Virtual Screening Based on Docking and Molecular Dynamics Simulations of Potential Ebola Receptor Inhibitors DOI
Prashasti Sinha, Anil Kumar Yadav

ChemistrySelect, Journal Year: 2023, Volume and Issue: 8(42)

Published: Nov. 8, 2023

Abstract Galidesivir (BCX4430) is known to treat different viruses under Filoviridae family and it has proved as a potential antiviral drug against Ebola virus. Therefore, for treating virus in particular there need the identification compound. In this work, derivatives of Pyrrolopyrimidine are designed investigate their activity receptors (VP24, VP30, VP35 VP40). FBDD‐based virtual screening resulted eight compounds, based on pharmacokinetics Density Functional Theory (DFT) analysis; four compounds were shortlisted. Further, docking simulation that, compound 4 exhibited −9.8, −9.6, −9.7, −9.5 kcal/mol binding energy each receptor, respectively. The predicted results above receptor better than BCX4430. Docking validated compared BCX4430 by performing Molecular Dynamic simulations at 100 ns, order study Root Mean Square Deviation, Fluctuation, Radius Gyration MM/PBSA docked complexes. lays foundation screened act probable Ebola.

Language: Английский

Molecular docking, molecular dynamics and binding free energy based identification of novel potential multitarget inhibitors of Nipah virus DOI
Prashasti Sinha, Anil Kumar Yadav

Journal of Biomolecular Structure and Dynamics, Journal Year: 2023, Volume and Issue: unknown, P. 1 - 17

Published: Nov. 3, 2023

Nipah virus (NiV) is one of the most common viral diseases affecting brain and nervous system body. To date, there no significant antiviral drug specifically designed to inhibit NiV. In last ten years, has been a increase in interest multitarget development. Therefore, reported work focuses on designing inhibitor for Among twelve compounds, five exhibited better drug-likeness ADMET properties, hence being selected further analysis. molecular docking study, these compounds possessed binding affinity as compared Favipiravir. The RMSD was ≤2Å number H-bonds signified stability complexes formed. ΔGbind C4, C6 C7 found be comparatively higher than other screened revealing their greater ability bind efficiently with NiV-G, NiV-F NiV-N receptors, respectively. based docking, dynamics, MM/PBSA analysis, can act potential inhibitors multitargets NiV.Communicated by Ramaswamy H. Sarma.

Language: Английский

Citations

4
Unraveling the anti-breast cancer activity of Cimicifugae rhizoma using biological network pathways and molecular dynamics simulation DOI
Prashasti Sinha, Anil Kumar Yadav

Molecular Diversity, Journal Year: 2024, Volume and Issue: 29(1), P. 241 - 254

Published: April 13, 2024

Language: Английский

Citations

1
Computational exploration of nonlinear optical properties in supramolecular naphthalene diimides and nucleotide complexes DOI
Wajid Hussain, Muhammad Sulaman, Yahya Sandali

et al.

Materials Science and Engineering B, Journal Year: 2024, Volume and Issue: 305, P. 117429 - 117429

Published: May 17, 2024

Language: Английский

Citations

1
Identification of 3, 4-dihydroxy complexes as potential antiviral via DFT, molecular docking, molecular dynamics and MM/PBSA against rabies and dengue receptors DOI
Prashasti Sinha, Anil Kumar Yadav

Journal of Biomolecular Structure and Dynamics, Journal Year: 2023, Volume and Issue: 42(13), P. 7037 - 7053

Published: Aug. 14, 2023

AbstractThe quest to identify antiviral drug candidates for dengue and rabies viral diseases is a great challenge the researchers. While different research being conducted on repurposed drugs against these two viruses, no compound has gained success in treating them. Therefore, this study, 3, 4-dihydroxy complexes have been virtually designed investigate their properties analyze efficiency interaction with concerned diseases. DFT calculations are carried out study electronic thermodynamic understand stability reactivity of reported compounds. These compounds were subjected molecular docking studies binding interactions NS5 Dengue virus mRNA 2'-O-methyltransferase phosphoprotein C-terminal domain Rabies virus. MD simulation, hydrogen bond analysis, MM/PBSA performed at 100 ns support obtained results.Communicated by Ramaswamy H. SarmaKeywords: 3,4-dihydroxy complexesmolecular dockingmolecular dynamics AcknowledgmentsAuthor, Prashasti Sinha very thankful University Grant Commission (UGC), New Delhi, India, financial doctoral work. Authors would like acknowledge IIT India allowing access SCFBio web server.Authors' contributionsAuthor P.S. primary contributor manuscript under supervision author A.K.Y.Disclosure statementAuthors declare conflict interests.Data availability statementAll relevant data available manuscript.Additional informationFundingThe author(s) there funding associated work featured article.

Language: Английский

Citations

3
Repurposing integrase inhibitors against human T-lymphotropic virus type-1: a computational approach DOI
Prashasti Sinha, Anil Kumar Yadav

Journal of Biomolecular Structure and Dynamics, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 12

Published: Jan. 17, 2024

Adult T-cell Lymphoma (ATL) is caused by the delta retrovirus family member known as Human Leukaemia Type I (HTLV-1). Due to unavailability of any cure, study gained motivation identify some repurposed drugs against virus. A quick and accurate method screening licensed medications for finding a treatment HTLV-1 cheminformatics drug repurposing in order analyze dataset FDA approved integrase antivirals infection. To determine how antiviral interacted with important residues active regions, molecular docking modeling was used. The steady behavior ligands inside region then confirmed dynamics probable receptor-drug complexes. Cabotegravir, Raltegravir Elvitegravir had best scores target, indicating that they can tightly bind integrase. Moreover, MD simulation revealed Cabotegravir-HTLV-1, Raltegravir-HTLV-1 Elvitegravir-HTLV-1 interactions were stable. It obvious more testing these medicines both clinical trials experimental tests necessary demonstrate their efficacy

Language: Английский

Citations

0
In silico identification of cyclosporin derivatives as potential inhibitors for RdRp of rotavirus by molecular docking and molecular dynamic studies DOI
Prashasti Sinha, Anil Kumar Yadav

Journal of Biomolecular Structure and Dynamics, Journal Year: 2023, Volume and Issue: 42(10), P. 5001 - 5014

Published: July 30, 2023

AbstractRotavirus is one of the most common gastrointestinal viral diseases. Till date, there are only two vaccines available in markets, which specifically to be administered young babies. In this study, VP1 RdRp selected as potential target carry out inhibitory activities. Cyclosporin A (Cys A) derivatives were designed via FBDD, pharmacokinetics, molecular docking, dynamics (MD) simulation and mechanics generalized born surface area was applied on these compounds. The results from investigations analyzed it found that considered study nontoxic docking revealed made some important bonds inside active site receptors within a catalytic triad (Serine–Histidine–Aspartate). After analyzing mean values root square density (RMSD), fluctuation (RMSF), radius gyration (RoG) solvent accessible (SASA) at 100 ns MD compounds, compound 1 exhibits RMSD 0.74 ± 0.10 Å, RMSF 0.85 0.15 RoG 16.45 0.40 SASA 66.55 0.35 nm2 ΔGbind −32.76 0.02 kcal/mol. Therefore, amongst reported more stable region also possesses lower binding free energy compared other compounds Cys well.Communicated by Ramaswamy H. SarmaKeywords: RotavirusCyclosporin derivativesMolecular dockingMD simulationMM/PBSA AcknowledgmentsThe authors would like acknowledge IIT Delhi, India for allowing access SCFBio web server.Disclosure statementThe declare no conflict interests.Additional informationFundingThe author Prashasti Sinha very thankful University Grants Commission (UGC), New India, financial support doctoral research work.

Language: Английский

Citations

1
Computational Analysis on Molecular Stability and Binding Affinity of 3-(Aminothiazolyl)Quinolone Derivative as Multitargeting Antibacterial Agents through Ab Initio Methods and Molecular Docking DOI
Prashasti Sinha, Anil Kumar Yadav

Polycyclic aromatic compounds, Journal Year: 2023, Volume and Issue: unknown, P. 1 - 22

Published: Oct. 25, 2023

The present study deals with the application of ab initio method using density functional theory (DFT) at M06-2X/6-311++G(d,p) to characterize considered molecule completely. Though anti-bacterial activity 3-(amino thiazolyl)quinolone derivatives was studied, effects intermolecular hydrogen bonding on chemical and biological processes remain unexplored or have not been thoroughly investigated so far. Investigations into non-covalent interactions were carried out reduced gradient methodology quantum atoms in molecules. An electron localization function used investigate electronic vicinity each atom a molecule. Natural bond orbital analysis determine correlated stabilization energies for bonds (H-bonds) that are responsible molecular stability dimer structure. electrophilic nucleophilic sites predicted electrostatic potential. states partial also represent frontier orbitals. inhibitory activities compound different classes bacteria docking simulation.

Language: Английский

Citations

0
Virtual Screening Based on Docking and Molecular Dynamics Simulations of Potential Ebola Receptor Inhibitors DOI
Prashasti Sinha, Anil Kumar Yadav

ChemistrySelect, Journal Year: 2023, Volume and Issue: 8(42)

Published: Nov. 8, 2023

Abstract Galidesivir (BCX4430) is known to treat different viruses under Filoviridae family and it has proved as a potential antiviral drug against Ebola virus. Therefore, for treating virus in particular there need the identification compound. In this work, derivatives of Pyrrolopyrimidine are designed investigate their activity receptors (VP24, VP30, VP35 VP40). FBDD‐based virtual screening resulted eight compounds, based on pharmacokinetics Density Functional Theory (DFT) analysis; four compounds were shortlisted. Further, docking simulation that, compound 4 exhibited −9.8, −9.6, −9.7, −9.5 kcal/mol binding energy each receptor, respectively. The predicted results above receptor better than BCX4430. Docking validated compared BCX4430 by performing Molecular Dynamic simulations at 100 ns, order study Root Mean Square Deviation, Fluctuation, Radius Gyration MM/PBSA docked complexes. lays foundation screened act probable Ebola.

Language: Английский

Citations

0