Computational design of a broad-spectrum multi-epitope vaccine candidate against seven strains of human coronaviruses DOI Creative Commons
Avinash Kumar, Ekta Rathi, Suvarna G. Kini

et al.

3 Biotech, Journal Year: 2022, Volume and Issue: 12(9)

Published: Aug. 23, 2022

Spike (S) proteins are an attractive target as it mediates the binding of SARS-CoV-2 to host through ACE-2 receptors. We hypothesize that screening S protein sequences all seven known HCoVs would result in identification potential multi-epitope vaccine candidates capable conferring immunity against various HCoVs. In present study, several machine learning-based in-silico tools were employed design a broad-spectrum candidate targeting strains human coronaviruses. Herein, multiple B-cell epitopes and T-cell (CTL HTL) predicted from Post-prediction they linked together with adjuvant construct candidate. Secondary tertiary structures validated, refined 3D-model was docked immune receptor. The evaluated for antigenicity, allergenicity, solubility, its ability achieve high-level expression bacterial hosts. Finally, simulation carried out evaluate response after three doses. designed is antigenic (with or without adjuvant), non-allergenic, binds well TLR-3 receptor might elicit diverse strong response.The online version contains supplementary material available at 10.1007/s13205-022-03286-0.

Language: Английский

Deciphering molecular mechanisms of SARS-CoV-2 pathogenesis and drug repurposing through GRN motifs: a comprehensive systems biology study DOI Open Access
Marzieh Sameni, Seyed Amir Mirmotalebisohi, Zeinab Dehghan

et al.

3 Biotech, Journal Year: 2023, Volume and Issue: 13(4)

Published: March 13, 2023

Language: Английский

Citations

5
Phytochemicals of Cocculus hirsutus deciphered SARS-CoV-2 inhibition by targeting main proteases in molecular docking, simulation, and pharmacological analyses DOI

Mariappan Rajan,

Selvakani Prabhakaran,

Jyoti Sankar Prusty

et al.

Journal of Biomolecular Structure and Dynamics, Journal Year: 2022, Volume and Issue: 41(15), P. 7406 - 7420

Published: Sept. 13, 2022

The COVID-19 pandemic is spreading rapidly due to the outbreak of novel coronavirus SARS-CoV-2 across globe. Anti-COVID-19 drugs are urgently required in this situation. In regard, discovery promising new anti-COVID-19 moieties expected from traditional medicine. study aimed discover phytochemicals Cocculus hirsutus having activity via inhibiting main proteases SARS-CoV-2. Main (Mpro) serve as a protuberant target for drug because it key enzyme coronaviruses and has pivotal role mediating viral replication transcription that makes an attractive target. Recent studies indicated utility C. treatment disorders like Dengue. Phytochemicals were docked against (6LU7, 5R7Y, 5R7Z, 5R80, 5R81, 5R82) using PyRx virtual screen tool studio visualizer. Further, molecular dynamics simulations performed (for 100 ns) see conformational stability all complexes. Pharmacokinetic properties drug-likeness prediction selected phytoconstituents also performed. Betulin, coclaurine, quinic acid found with significant binding affinity Mpro comparison control. They have shown stable interactions amino residues present on active site most candidates. These compounds could be potential leads development target-specific therapeutics while ethnomedicinal uses herb further needed its detailed antiviral therapeutic exploration.Communicated by Ramaswamy H. Sarma.

Language: Английский

Citations

8
Investigation of the effects of N-Acetylglucosamine on the stability of the spike protein in SARS-CoV-2 by molecular dynamics simulations DOI Open Access
E. Deniz Tekin

Computational and Theoretical Chemistry, Journal Year: 2023, Volume and Issue: 1222, P. 114049 - 114049

Published: Feb. 1, 2023

Language: Английский

Citations

4
Structure based exploration of potential lead molecules against the extracellular cysteine protease (EcpA) of Staphylococcus epidermidis: a therapeutic halt DOI
Guneswar Sethi, Jeong Ho Hwang, R. Krishna

et al.

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

Published: Aug. 24, 2023

Nosocomial infection caused by Staphylococcus epidermidis is one of the most widely spread diseases affecting world's population. No strategies have been developed to overcome this and inhibit its in immunocompromised patients or with indwelling medical devices. EcpA an extracellular cysteine protease protein involved biofilm formation on Thus, blocking mechanism may be viable for developing a drug against S. epidermidis. The current research aimed find new, potent inhibitors that could stop from functioning. This study attempted identify promising candidates using structure-based virtual screening (SBVS) libraries natural ligands. top-scored molecules were shortlisted based their IC50 values pharmacophore properties further validated through density functional theory (DFT) studies. We found five screening, results indicate these drugs had highest energy binding potential towards targets when compared reference molecule E-64, known inhibitor. In order evaluate conformational stability protein-ligand complexes, molecular dynamics (MD) simulations performed triplicate 100 ns, revealing significant anticipated at docked site. Furthermore, principal component analysis free calculations understand complexes. indicated compounds looked suitable novel pave path discovery EcpA.Communicated Ramaswamy H. Sarma.

Language: Английский

Citations

4
Computational design of a broad-spectrum multi-epitope vaccine candidate against seven strains of human coronaviruses DOI Creative Commons
Avinash Kumar, Ekta Rathi, Suvarna G. Kini

et al.

3 Biotech, Journal Year: 2022, Volume and Issue: 12(9)

Published: Aug. 23, 2022

Spike (S) proteins are an attractive target as it mediates the binding of SARS-CoV-2 to host through ACE-2 receptors. We hypothesize that screening S protein sequences all seven known HCoVs would result in identification potential multi-epitope vaccine candidates capable conferring immunity against various HCoVs. In present study, several machine learning-based in-silico tools were employed design a broad-spectrum candidate targeting strains human coronaviruses. Herein, multiple B-cell epitopes and T-cell (CTL HTL) predicted from Post-prediction they linked together with adjuvant construct candidate. Secondary tertiary structures validated, refined 3D-model was docked immune receptor. The evaluated for antigenicity, allergenicity, solubility, its ability achieve high-level expression bacterial hosts. Finally, simulation carried out evaluate response after three doses. designed is antigenic (with or without adjuvant), non-allergenic, binds well TLR-3 receptor might elicit diverse strong response.The online version contains supplementary material available at 10.1007/s13205-022-03286-0.

Language: Английский

Citations

7