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Subbarayan R, Srinivasan D, Shadula Osmania S, Murugan Girija D, Ikhlas S, Srivastav N, Balakrishnan R, Shrestha R, Chauhan A. Molecular insights on Eltrombopag: potential mitogen stimulants, angiogenesis, and therapeutic radioprotectant through TPO-R activation. Platelets 2024; 35:2359028. [PMID: 38832545 DOI: 10.1080/09537104.2024.2359028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/17/2024] [Indexed: 06/05/2024]
Abstract
The purpose of this study is to investigate the molecular interactions and potential therapeutic uses of Eltrombopag (EPAG), a small molecule that activates the cMPL receptor. EPAG has been found to be effective in increasing platelet levels and alleviating thrombocytopenia. We utilized computational techniques to predict and confirm the complex formed by the ligand (EPAG) and the Thrombopoietin receptor (TPO-R) cMPL, elucidating the role of RAS, JAK-2, STAT-3, and other essential elements for downstream signaling. Molecular dynamics (MD) simulations were employed to evaluate the stability of the ligand across specific proteins, showing favorable characteristics. For the first time, we examined the presence of TPO-R in human umbilical cord mesenchymal stem cells (hUCMSC) and human gingival mesenchymal stem cells (hGMSC) proliferation. Furthermore, treatment with EPAG demonstrated angiogenesis and vasculature formation of endothelial lineage derived from both MSCs. It also indicated the activation of critical factors such as RUNX-1, GFI-1b, VEGF-A, MYB, GOF-1, and FLI-1. Additional experiments confirmed that EPAG could be an ideal molecule for protecting against UVB radiation damage, as gene expression (JAK-2, ERK-2, MCL-1, NFkB, and STAT-3) and protein CD90/cMPL analysis showed TPO-R activation in both hUCMSC and hGMSC. Overall, EPAG exhibits significant potential in treating radiation damage and mitigating the side effects of radiotherapy, warranting further clinical exploration.
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Affiliation(s)
- Rajasekaran Subbarayan
- Centre for Advanced Biotherapeutics and Regenerative Medicine, Research-FAHS, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
| | - Dhasarathdev Srinivasan
- Centre for Advanced Biotherapeutics and Regenerative Medicine, Research-FAHS, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
| | - Salman Shadula Osmania
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Shoeb Ikhlas
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nityanand Srivastav
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ranjith Balakrishnan
- Centre for Advanced Biotherapeutics and Regenerative Medicine, Research-FAHS, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
| | | | - Ankush Chauhan
- Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
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Muruganantham JK, Veerabathiran R. The influence of Omicron on vaccine efficacy and durability: a neurology perspective. Clin Exp Vaccine Res 2024; 13:175-183. [PMID: 39144125 PMCID: PMC11319109 DOI: 10.7774/cevr.2024.13.3.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 07/01/2024] [Indexed: 08/16/2024] Open
Abstract
Omicron variants present new challenges when it comes to understanding their impact on vaccines, antiviral strategies, and possible neurological consequences. This article describes the characteristics of the Omicron variant, its epidemiology, the efficacy of vaccines and monoclonal antibodies, and its association with lymphoid depletion. We also explore the neurological implications of Omicron, focusing on its association with encephalopathy and encephalitis. There are unique challenges associated with the Omicron variant, which is characterized by distinct mutations and increased transmissibility. For a better understanding of the effects of this disease and developing strategies to combat its spread, especially concerning neurological complications, ongoing research is necessary.
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Affiliation(s)
- Jethendra Kumar Muruganantham
- Human Cytogenetics and Genomics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
| | - Ramakrishnan Veerabathiran
- Human Cytogenetics and Genomics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
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Taysi MR, Kirici M, Kirici M, Tuzun B, Poustforoosh A. Antioxidant enzyme activities, molecular docking studies, MM-GBSA, and molecular dynamic of chlorpyrifos in freshwater fish Capoeta umbla. J Biomol Struct Dyn 2024; 42:163-176. [PMID: 36974945 DOI: 10.1080/07391102.2023.2192807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
Abstract
Chlorpyrifos (CPF), which was started to be used in 1965, is a broad spectrum organophosphate insecticide that is used more and more day by day. Commonly used to control pests in farmland and homes, CPF is more toxic to fish than organochlorine compounds. CPF poses a serious threat to the health of humans and aquatic organisms. This paper studies the relationship between CPF exposure and antioxidant enzyme activities in gill, kidney and liver tissues of Capoeta umbla. Different time intervals (12, 24, 48, 72, and 96 h) and CPF doses (55 and 110 µg L-1) were used in the study. Spectrophotometrical measures were taken in all tissues for antioxidant enzyme activities and malondialdehyde (MDA) levels, as indices of the lipid peroxidation (LPO). A positive relationship between CPF and MDA levels was found in the study at a statistically significant level (p < 0.05). The study also found a negative relationship between CPF levels and catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), and glutathione reductase (GR) activity. Independent variables in the study can act as biomarkers of CPF exposure. The study recommends employing proper ecotoxicological risk evaluations in cases of CPF usage as a pesticide. The activities of the studied molecules against various proteins that are crystal structure of human peroxiredoxin 5 (PDB ID: 1HD2) has docking score value is -2.67, crystal structure of Bovine Xanthine Oxidase (PDB ID: 3NRZ) has docking score value is -3.76, and crystal structure of antibacterial FabH (PDB ID: 4Z8D) has docking score value is -3.16, were compared. Molecular dynamic (MD) calculations were made in 100 ns. MM/GBSA methods are calculated binding free energy. Afterwards, ADME/T analysis was performed to examine the some properties of the molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mehmet Reşit Taysi
- Department of Fisheries, Faculty of Agriculture, Bingol University, Bingöl, Turkey
| | - Muammer Kirici
- Department of Veterinary Health, Food Agriculture and Livestock Vocational School, Bingöl University, Bingöl, Turkey
| | - Mahinur Kirici
- Department of Chemistry, Faculty of Arts and Science, Bingöl University, Bingöl, Turkey
| | - Burak Tuzun
- Plant and Animal Production Department, Technical Sciences Vocational School of Sivas, Sivas Cumhuriyet University, Sivas, Turkey
| | - Alireza Poustforoosh
- Chemical Engineering Department, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
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Dey A, Vaishak K, Deka D, Radhakrishnan AK, Paul S, Shanmugam P, Daniel AP, Pathak S, Duttaroy AK, Banerjee A. Epigenetic perspectives associated with COVID-19 infection and related cytokine storm: an updated review. Infection 2023; 51:1603-1618. [PMID: 36906872 PMCID: PMC10008189 DOI: 10.1007/s15010-023-02017-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/27/2023] [Indexed: 03/13/2023]
Abstract
PURPOSE The COVID-19 pandemic caused by the novel Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has put the world in a medical crisis for the past three years; nearly 6.3 million lives have been diminished due to the virus outbreak. This review aims to update the recent findings on COVID-19 infections from an epigenetic scenario and develop future perspectives of epi-drugs to treat the disease. METHODS Original research articles and review studies related to COVID-19 were searched and analyzed from the Google Scholar/PubMed/Medline databases mainly between 2019 and 2022 to brief the recent work. RESULTS Numerous in-depth studies of the mechanisms used by SARS-CoV-2 have been going on to minimize the consequences of the viral outburst. Angiotensin-Converting Enzyme 2 receptors and Transmembrane serine protease 2 facilitate viral entry to the host cells. Upon internalization, it uses the host machinery to replicate viral copies and alter the downstream regulation of the normal cells, causing infection-related morbidities and mortalities. In addition, several epigenetic regulations such as DNA methylation, acetylation, histone modifications, microRNA, and other factors (age, sex, etc.) are responsible for the regulations of viral entry, its immune evasion, and cytokine responses also play a major modulatory role in COVID-19 severity, which has been discussed in detail in this review. CONCLUSION Findings of epigenetic regulation of viral pathogenicity open a new window for epi-drugs as a possible therapeutical approach against COVID-19.
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Affiliation(s)
- Amit Dey
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, TN, 603103, India
| | - K Vaishak
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, TN, 603103, India
| | - Dikshita Deka
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, TN, 603103, India
| | - Arun Kumar Radhakrishnan
- Department of Pharmacology, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chennai, TN, India
| | - Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No.500 Fracc., CP 76130, San Pablo, Querétaro, Mexico
| | - Priyadarshini Shanmugam
- Department of Microbiology, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chennai, TN, 603103, India
| | - Alice Peace Daniel
- Department of Microbiology, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chennai, TN, 603103, India
| | - Surajit Pathak
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, TN, 603103, India
| | - Asim K Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Antara Banerjee
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, TN, 603103, India.
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Vardhan S, Sahoo SK. Computational studies on the interaction of Omicron subvariants (BA.1, BA.2, and BA.3) with ACE2 and polyphenols. PHYTOCHEMICAL ANALYSIS : PCA 2023; 34:800-815. [PMID: 36606391 DOI: 10.1002/pca.3204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/05/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION The SARS-CoV-2 Omicron variant BA.2 is spreading widely across the globe. The World Health Organization (WHO) designated BA.2 as a variant of concern due to its high transmission rate and pathogenicity. To elucidate the structural changes caused by mutations, we conducted a comparative analysis of BA.2 with variants BA.1 and BA.3. OBJECTIVE In the present study, we aimed to investigate the interactions of the spike glycoprotein receptor-binding domain (SGp RBD) of Omicron variants BA.1, BA.2, and BA.3 with the human receptor hACE2. Further, a library of 233 polyphenols was screened by molecular docking with the SGp RBDs of Omicron variants BA.1, BA.2, and BA.3. METHODS Protein-protein and protein-ligand molecular docking simulations were performed with AutoDock Vina and the ClusPro 2.0 server, respectively. The protein-ligand interactions were evaluated by BIOVIA Discovery Studio and ChimeraX 1.4. The molecular dynamics simulations for 100 ns were performed using GROMACS 2021. RESULTS Compared to other variants of concern, the structural changes in Omicron caused by mutations at key positions improved its ability to cause infection. Despite multiple mutations, many important polyphenols bind effectively at the RBDs of Omicron variants, with the required pharmacokinetic and ADME features and obeying the Lipinski rule. CONCLUSION Even though Omicron variants have multiple mutations and their transmission rate is relatively high, the computed binding affinities of lead polyphenols like epigallocatechin-3-O-gallate (EGCG) and luteolin-7-O-glucuronide (L7G) indicate that traditional medicines and proper immunity booster diets may be useful in the long-term fight against SARS-CoV-2.
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Affiliation(s)
- Seshu Vardhan
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology (SVNIT), Surat, Gujarat, India
| | - Suban K Sahoo
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology (SVNIT), Surat, Gujarat, India
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Molecular modeling and simulations of some antiviral drugs, benzylisoquinoline alkaloid, and coumarin molecules to investigate the effects on Mpro main viral protease inhibition. Biochem Biophys Rep 2023; 34:101459. [PMID: 36987522 PMCID: PMC10037929 DOI: 10.1016/j.bbrep.2023.101459] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/26/2023] Open
Abstract
Background SARS-CoV-2 is a deadly viral disease and uncounted deaths occurs since its first appearance in the year 2019. The antiviral drugs, benzylisoquinoline alkaloids, and coumarin molecules were searched using different online engines for drug repurposing with SARS-CoV-2 and to investigate the effects on main viral protease (Mpro) upon their bindings. Methods A database composed of antiviral drugs, benzylisoquinoline alkaloids, and Coumarin molecules was screened through a molecular docking strategy to uncover the interactions of collected molecules with SARS-CoV-2 Mpro. Further, molecular dynamics simulations (MDS) were implemented for 100 ns to calculate the stability of the best complexed molecular scaffold with Mpro. The conformations of the simulated complexes were investigated by using principal component analysis (PCA) and Gibbs energy landscape (FEL) and DSSP together. Next, free binding energy (ΔGbind) was calculated using the mmpbsa method. Results Molecular docking simulations demonstrate 17 molecules exhibited better binding affinity out of 99 molecules present in the database with the viral protease Mpro, followed ADMET properties and were documented. The Coumarin-EM04 molecular scaffold exhibited interactions with catalytical dyad HIS41, CYS145, and neighboring amino acids SER165 and GLN189 in the catalytical site. The crucial factor RMSD was calculated to determine the orientations of Coumarin-EM04. The Coumarin-EM04 complexed with Mpro was found stable in the binding site during MDS. Furthermore, the free energy binding ΔGbind of Coumarin-EM04 was found to be −187.471 ± 2.230 kJ/mol, and for Remdesivir ΔGbind was −171.926 ± 2.237 kJ/mol with SARS-CoV-2 Mpro. Conclusion In this study, we identify potent molecules that exhibit interactions with catalytical dyad HIS41 and CYS145 amino acids and unravel Coumarin-EM04 exhibited ΔGbind higher than Remdesivir against Mpro and thus may serve better antiviral agent against SARS-CoV-2.
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Rafiq A, Jabeen T, Aslam S, Ahmad M, Ashfaq UA, Mohsin NUA, Zaki MEA, Al-Hussain SA. A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products. Molecules 2023; 28:4860. [PMID: 37375415 DOI: 10.3390/molecules28124860] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The ongoing COVID-19 pandemic has resulted in a global panic because of its continual evolution and recurring spikes. This serious malignancy is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the outbreak, millions of people have been affected from December 2019 till now, which has led to a great surge in finding treatments. Despite trying to handle the pandemic with the repurposing of some drugs, such as chloroquine, hydroxychloroquine, remdesivir, lopinavir, ivermectin, etc., against COVID-19, the SARS-CoV-2 virus continues its out-of-control spread. There is a dire need to identify a new regimen of natural products to combat the deadly viral disease. This article deals with the literature reports to date of natural products showing inhibitory activity towards SARS-CoV-2 through different approaches, such as in vivo, in vitro, and in silico studies. Natural compounds targeting the proteins of SARS-CoV-2-the main protease (Mpro), papain-like protease (PLpro), spike proteins, RNA-dependent RNA polymerase (RdRp), endoribonuclease, exoribonuclease, helicase, nucleocapsid, methyltransferase, adeno diphosphate (ADP) phosphatase, other nonstructural proteins, and envelope proteins-were extracted mainly from plants, and some were isolated from bacteria, algae, fungi, and a few marine organisms.
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Affiliation(s)
- Ayesha Rafiq
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Tooba Jabeen
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Sana Aslam
- Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Noor Ul Amin Mohsin
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Sami A Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
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Hasanzadeh Esfahani M, Ghasemi L, Behzad M, Skorepova E, Dusek M. Design, Spectroscopic, and Crystal Structural Characterization of New Pyrazolone-Based Schiff Bases: Molecular Docking Investigations against SARS-Covid-19 Main Proteases (PDB Ids: 6LU7 and 7TLL). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2157026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Liana Ghasemi
- Faculty of Chemistry, Semnan University, Semnan, Iran
| | - Mahdi Behzad
- Faculty of Chemistry, Semnan University, Semnan, Iran
| | - Eliska Skorepova
- Department of Structure Analysis, Institute of Physics ASCR, Prague, Czech Republic
| | - Michal Dusek
- Department of Structure Analysis, Institute of Physics ASCR, Prague, Czech Republic
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Arumuganainar D, Yadalam PK, Alzahrani KJ, Alsharif KF, Alzahrani FM, Alshammeri S, Ahmed SSSJ, Vinothkumar TS, Baeshen HA, Patil S. Inhibitory effect of lupeol, quercetin, and solasodine on Rhizopus oryzae: A molecular docking and dynamic simulation study. J Infect Public Health 2022; 16:117-124. [PMID: 36512968 DOI: 10.1016/j.jiph.2022.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mucormycosis is an infection caused by fungi belonging to the order Mucorales. Rhizopus oryzae is one of the most prevalent organisms identified in mucormycosis patients. Because it spreads quickly through the blood vessels, this opportunistic illness has an exceptionally high fatality rate, even when vigorous treatment is administered. Nonetheless, it has a high tolerance to antifungal medicines, limiting treatment options. As a result, improved methods for preventing and treating mucormycosis are desperately needed. Hence, this study was aimed at assessing the effect of lupeol, quercetin, and solasodine against mucormycosis based on computational approaches. METHODS The Rhizopus oryzae RNA-dependent RNA polymerase (RdRp) was the target for the design of drugs against the deadly mucormycosis. The three-dimensional structure of the RdRp was modelled with a Swiss model and validated using PROCHECK, VERIFY 3D, and QMEAN. Using the Schrodinger maestro module, a molecular docking study was performed between RdRp and the antimicrobial phytochemicals lupeol, quercetin, and solasodine. A molecular dynamics (MD) simulation study was used to assess the stability and interaction of the RdRp with these phytochemicals. RESULTS The RdRp protein binds strongly to lupeol (-7.2 kcal/mol), quercetin (-9.1 kcal/mol), and solasodine (-9.6 kcal/mol), according to molecular docking assessment based on the lowest binding energy, confirmation, and bond interaction. Simulations suggest that lupeol, quercetin, and solasodine complexes with RdRp and showed stable confirmation with minimal fluctuation throughout the 200 nanoseconds based on the RMSD and RMSF trajectory assessments. CONCLUSION The molecular docking and MD simulation investigation improved our understanding of phytochemical-RdRp interactions. Due to its high affinity for RdRp, solasodine may be a better treatment option for mucormycosis.
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Affiliation(s)
- Deepavalli Arumuganainar
- Department of Periodontics, Ragas Dental College and Hospital, 2/102, East Coast Road, Uthandi, Chennai 600119, India.
| | - Pradeep Kumar Yadalam
- Department of Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Khalid J Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied medical sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Khalaf F Alsharif
- Department of Clinical Laboratory Sciences, College of Applied medical sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Fuad M Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied medical sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Saleh Alshammeri
- Department of Optometry, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia.
| | - Sheik S S J Ahmed
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India.
| | - Thilla Sekar Vinothkumar
- Department of Restorative Dental Sciences, College of Dentistry, Jazan University, Jazan 45142, Saudi Arabia; Department of Conservative Dentistry and Endodontics, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Hosam Ali Baeshen
- Department of Orthodontics, College of Dentistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan UTAH - 84095, USA; Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
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Alzain AA. Insights from computational studies on the potential of natural compounds as inhibitors against SARS-CoV-2 spike omicron variant. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:953-968. [PMID: 36469669 DOI: 10.1080/1062936x.2022.2152486] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a major global health emergency, with more than six million deaths worldwide. It is becoming increasingly challenging to treat COVID-19 due to the emergence of novel variants. The omicron variant is capable to evade defences and spread quickly. Among many validated COVID-19 targets, the spike (S) protein plays an important role in receptor recognition (via the S1 subunit) and membrane fusion (via the S2 subunit). The S protein is one of the vital targets for the development of drugs to combat this illness. In this research, we applied various computational methods such as molecular docking, molecular dynamics, MM-GBSA calculations, and ADMET prediction to identify potential natural products from Saudi medicinal plants against the spike omicron variant. As a result, three compounds (LTS0002490, LTS0117007, and LTS0217912) were identified with better binding affinity to the spike omicron variant compared to the reference compound (VE607). In addition, these compounds showed stable interactions with the target during molecular dynamics simulations for 140 ns. Last, these compounds have optimal ADMET properties. We suggest that these compounds may be considered promising hits to treat COVID-19 if experimentally validated.
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Affiliation(s)
- A A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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Rahmatullah M, Jahan R, Nissapatorn V, Pereira MDL, Wiart C. Editorial: Emerging and old viral diseases: Antiviral drug discovery from medicinal plants. Front Pharmacol 2022; 13:976592. [PMID: 36059941 PMCID: PMC9437638 DOI: 10.3389/fphar.2022.976592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mohammed Rahmatullah
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, University of Development Alternative, Dhaka, Bangladesh
- *Correspondence: Mohammed Rahmatullah,
| | - Rownak Jahan
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, University of Development Alternative, Dhaka, Bangladesh
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Maria De Lourdes Pereira
- CICECO-Aveiro Institute of Materials and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Christophe Wiart
- School of Pharmacy, University of Nottingham Malaysia Campus, Selangor, Malaysia
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