1
|
Bhattacharya P, Mandal A. Identification of amentoflavone as a potent SARS-CoV-2 M pro inhibitor: a combination of computational studies and in vitro biological evaluation. J Biomol Struct Dyn 2024:1-19. [PMID: 38263736 DOI: 10.1080/07391102.2024.2304676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/07/2024] [Indexed: 01/25/2024]
Abstract
Small-molecule inhibitors of SARS-CoV-2 Mpro that block the active site pocket of the viral main protease have been considered potential therapeutics for the development of drugs against SARS-CoV-2. Here, we report the identification of amentoflavone (a biflavonoid) through docking-based virtual screening of a library comprised of 231 compounds consisting of flavonoids and isoflavonoids. The docking results were further substantiated through extensive analysis of the data obtained from all-atom 150 ns MD simulation. End-state effective free energy calculations using MM-PBSA calculations further suggested that (Ra)-amentoflavone (C3'-C8''-atropisomer) may show a greater binding affinity towards the Mpro than (Sa)-amentoflavone. In vitro cytotoxicity assay established that amentoflavone showed a high CC50 value indicating much lower toxicity. Further, potent inhibition of the Mpro by amentoflavone was established by studying the effect on HEK293T cells treated with SARS-CoV-2 Mpro expressing plasmid.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Anirban Mandal
- Department of Microbiology, Mrinalini Datta Mahavidyapith, Kolkata, India
| |
Collapse
|
2
|
Varshney N, Murmu S, Baral B, Kashyap D, Singh S, Kandpal M, Bhandari V, Chaurasia A, Kumar S, Jha HC. Unraveling the Aurora kinase A and Epstein-Barr nuclear antigen 1 axis in Epstein Barr virus associated gastric cancer. Virology 2023; 588:109901. [PMID: 37839162 DOI: 10.1016/j.virol.2023.109901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/18/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
Aurora kinase A (AURKA) is one of the crucial cell cycle regulators associated with gastric cancer. Here, we explored Epstein Barr Virus-induced gastric cancer progression through EBV protein EBNA1 with AURKA. We found that EBV infection enhanced cell proliferation and migration of AGS cells and upregulation of AURKA levels. AURKA knockdown markedly reduced the proliferation and migration of the AGS cells even with EBV infection. Moreover, MD-simulation data deciphered the probable connection between EBNA1 and AURKA. The in-vitro analysis through the transcript and protein expression showed that AURKA knockdown reduces the expression of EBNA1. Moreover, EBNA1 alone can enhance AURKA protein expression in AGS cells. Co-immunoprecipitation and NMR analysis between AURKA and EBNA1 depicts the interaction between two proteins. In addition, AURKA knockdown promotes apoptosis in EBV-infected AGS cells through cleavage of Caspase-3, -9, and PARP1. This study demonstrates that EBV oncogenic modulators EBNA1 possibly modulate AURKA in EBV-mediated gastric cancer progression.
Collapse
Affiliation(s)
- Nidhi Varshney
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Sneha Murmu
- Division of Agricultural Bioinformatics (DABin), ICAR-Indian Agricultural Statistics Research Institute (IASRI), India
| | - Budhadev Baral
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Dharmendra Kashyap
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Siddharth Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Meenakshi Kandpal
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Vasundhra Bhandari
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Hyderabad, India
| | | | - Sunil Kumar
- Division of Agricultural Bioinformatics (DABin), ICAR-Indian Agricultural Statistics Research Institute (IASRI), India.
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India.
| |
Collapse
|
3
|
Udunwa DI, Onukwuli OD, Menkiti MC, Anadebe VC, Chidiebere MA. 1-Butyl-3-methylimidazolium methane sulfonate ionic liquid corrosion inhibitor for mild steel alloy: Experimental, optimization and theoretical studies. Heliyon 2023; 9:e18353. [PMID: 37539257 PMCID: PMC10395542 DOI: 10.1016/j.heliyon.2023.e18353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 08/05/2023] Open
Abstract
The current research reports the performance of 1-butyl-3-methylimidazolium methane sulfonate ([C4MIM][OMs](IL)) as effective corrosion inhibitor for mild steel in 1 M H2SO4 electrolyte. For proper evaluation, weight loss, electrochemical study, theoretical modeling and optimization techniques were used. Weight loss and electrochemical methods shows that the inhibition performance of [C4MIM][OMs] on the metal surface strengthens as the concentration increases. Maximum inhibition efficiency of 85.71%, 92.5% and 91.1% at 0.8 g L-1 concentration of [C4MIM][OMs] were obtained from the weight loss, polarization and impedance studies, respectively. In addition, response surface methodology (RSM) a statistical tool was used for modeling and optimization of the empirical data. The RSM model validates the empirical findings. Also, DFT/MD-simulation investigations evidenced that [C4MIM][OMs] forms a barrier film on the mild steel surface. The result shows that the synthesized [C4MIM][OMs] could open up opportunities in corrosion and materials protection for sustainability.
Collapse
Affiliation(s)
- Daniel Iheanacho Udunwa
- Department of Polymer and Textile Engineering, Federal University of Technology, Owerri, Imo State, Nigeria
- Department of Chemical Engineering, Nnamdi Azikiwe University, Awka, Anambra State, Nigeria
| | | | | | - Valentine Chikaodili Anadebe
- Corrosion and Materials Protection Division, CSIR-Central Electrochemical Research Institute, Karaikudi 630003, Tami Nadu, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Department of Chemical Engineering, Alex Ekwueme Federal University, Ndufu Alike, P.M.B. 1010, Abakaliki, Ebonyi State, Nigeria
| | | |
Collapse
|
4
|
Baildya N, Ghosh NN, Chattopadhyay AP. Inhibitory activity of hydroxychloroquine on COVID-19 main protease: An insight from MD-simulation studies. J Mol Struct 2020; 1219:128595. [PMID: 32834108 PMCID: PMC7266611 DOI: 10.1016/j.molstruc.2020.128595] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
The present work is an investigation to test hydroxychloroquine as an inhibitor for the COVID-19 main protease. Molecular docking studies revealed a high docking score and interaction energies and decent level of docking within the cavity in protease moiety. Molecular dynamics simulations also lead to the evaluation of conformational energies, average H-bonding distance, RMSD plots etc. Large RMSD fluctuations for the first 2 ns seem to provide the conformational and rotational changes associated with the drug molecule when it comes into the vicinity on the protease matrix. Snapshots of structural changes with respect to time vividly indicates that drug molecule has a profound impact on the binding sites as well as overall geometry of the protease moiety. On the whole, hydroxyxhloroquine confers good inhibitory response to COVID-19 main protease. We hope the present study should help workers in the field to develop potential vaccines and therapeutics against the novel coronavirus. Molecular Docking studies reveals that hydroxychloroquine (HCQ) possesses a high docking score and interaction energy compared to other small drug molecule with the COVID-19 main protease. Atomistic Molecular Dynamics simulation indicates considerable interaction between HCQ and COVID-19 protease. RMSD plot suggests complex formation between HCQ and COVID-19 protease after 2 ns. Equilibration of binding occurs between HCQ and COVID-19 protease between 7 and 10 ns. Binding with HCQ induced large structural change in COVID-19 protease, hence change in its activity.
Collapse
Affiliation(s)
- Nabajyoti Baildya
- Department of Chemistry, University of Kalyani, Kalyani, 741235, India
| | - Narendra Nath Ghosh
- Department of Chemistry, University of Gour Banga, Mokdumpur, Malda, 732103, India
| | | |
Collapse
|
5
|
Vijayababu P, Samykannu G, Antonyraj CB, Narayanan S, Basheer Ahamed SI, Perumal P, Piramanayagam S. B-cell and T-cell epitope identification with stability analysis of AI-2 import ATP-binding cassette LsrA from S. typhiIn silico approach. Microb Pathog 2018; 123:487-495. [PMID: 30098402 DOI: 10.1016/j.micpath.2018.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/07/2018] [Accepted: 08/07/2018] [Indexed: 12/14/2022]
Abstract
Typhoid fever is a severe illness in humans, caused by Salmonella typhi, a Gram-negative bacterium. Membrane proteins of S. typhi have strong potential for its use in development of subunit vaccine against typhoid. In current study, peptide-based subunit vaccine constructed from AI-2 import ATP-binding cassette transporter protein (LsrA) against S. typhi. B-cell and T-cell epitopes were identified at fold level with validated 3-D theoretical modelled structure. T-cell epitope from LsrA (LELPGSRPQ) has binds to maximum number (82.93%) of MHC class I and class II alleles. LsrA epitope was docked with HLA-DR4 and contact map were constructed to analyze molecular interaction (docking) studies. Simulation search for the binding site for full flexibility of the peptide from CABS-dock shows the stable interactions. MD simulation analysis reveals that LsrA epitope was binding and interacting firmly with the HLA-DR4. Hence, we are proposing that LsrA epitope would be a prominent epitope vaccine for human specific pathogen of S. typhi, which requires further steps to be elevated as a vaccine drug in near future.
Collapse
Affiliation(s)
- Princy Vijayababu
- Structural Biology Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
| | - Gopinath Samykannu
- Structural Biology Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | | | - SundaraBaalaji Narayanan
- Structural Biology Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | | | - Perumal Perumal
- Membrane Protein Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shanmughavel Piramanayagam
- Computational Biology Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| |
Collapse
|