Comparative molecular investigation of the potential inhibitors against SARS-CoV-2 main protease: a molecular docking study.
Arif Khan,Shafi Mahmud,A. S. M. Rubayet Ul Alam,Ekhtiar Rahman,Firoz Ahmed,Mohammed Rahmatullah +5 more
TLDR
The overall prediction findings indicate that Epirubicin, Vapreotida, and Saquinavir may inhibit COVID-19 by synergistic interactions in the active cavity and those results can pave the way in drug discovery although it has to be further validated by in-vitro and in- vivo investigations.Abstract:
Recent outbreak of novel coronavirus and its rapid pandemic escalation in all over the world has drawn the attention to urgent need for effective drug development. However, due to prolonged vaccine and drug development procedure against a newly emerged devastating SARS-CoV-2 virus pathogen, repurposing of existing potential pertinent drug molecules would be preferable strategy to reduce mortality immediately and further development of new drugs to combat overall global Covid-19 crisis in all over the world. Herein, we have filtered 23 prospective drug candidates through literature review. Assessing evidences from molecular docking studies, it was clearly seen that, Epirubicin, Vapreotida, and Saquinavir exhibited better binding affinity against SARS-CoV-2 Main Protease than other drug molecules among the 23 potential inhibitors. However, 50 ns molecular dynamics simulation indicated the less mobile nature of the docked complex maintaining structural integrity. Our overall prediction findings indicate that Epirubicin, Vapreotida, and Saquinavir may inhibit COVID-19 by synergistic interactions in the active cavity and those results can pave the way in drug discovery although it has to be further validated by in-vitro and in-vivo investigations. Communicated by Ramaswamy H. Sarma.read more
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Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA-dependent RNA polymerase (RdRp) inhibition: an in-silico analysis.
TL;DR: It is suggested that EGCG, TF2a,TF2b, TF3 can inhibit RdRp and represent an effective therapy for COVID-19, and the binding free energy components calculated by the MM-PBSA also confirm the stability of the complexes.
Journal ArticleDOI
Virtual screening and molecular dynamics simulation study of plant-derived compounds to identify potential inhibitors of main protease from SARS-CoV-2.
Shafi Mahmud,Mohammad Abu Raihan Uddin,Gobindo Kumar Paul,Mst Sharmin Sultana Shimu,Saiful Islam,Ekhtiar Rahman,Ariful Islam,Samiul Islam,Maria Meha Promi,Talha Bin Emran,Talha Bin Emran,Abu Saleh +11 more
TL;DR: In this paper, the authors employed a rigorous literature review pipeline to enlist 3063 compounds from more than 200 plants from the Asian region and employed a virtual screening procedure to shortlist the total compounds into 19 based on their better binding energy.
Journal ArticleDOI
Efficacy of Phytochemicals Derived from Avicennia officinalis for the Management of COVID-19: A Combined In Silico and Biochemical Study.
Shafi Mahmud,Gobindo Kumar Paul,Mirola Afroze,Shirmin Islam,Swagota Briti Ray Gupt,Mamudul Hasan Razu,Suvro Biswas,Shahriar Zaman,Salah Uddin,Mala Khan,Nunzio Antonio Cacciola,Talha Bin Emran,Abu Saleh,Raffaele Capasso,Jesus Simal-Gandara +14 more
TL;DR: In this article, the authors examined phytochemicals extracted from Avicennia officinalis and evaluated their potential effects against the main protease of SARS-CoV-2.
Journal ArticleDOI
Screening of phytochemicals as potent inhibitor of 3-chymotrypsin and papain-like proteases of SARS-CoV2: an in silico approach to combat COVID-19.
TL;DR: Amentoflavone and Gallocatechin gallate may be potential inhibitors of 3CLpro and PLpro proteins and effective drug candidates for SARS-CoV2, but the findings need to be supported by in vivo studies to establish the exact mode of action.
Journal ArticleDOI
A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that inhibit the main protease of SARS-CoV-2: an in silico investigation.
Ahmed Rakib,Zulkar Nain,Saad Ahmed Sami,Shafi Mahmud,Ashiqul Islam,Shahriar Ahmed,Adnan Bin Faisul Siddiqui,S.M. Omar Faruque Babu,Payar Hossain,Asif Shahriar,Firzan Nainu,Talha Bin Emran,Jesus Simal-Gandara +12 more
TL;DR: In this article, the authors performed a molecular docking analysis and found that several of the selected selenocompounds showed potential binding affinities for SARS-CoV-2 Mpro, especially ethaselen (49), which exhibited a docking score of -6.7
References
More filters
Journal ArticleDOI
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott,Arthur J. Olson +1 more
TL;DR: AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in the lab, while also significantly improving the accuracy of the binding mode predictions, judging by tests on the training set used in AutoDock 4 development.
Journal ArticleDOI
The Amber biomolecular simulation programs
David A. Case,Thomas E. Cheatham,Tom Darden,Holger Gohlke,Ray Luo,Kenneth M. Merz,Alexey V. Onufriev,Carlos Simmerling,Bing Wang,Robert J. Woods +9 more
TL;DR: The development, current features, and some directions for future development of the Amber package of computer programs, which contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
Journal ArticleDOI
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
TL;DR: The first published version of the Merck molecular force field (MMFF) is MMFF94 as mentioned in this paper, which is based on the OPLS force field and has been applied to condensed-phase processes.
Journal ArticleDOI
PubChem Substance and Compound databases
Sunghwan Kim,Paul A. Thiessen,Evan E Bolton,Jie Chen,Gang Fu,Asta Gindulyte,Lianyi Han,Jane He,Siqian He,Benjamin A. Shoemaker,Jiyao Wang,Bo Yu,Jian-Jian Zhang,Stephen H. Bryant +13 more
TL;DR: An overview of the PubChem Substance and Compound databases is provided, including data sources and contents, data organization, data submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access.