Journal ArticleDOI
Exploring the potent inhibitors and binding modes of phospholipase A2 through in silico investigation.
Shafi Mahmud,Md. Rimon Parves,Yasir Mohamed Riza,Khaled Mahmud Sujon,Suvendu Ray,Fahmida Alam Tithi,Zannati Ferdous Zaoti,Sanjida Alam,Nurul Absar +8 more
TLDR
34 experimentally proven and diverse synthetic inhibitors of PLA2 were screened primarily on the basis of Glide extra precision docking and MM-GBSA rescoring function and showed positive remarks on various physiochemical properties and pharmacologically relevant descriptors, and could be used for targeted inhibition.Abstract:
Snake venom of Naja naja comprises of several types of enzymes, and among them, water-soluble proteolytic enzyme, phospholipase A2 (PLA2), is noteworthy for its numerous adverse effects, such as cy...read more
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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
Journal ArticleDOI
Plant-Based Phytochemical Screening by Targeting Main Protease of SARS-CoV-2 to Design Effective Potent Inhibitors
Shafi Mahmud,Suvro Biswas,Gobindo Kumar Paul,Mohasana Akter Mita,Maria Meha Promi,Shamima Afrose,Md. Robiul Hasan,Shahriar Zaman,Md. Salah Uddin,Kuldeep Dhama,Talha Bin Emran,Md. Abu Saleh,Jesus Simal-Gandara +12 more
TL;DR: A molecular docking program was used to screen the top three candidate compounds: epicatechin-3-O-gallate, psi-taraxasterol, and catechin gallate as mentioned in this paper.
References
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Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
TL;DR: Numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, show that density-functional formulas for the correlation energy and correlation potential give correlation energies within a few percent.
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The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
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
SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules
TL;DR: The new SwissADME web tool is presented that gives free access to a pool of fast yet robust predictive models for physicochemical properties, pharmacokinetics, drug-likeness and medicinal chemistry friendliness, among which in-house proficient methods such as the BOILED-Egg, iLOGP and Bioavailability Radar are presented.