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Ab-initio, Molecular Docking and MD Simulation of an Anti-HIV Drug (Lamivudine): An In-silico Approach

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Abstract

Lamivudine (3TC), a nucleoside analogue reverse transcriptase inhibitor (NARTI) that is being widely used to treat HIV infection, has been chosen in this study to investigate its electronic properties, non-linear optical properties (NLO) and absorption spectra along with its inhibition activity with deoxycytidine kinase receptor (PDB ID: 2NOA). For DFT calculations, B3LYP and ωB97XD functionals with 6–311 + G(d,p) basis set have been employed in gas, water and methanol mediums. In molecular docking, it is observed that the binding energies of the 2NOA receptor with lamivudine allow a variety of binding sites, however, the most preferred binding site, has been taken into account for molecular dynamics (MD) simulation. The molecular docking and molecular dynamics simulation results elucidate that lamivudine exhibits better binding and stability with 2NOA protein receptor.

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Acknowledgements

For his informative remarks and helpful conversation, we are grateful to Prof. S N Tiwari of the Department of Physics, D.D.U. Gorakhpur University, Gorakhpur. D. Sharma is appreciative of the financial assistance provided by UGC, New Delhi, India, in the form of the Start-Up Project [F.30-505/2020(BSR)].

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Authors and Affiliations

  1. Department of Physics, Patna University, Patna, 800005, India

    Gargi Tiwari

  2. Department of Physics, DDU Gorakhpur University, Gorakhpur, 273009, India

    Shiv Kumar, Madan Singh Chauhan & Dipendra Sharma

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  1. Gargi Tiwari
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Correspondence to Dipendra Sharma.

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Tiwari, G., Kumar, S., Chauhan, M.S. et al. Ab-initio, Molecular Docking and MD Simulation of an Anti-HIV Drug (Lamivudine): An In-silico Approach. Biomedical Materials & Devices (2023). https://doi.org/10.1007/s44174-023-00131-7

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