Department, 33 El−Bohouth St., Dokki, Giza 12622, Egypt; (T.A.M.); (S.K.A.); (M.-E.F.H.)
| | - Abdelsamed I. Elshamy
- National Research Centre, Chemistry of Natural Compounds Department, Dokki, Giza 12622, Egypt; (A.I.E.); (R.F.A.)
| | - Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt;
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Rania F. Ahmed
- National Research Centre, Chemistry of Natural Compounds Department, Dokki, Giza 12622, Egypt; (A.I.E.); (R.F.A.)
| | - Sherin K. Ali
- National Research Centre, Chemistry of Medicinal Plants Department, 33 El−Bohouth St., Dokki, Giza 12622, Egypt; (T.A.M.); (S.K.A.); (M.-E.F.H.)
| | - Karam A. Mahdy
- National Research Centre, Medical Biochemistry Department, 33 El Bohouth St., Dokki, Giza 12622, Egypt;
| | - Shifaa O. Alshammari
- Department of Biology, College of Science, University of Hafr Al Batin, Hafar Al Batin 39524, Saudi Arabia;
| | - Ahmed M. Al-Abd
- Department of Pharmaceutical Sciences, College of Pharmacy & Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates
- Pharmacology Department, Medical Division, National Research Centre, Cairo 12622, Egypt
| | - Mahmoud F. Moustafa
- Department of Biology, College of Science, King Khalid University, Abha 9004, Saudi Arabia;
- Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - Abdel Razik H. Farrag
- National Research Centre, Pathology Department, 33 El Bohouth St., Dokki, Giza 12622, Egypt;
| | - Mohamed-Elamir F. Hegazy
- National Research Centre, Chemistry of Medicinal Plants Department, 33 El−Bohouth St., Dokki, Giza 12622, Egypt; (T.A.M.); (S.K.A.); (M.-E.F.H.)
| |
Collapse
|
15
|
Ibrahim MAA, Abdelrahman AHM, Atia MAM, Mohamed TA, Moustafa MF, Hakami AR, Khalifa SAM, Alhumaydhi FA, Alrumaihi F, Abidi SH, Allemailem KS, Efferth T, Soliman ME, Paré PW, El-Seedi HR, Hegazy MEF. Blue Biotechnology: Computational Screening of Sarcophyton Cembranoid Diterpenes for SARS-CoV-2 Main Protease Inhibition. Mar Drugs 2021; 19:391. [PMID: 34356816 PMCID: PMC8308023 DOI: 10.3390/md19070391] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 12/29/2022] Open
Abstract
The coronavirus pandemic has affected more than 150 million people, while over 3.25 million people have died from the coronavirus disease 2019 (COVID-19). As there are no established therapies for COVID-19 treatment, drugs that inhibit viral replication are a promising target; specifically, the main protease (Mpro) that process CoV-encoded polyproteins serves as an Achilles heel for assembly of replication-transcription machinery as well as down-stream viral replication. In the search for potential antiviral drugs that target Mpro, a series of cembranoid diterpenes from the biologically active soft-coral genus Sarcophyton have been examined as SARS-CoV-2 Mpro inhibitors. Over 360 metabolites from the genus were screened using molecular docking calculations. Promising diterpenes were further characterized by molecular dynamics (MD) simulations based on molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations. According to in silico calculations, five cembranoid diterpenes manifested adequate binding affinities as Mpro inhibitors with ΔGbinding < -33.0 kcal/mol. Binding energy and structural analyses of the most potent Sarcophyton inhibitor, bislatumlide A (340), was compared to darunavir, an HIV protease inhibitor that has been recently subjected to clinical-trial as an anti-COVID-19 drug. In silico analysis indicates that 340 has a higher binding affinity against Mpro than darunavir with ΔGbinding values of -43.8 and -34.8 kcal/mol, respectively throughout 100 ns MD simulations. Drug-likeness calculations revealed robust bioavailability and protein-protein interactions were identified for 340; biochemical signaling genes included ACE, MAPK14 and ESR1 as identified based on a STRING database. Pathway enrichment analysis combined with reactome mining revealed that 340 has the capability to re-modulate the p38 MAPK pathway hijacked by SARS-CoV-2 and antagonize injurious effects. These findings justify further in vivo and in vitro testing of 340 as an antiviral agent against SARS-CoV-2.
Collapse
Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt;
| | - Alaa H. M. Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt;
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Tarik A. Mohamed
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt;
| | - Mahmoud F. Moustafa
- Department of Biology, College of Science, King Khalid University, Abha 9004, Saudi Arabia; or
- Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - Abdulrahim R. Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61481, Saudi Arabia;
| | - Shaden A. M. Khalifa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden;
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.A.A.); (F.A.); (K.S.A.)
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.A.A.); (F.A.); (K.S.A.)
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan;
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.A.A.); (F.A.); (K.S.A.)
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany;
| | - Mahmoud E. Soliman
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa;
| | - Paul W. Paré
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
| | - Hesham R. El-Seedi
- Department of Chemistry, Faculty of Science, El-Menoufia University, Shebin El-Kom 32512, Egypt
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Pharmacognosy Group, Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Box 574, 751 23 Uppsala, Sweden
| | - Mohamed-Elamir F. Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt;
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany;
| |
Collapse
|
16
|
Atia MAM, El-Khateeb EA, Abd El-Maksoud RM, Abou-Zeid MA, Salah A, Abdel-Hamid AME. Mining of Leaf Rust Resistance Genes Content in Egyptian Bread Wheat Collection. Plants (Basel) 2021; 10:1378. [PMID: 34371581 PMCID: PMC8309345 DOI: 10.3390/plants10071378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/15/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022]
Abstract
Wheat is a major nutritional cereal crop that has economic and strategic value worldwide. The sustainability of this extraordinary crop is facing critical challenges globally, particularly leaf rust disease, which causes endless problems for wheat farmers and countries and negatively affects humanity's food security. Developing effective marker-assisted selection programs for leaf rust resistance in wheat mainly depends on the availability of deep mining of resistance genes within the germplasm collections. This is the first study that evaluated the leaf rust resistance of 50 Egyptian wheat varieties at the adult plant stage for two successive seasons and identified the absence/presence of 28 leaf rust resistance (Lr) genes within the studied wheat collection. The field evaluation results indicated that most of these varieties demonstrated high to moderate leaf rust resistance levels except Gemmeiza 1, Gemmeiza 9, Giza162, Giza 163, Giza 164, Giza 165, Sids 1, Sids 2, Sids 3, Sakha 62, Sakha 69, Sohag 3 and Bany Swif 4, which showed fast rusting behavior. On the other hand, out of these 28 Lr genes tested against the wheat collection, 21 Lr genes were successfully identified. Out of 15 Lr genes reported conferring the adult plant resistant or slow rusting behavior in wheat, only five genes (Lr13, Lr22a, Lr34, Lr37, and Lr67) were detected within the Egyptian collection. Remarkedly, the genes Lr13, Lr19, Lr20, Lr22a, Lr28, Lr29, Lr32, Lr34, Lr36, Lr47, and Lr60, were found to be the most predominant Lr genes across the 50 Egyptian wheat varieties. The molecular phylogeny results also inferred the same classification of field evaluation, through grouping genotypes characterized by high to moderate leaf rust resistance in one cluster while being highly susceptible in a separate cluster, with few exceptions.
Collapse
Affiliation(s)
- Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Eman A. El-Khateeb
- Department of Botany, Faculty of Science, Tanta University, Tanta 31527, Egypt;
| | - Reem M. Abd El-Maksoud
- Department of Nucleic Acid & Protein Structure, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Mohamed A. Abou-Zeid
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Arwa Salah
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Amal M. E. Abdel-Hamid
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Roxy, Cairo 11341, Egypt;
| |
Collapse
|
17
|
Elshamy AI, Mohamed TA, Ibrahim MAA, Atia MAM, Yoneyama T, Umeyama A, Hegazy MEF. Two novel oxetane containing lignans and a new megastigmane from Paronychia arabica and in silico analysis of them as prospective SARS-CoV-2 inhibitors. RSC Adv 2021; 11:20151-20163. [PMID: 35479905 PMCID: PMC9033657 DOI: 10.1039/d1ra02486h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/15/2021] [Indexed: 12/22/2022] Open
Abstract
The chemical characterization of the extract of the aerial parts of Paronychia arabica afforded two oxetane containing lignans, paronychiarabicine A (1) and B (2), and one new megastigmane, paronychiarabicastigmane A (3), alongside a known lignan (4), eight known phenolic compounds (5–12), one known elemene sesquiterpene (13) and one steroid glycoside (14). The chemical structures of the isolated compounds were constructed based upon the HRMS, 1D, and 2D-NMR results. The absolute configurations were established via NOESY experiments as well as experimental and TDDFT-calculated electronic circular dichroism (ECD). Utilizing molecular docking, the binding scores and modes of compounds 1–3 towards the SARS-CoV-2 main protease (Mpro), papain-like protease (PLpro), and RNA-dependent RNA polymerase (RdRp) were revealed. Compound 3 exhibited a promising docking score (−9.8 kcal mol−1) against SARS-CoV-2 Mpro by forming seven hydrogen bonds inside the active site with the key amino acids. The reactome pathway enrichment analysis revealed a correlation between the inhibition of GSK3 and GSK3B genes (identified as the main targets of megastigmane treatment) and significant inhibition of SARS-CoV-1 viral replication in infected Vero E6 cells. Our results manifest a novel understanding of genes, proteins and corresponding pathways against SARS-CoV-2 infection and could facilitate the identification and characterization of novel therapeutic targets as treatments of SARS-CoV-2 infection. The hydromethanolic extract of Paronychia arabica aerial parts afforded two oxetane containing lignans, paronychiarabicine A (1) and B (2), and one new megastigmane, paronychiarabicastigmane A (3), alongside a known secondary metabolites (4–14).![]()
Collapse
Affiliation(s)
- Abdelsamed I Elshamy
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University Yamashiro-cho Tokushima 770-8514 Japan.,Chemistry of Natural Compounds Department, National Research Centre Dokki Giza 12622 Egypt
| | - Tarik A Mohamed
- Chemistry of Medicinal Plants Department, National Research Centre 33 El-Bohouth St., Dokki Giza 12622 Egypt +20-233370931 +20-233371635
| | - Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC) Giza 12619 Egypt
| | - Tatsuro Yoneyama
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University Yamashiro-cho Tokushima 770-8514 Japan
| | - Akemi Umeyama
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University Yamashiro-cho Tokushima 770-8514 Japan
| | - Mohamed-Elamir F Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre 33 El-Bohouth St., Dokki Giza 12622 Egypt +20-233370931 +20-233371635.,Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Staudinger Weg 5 55128 Mainz Germany
| |
Collapse
|
18
|
Ibrahim MAA, Badr EAA, Abdelrahman AHM, Almansour NM, Shawky AM, Mekhemer GAH, Alrumaihi F, Moustafa MF, Atia MAM. Prospective Drug Candidates as Human Multidrug Transporter ABCG2 Inhibitors: an In Silico Drug Discovery Study. Cell Biochem Biophys 2021; 79:189-200. [PMID: 33954893 DOI: 10.1007/s12013-021-00985-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 12/22/2022]
Abstract
Breast cancer resistance protein (ABCG2) is a human ATP-binding cassette (ABC) that plays a paramount role in multidrug resistance (MDR) in cancer therapy. The discovery of ABCG2 inhibitors could assist in designing unprecedented therapeutic strategies for cancer treatment. There is as yet no approved drug targeting ABCG2, although a large number of drug candidates have been clinically investigated. In this work, binding affinities of 181 drug candidates in clinical-trial or investigational stages as ABCG2 inhibitors were inspected using in silico techniques. Based on available experimental data, the performance of AutoDock4.2.6 software was first validated to predict the inhibitor-ABCG2 binding mode and affinity. Combined molecular docking calculations and molecular dynamics (MD) simulations, followed by molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations, were then performed to filter out the studied drug candidates. From the estimated docking scores and MM-GBSA binding energies, six auspicious drug candidates-namely, pibrentasvir, venetoclax, ledipasvir, avatrombopag, cobicistat, and revefenacin-exhibited auspicious binding energies with value < -70.0 kcal/mol. Interestingly, pibrentasvir, venetoclax, and ledipasvir were observed to show even higher binding affinities with the ABCG2 transporter with binding energies of < -80.0 kcal/mol over long MD simulations of 100 ns. The stabilities of these three promising candidates in complex with ABCG2 transporter were demonstrated by their energetics and structural analyses throughout the 100 ns MD simulations. The current study throws new light on pibrentasvir, venetoclax, and ledipasvir as curative options for multidrug resistant cancers by inhibiting ABCG2 transporter.
Collapse
Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt.
| | - Esraa A A Badr
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Alaa H M Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Nahlah Makki Almansour
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, Saudi Arabia
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mahmoud F Moustafa
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
- Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena, Egypt
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt.
| |
Collapse
|
19
|
Ibrahim MAA, Abdelrahman AHM, Mohamed TA, Atia MAM, Al-Hammady MAM, Abdeljawaad KAA, Elkady EM, Moustafa MF, Alrumaihi F, Allemailem KS, El-Seedi HR, Paré PW, Efferth T, Hegazy MEF. In Silico Mining of Terpenes from Red-Sea Invertebrates for SARS-CoV-2 Main Protease (M pro) Inhibitors. Molecules 2021; 26:2082. [PMID: 33916461 PMCID: PMC8038614 DOI: 10.3390/molecules26072082] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19 pandemic, which generated more than 1.82 million deaths in 2020 alone, in addition to 83.8 million infections. Currently, there is no antiviral medication to treat COVID-19. In the search for drug leads, marine-derived metabolites are reported here as prospective SARS-CoV-2 inhibitors. Two hundred and twenty-seven terpene natural products isolated from the biodiverse Red-Sea ecosystem were screened for inhibitor activity against the SARS-CoV-2 main protease (Mpro) using molecular docking and molecular dynamics (MD) simulations combined with molecular mechanics/generalized Born surface area binding energy calculations. On the basis of in silico analyses, six terpenes demonstrated high potency as Mpro inhibitors with ΔGbinding ≤ -40.0 kcal/mol. The stability and binding affinity of the most potent metabolite, erylosides B, were compared to the human immunodeficiency virus protease inhibitor, lopinavir. Erylosides B showed greater binding affinity towards SARS-CoV-2 Mpro than lopinavir over 100 ns with ΔGbinding values of -51.9 vs. -33.6 kcal/mol, respectively. Protein-protein interactions indicate that erylosides B biochemical signaling shares gene components that mediate severe acute respiratory syndrome diseases, including the cytokine- and immune-signaling components BCL2L1, IL2, and PRKC. Pathway enrichment analysis and Boolean network modeling were performed towards a deep dissection and mining of the erylosides B target-function interactions. The current study identifies erylosides B as a promising anti-COVID-19 drug lead that warrants further in vitro and in vivo testing.
Collapse
Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt; (A.H.M.A.); (K.A.A.A.)
| | - Alaa H. M. Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt; (A.H.M.A.); (K.A.A.A.)
| | - Tarik A. Mohamed
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt;
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | | | - Khlood A. A. Abdeljawaad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt; (A.H.M.A.); (K.A.A.A.)
| | - Eman M. Elkady
- National Institute of Oceanography & Fisheries, NIOF, Cairo 11516, Egypt; (M.A.M.A.-H.); (E.M.E.)
| | - Mahmoud F. Moustafa
- Department of Biology, College of Science, King Khalid University, Abha 9004, Saudi Arabia;
- Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.A.); (K.S.A.)
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.A.); (K.S.A.)
| | - Hesham R. El-Seedi
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
- Department of Chemistry, Faculty of Science, El-Menoufia University, Shebin El-Kom 32512, Egypt
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
| | - Paul W. Paré
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany;
| | - Mohamed-Elamir F. Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt;
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany;
| |
Collapse
|
20
|
Ibrahim MAA, Mohamed EAR, Abdelrahman AHM, Allemailem KS, Moustafa MF, Shawky AM, Mahzari A, Hakami AR, Abdeljawaad KAA, Atia MAM. Rutin and flavone analogs as prospective SARS-CoV-2 main protease inhibitors: In silico drug discovery study. J Mol Graph Model 2021; 105:107904. [PMID: 33798836 PMCID: PMC7980232 DOI: 10.1016/j.jmgm.2021.107904] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 03/14/2021] [Accepted: 03/15/2021] [Indexed: 01/12/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a new pandemic characterized by quick spreading and illness of the respiratory system. To date, there is no specific therapy for Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). Flavonoids, especially rutin, have attracted considerable interest as a prospective SARS-CoV-2 main protease (Mpro) inhibitor. In this study, a database containing 2017 flavone analogs was prepared and screened against SARS-CoV-2 Mpro using the molecular docking technique. According to the results, 371 flavone analogs exhibited good potency towards Mpro with docking scores less than −9.0 kcal/mol. Molecular dynamics (MD) simulations, followed by molecular mechanics-generalized Born surface area (MM/GBSA) binding energy calculations, were performed for the top potent analogs in complex with Mpro. Compared to rutin, PubChem-129-716-607 and PubChem-885-071-27 showed better binding affinities against SARS-CoV-2 Mpro over 150 ns MD course with ΔGbinding values of −69.0 and −68.1 kcal/mol, respectively. Structural and energetic analyses demonstrated high stability of the identified analogs inside the SARS-CoV-2 Mpro active site over 150 ns MD simulations. The oral bioavailabilities of probable SARS-CoV-2 Mpro inhibitors were underpinned using drug-likeness parameters. A comparison of the binding affinities demonstrated that the MM/GBSA binding energies of the identified flavone analogs were approximately three and two times less than those of lopinavir and baicalein, respectively. In conclusion, PubChem-129-716-607 and PubChem-885-071-27 are promising anti-COVID-19 drug candidates that warrant further clinical investigations.
Collapse
Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt.
| | - Eslam A R Mohamed
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Alaa H M Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mahmoud F Moustafa
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia; Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena, Egypt
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Ali Mahzari
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Abdulrahim Refdan Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, 61481, Saudi Arabia
| | - Khlood A A Abdeljawaad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, 12619, Egypt.
| |
Collapse
|
21
|
Reda EH, Shakour ZTA, El-Halawany AM, El-Kashoury ESA, Shams KA, Mohamed TA, Saleh I, Elshamy AI, Atia MAM, El-Beih AA, Abdel-Azim NS, El-Seedi HR, Hegazy MEF. Comparative Study on the Essential Oils from Five Wild Egyptian Centaurea Species: Effective Extraction Techniques, Antimicrobial Activity and In-Silico Analyses. Antibiotics (Basel) 2021; 10:252. [PMID: 33802470 PMCID: PMC8000757 DOI: 10.3390/antibiotics10030252] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 11/17/2022] Open
Abstract
The genus Centaurea is recognized in folk medicine for anti-inflammatory, anti-itch, antitussive, purgative, astringent, and tonic activities. To study the chemical determinant for antimicrobial activity essential oils (EOs), five Centaurea species were analyzed including: C. scoparia, C. calcitrapa, C. glomerata, C. lipii and C. alexandrina. Conventional hydro-distillation (HD) and microwave-assisted extraction (MAE), as new green technologies, were compared for the extraction of essential oils. GC/MS analysis identified 120 EOs including mostly terpenoid except from C. lipii and C. alexandrina in which nonterpenoids were the major constituents. Major terpenoids included spathulenol, caryophyllene oxide and alloaromadendrene oxide-2. To probe antibacterial activity, potential EO inhibitors of a bacterial type II DNA topoisomerase, DNA gyrase B were screened via an in silico molecular docking approach. Spathulenol and alloaromadendrene oxide-2 possessed the best binding affinity in the ATP- binding pocket of Gyrase B enzyme. Principal component analysis and agglomerative hierarchical clustering were used for sample classification and revealed that sesquiterpenes contributed the most for accessions classification. In vitro antimicrobial activity against Staphylococcus aureus, Escherichia coli and Aspergillus niger for all EOs were also evaluated. EOs from C. lipii, C. glomerata and C. calcitrapa exhibited significant MIC against S. aureus with an MIC value of 31.25 µg/mL.
Collapse
Affiliation(s)
- Eman H. Reda
- Phytochemistry Laboratory, National Organization for Drug Control and Research, Giza 12622, Egypt; (E.H.R.); (Z.T.A.S.)
| | - Zienab T. Abdel Shakour
- Phytochemistry Laboratory, National Organization for Drug Control and Research, Giza 12622, Egypt; (E.H.R.); (Z.T.A.S.)
| | - Ali M. El-Halawany
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt;
| | | | - Khaled A. Shams
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt; (K.A.S.); (T.A.M.); (I.S.); (N.S.A.-A.)
| | - Tarik A. Mohamed
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt; (K.A.S.); (T.A.M.); (I.S.); (N.S.A.-A.)
| | - Ibrahim Saleh
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt; (K.A.S.); (T.A.M.); (I.S.); (N.S.A.-A.)
| | - Abdelsamed I. Elshamy
- Department of Natural Compounds Chemistry, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt;
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Ahmed A. El-Beih
- Chemistry of Natural & Microbial Products Department, National Research Centre, Dokki, Giza 12622, Egypt;
| | - Nahla S. Abdel-Azim
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt; (K.A.S.); (T.A.M.); (I.S.); (N.S.A.-A.)
| | - Hesham R. El-Seedi
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
| | - Mohamed-Elamir F. Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt; (K.A.S.); (T.A.M.); (I.S.); (N.S.A.-A.)
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| |
Collapse
|
22
|
Mokhtar MM, Hussein EHA, El-Assal SEDS, Atia MAM. VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba. AoB Plants 2020; 12:plaa064. [PMID: 33408850 PMCID: PMC7759246 DOI: 10.1093/aobpla/plaa064] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/21/2020] [Indexed: 05/20/2023]
Abstract
Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.
Collapse
Affiliation(s)
- Morad M Mokhtar
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | | | | | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- Corresponding author’s e-mail address:
| |
Collapse
|
23
|
Mokhtar MM, Atia MAM. SSRome: an integrated database and pipelines for exploring microsatellites in all organisms. Nucleic Acids Res 2020; 47:D244-D252. [PMID: 30365025 PMCID: PMC6323889 DOI: 10.1093/nar/gky998] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/14/2018] [Indexed: 11/23/2022] Open
Abstract
Over the past decade, many databases focusing on microsatellite mining on a genomic scale were released online with at least one of the following major deficiencies: (i) lacking the classification of microsatellites as genic or non-genic, (ii) not comparing microsatellite motifs at both genic and non-genic levels in order to identify unique motifs for each class or (iii) missing SSR marker development. In this study, we have developed ‘SSRome’ as a web-based, user-friendly, comprehensive and dynamic database with pipelines for exploring microsatellites in 6533 organisms. In the SSRome database, 158 million microsatellite motifs are identified across all taxa, in addition to all the mitochondrial and chloroplast genomes and expressed sequence tags available from NCBI. Moreover, 45.1 million microsatellite markers were developed and classified as genic or non-genic. All the stored motif and marker datasets can be downloaded freely. In addition, SSRome provides three user-friendly tools to identify, classify and compare motifs on either a genome- or transcriptome-wide scale. With the implementation of PHP, HTML and JavaScript, users can upload their data for analysis via a user-friendly GUI. SSRome represents a powerful database and mega-tool that will assist researchers in developing and dissecting microsatellite markers on a high-throughput scale.
Collapse
Affiliation(s)
- Morad M Mokhtar
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, 12619, Egypt
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, 12619, Egypt
| |
Collapse
|
24
|
Abouseadaa HH, Atia MAM, Younis IY, Issa MY, Ashour HA, Saleh I, Osman GH, Arif IA, Mohsen E. Gene-targeted molecular phylogeny, phytochemical profiling, and antioxidant activity of nine species belonging to family Cactaceae. Saudi J Biol Sci 2020; 27:1649-1658. [PMID: 32489307 PMCID: PMC7253903 DOI: 10.1016/j.sjbs.2020.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 12/21/2022] Open
Abstract
Cactaceae plant family comprises over 130 genera and 2000 species of succulent flowering plants. The genera Mammillaria and Notocactus (Parodia), which have medicinal and nutritional applications as well as aesthetic appeal, are considered to be among the major genera of the family. Several species of both genera show morphological and chemical similarities and diversities according to environmental conditions and genotypes. Here, we assessed the genetic relationships of nine species belonging to two major genera Mammillaria and Notocactus under the family Cactaceae, using two modern gene-targeting marker techniques, the Start Codon Targeted (SCoT) Polymorphism and the Conserved DNA-Derived Polymorphism (CDDP). Besides, we screened the various phytochemicals and evaluated the antioxidant activities of the nine species of cacti. Five out of the 10 SCoT and eight CDDP primers used to screen genetic variations within the nine species yielded species-specific reproducible bands. The entire 156 loci were detected, of which 107 were polymorphic, 26 were monomorphic, and 23 were unique loci. The nine species were categorized into two groups based on the dendrogram and similarity matrix. Phytochemical profiling revealed that sterols, triterpenes, flavonoids, and tannins were found in all the tested species. Additionally, two Notocactus species (N. shlosserii and N. roseoluteus) and one Mammillaria species (M. spinosissima) revealed a considerable antioxidant activity. Our results demonstrated that gene-targeting marker techniques were highly powerful tools for the classification and characterization of the nine investigated species, despite displaying high similarities at both morphological and phytochemical levels.
Collapse
Affiliation(s)
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Lab., Agriculture Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Egypt
| | - Inas Y Younis
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Egypt
| | - Marwa Y Issa
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Egypt
| | - Haraz A Ashour
- Pharmacy Department, King Abdullah medical complex, Jeddah, Saudi Arabia
| | - Ibrahim Saleh
- Prince Sultan Research Chair for Environment and Wildlife, Department of Botany & Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Gamal H Osman
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia.,Research Laboratories Center, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia.,Microbial Genetics Department, Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt
| | - Ibrahim A Arif
- Prince Sultan Research Chair for Environment and Wildlife, Department of Botany & Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Engy Mohsen
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Egypt
| |
Collapse
|
25
|
Atia MAM, Abdeldaym EA, Abdelsattar M, Ibrahim DSS, Saleh I, Elwahab MA, Osman GH, Arif IA, Abdelaziz ME. Piriformospora indica promotes cucumber tolerance against Root-knot nematode by modulating photosynthesis and innate responsive genes. Saudi J Biol Sci 2019; 27:279-287. [PMID: 31889848 PMCID: PMC6933207 DOI: 10.1016/j.sjbs.2019.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/01/2019] [Accepted: 09/09/2019] [Indexed: 02/09/2023] Open
Abstract
Root Knot Nematode (RKN, Meloidogyne incognita) is one of the greatest damaging soil pathogens causes severe yield losses in cucumber and many other economic crops. Here, we evaluated the potential antagonistic effect of the root mutualistic fungus Piriformospora indica against RKN and their impact on vegetative growth, yield, photosynthesis, endogenous salicylic acid (SA) and its responsive genes. Our results showed that P. indica dramatically decreased the damage on shoot and root architecture of cucumber plants, which consequently enhanced yield of infested plants. Likewise, P. indica colonization clearly improved the chlorophyll content and delimited the negative impact of RNK on photosynthesis. Moreover, P. indica colonization exhibited a significant reduction of different vital nematological parameters such as soil larva density, amount of eggs/eggmass, eggmasses, females and amount of galls at cucumber roots. Additionally, the results showed that SA level was significantly increased generally in the roots of all treatments especially in plants infested with RKN alone as compared to control. This suggests that P. indica promoting SA levels in host cucumber plant roots to antagonize the RKN and alleviate severity damages occurred in its roots. This higher levels of SA in cucumber roots was consistent with the higher expressional levels of SA pathway genes PR1 and PR3. Furthermore, P. indica colonization reduces PR1, PR3 and increased NPR1 in roots of RKN infested cucumber plants when compared to non-colonized plants. Interestingly, our in vitro results showed that direct application of P. indica suspension against the J2s exhibited a significant increase in mortality ratio. Our results collectively suggest that P. indica promoting morphological, physiological and SA levels that might together play a major important role to alleviate the adverse impact of RKN in cucumber.
Collapse
Affiliation(s)
- Mohamed A M Atia
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), 12619 Giza, Egypt
| | | | - Mohamed Abdelsattar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), 12619 Giza, Egypt
| | - Dina S S Ibrahim
- Nematology Department, Plant Pathology Institute, Agricultural Research Center (ARC), 12619 Giza, Egypt
| | - Ibrahim Saleh
- Prince Sultan Research Chair for Environment and Wildlife, Department of Botany & Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia
| | | | - Gamal H Osman
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makka, Saudi Arabia.,Microbial Genetics Department, Agricultural Genetic Engineering Research Institute (AGERI), Giza, Egypt.,Research Laboratories Center, Faculty of Applied Science, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Ibrahim A Arif
- Prince Sultan Research Chair for Environment and Wildlife, Department of Botany & Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia
| | | |
Collapse
|
26
|
Butt H, Eid A, Ali Z, Atia MAM, Mokhtar MM, Hassan N, Lee CM, Bao G, Mahfouz MM. Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule. Front Plant Sci 2017; 8:1441. [PMID: 28883826 PMCID: PMC5573723 DOI: 10.3389/fpls.2017.01441] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 08/03/2017] [Indexed: 05/17/2023]
Abstract
The CRISPR/Cas9 system has been applied in diverse eukaryotic organisms for targeted mutagenesis. However, targeted gene editing is inefficient and requires the simultaneous delivery of a DNA template for homology-directed repair (HDR). Here, we used CRISPR/Cas9 to generate targeted double-strand breaks and to deliver an RNA repair template for HDR in rice (Oryza sativa). We used chimeric single-guide RNA (cgRNA) molecules carrying both sequences for target site specificity (to generate the double-strand breaks) and repair template sequences (to direct HDR), flanked by regions of homology to the target. Gene editing was more efficient in rice protoplasts using repair templates complementary to the non-target DNA strand, rather than the target strand. We applied this cgRNA repair method to generate herbicide resistance in rice, which showed that this cgRNA repair method can be used for targeted gene editing in plants. Our findings will facilitate applications in functional genomics and targeted improvement of crop traits.
Collapse
Affiliation(s)
- Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute, Agricultural Research CenterGiza, Egypt
| | - Morad M. Mokhtar
- Molecular Genetics and Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute, Agricultural Research CenterGiza, Egypt
| | - Norhan Hassan
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Ciaran M. Lee
- Department of Bioengineering, Rice University, HoustonTX, United States
| | - Gang Bao
- Department of Bioengineering, Rice University, HoustonTX, United States
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
- *Correspondence: Magdy M. Mahfouz,
| |
Collapse
|
27
|
Atia MAM, Adawy SS, El-Itriby HA. Date Palm Sex Differentiation Based on Fluorescence In Situ Hybridization (FISH). Methods Mol Biol 2017; 1638:245-256. [PMID: 28755228 DOI: 10.1007/978-1-4939-7159-6_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In situ hybridization (ISH) is used to visualize defined DNA sequences in cellular preparations by hybridization of complementary probe sequences. Recently, the fluorescence in situ hybridization (FISH) technique has become a powerful and useful tool for the direct detection of specific DNA fragments in the genome. Ribosomal DNA genes (45S and 5S rDNA) are commonly used as markers for the physical mapping of plant chromosomes to analyze genomic organization. Here we describe cytological-based markers to differentiate date palm gender through localization of 45S and 5S rDNA markers on date palm chromosomes using FISH.
Collapse
Affiliation(s)
- Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory (MGGM), Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, 12619, Egypt.
| | - Sami S Adawy
- Molecular Genetics and Genome Mapping Laboratory (MGGM), Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, 12619, Egypt
| | | |
Collapse
|
28
|
Abstract
Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.
Collapse
Affiliation(s)
- Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory (MGGM), Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, P.O. Box 12619, Egypt.
| | - Mahmoud M Sakr
- Plant Biotechnology Department, National Research Center, Dokki, Giza, Egypt
| | - Sami S Adawy
- Molecular Genetics and Genome Mapping Laboratory (MGGM), Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, P.O. Box 12619, Egypt
| |
Collapse
|
29
|
Adawy SS, Diab AA, Atia MAM, Hussein EHA. Construction of genetic linkage map with chromosomal assigment and quantitative trait loci associated with some important agronomic traits in cotton. GM Crops Food 2013; 4:36-49. [PMID: 23333856 DOI: 10.4161/gmcr.23287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cotton is the world's leading natural fiber and second most important oilseed crop and has been a focus of genetic, systematic and breeding research. The genetic and physiological bases of some important agronomic traits in cotton were investigated by QTL mapping through constructing of genetic map with chromosomal assignment. A segregating F2 population derived from an interspecific cross (G. barbadense x G. hirsutum) between two genotypes, cvs. "Giza 83" and "Deltapine" was used in this study. Different molecular markers including SSR, EST, EST-SSR, AFLP and RAPD were employed to identify markers that reveal differences between the parents. In total 42 new markers were merged with 140 previously mapped markers to produce a new map with 182 loci covering a total length of 2370.5 cM. Among these new markers, some of them were used to assign chromosomes to the produced 26 linkage groups. The LG2, LG3, LG11 and LG26 were assigned to chromosomes 1, 6, 5 and 20 respectively. Single point analysis was used to identify genomic regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number of bolls. In total 40 significant QTL were identified for the five traits on 11 linkage groups (1, 2, 3, 4, 5, 10, 11, 12, 18, 19 and 23). This work represents an improvement of the previously constructed genetic map in addition to chromosomal assignment and detection of new significant QTL for the five traits in Egyptian cotton. The Significant QTLs detected in this study can be employed in marker assisted selection for molecular breeding programs aiming at developing cotton cultivars with improved agronomic traits.
Collapse
Affiliation(s)
- Sami S Adawy
- Molecular Markers and Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | | | | | | |
Collapse
|