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Harini M, Kavitha K, Prabakaran V, Krithika A, Dinesh S, Rajalakshmi A, Suresh G, Puvanakrishnan R, Ramesh B. Identification of apigenin-4'-glucoside as bacterial DNA gyrase inhibitor by QSAR modeling, molecular docking, DFT, molecular dynamics, and in vitro confirmation studies. J Mol Model 2024; 30:22. [PMID: 38170229 DOI: 10.1007/s00894-023-05813-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
CONTEXT It is well known that antibiotic resistance is a major health hazard. To eradicate antibiotic-resistant bacterial infections, it is essential to find a novel antibacterial agent. Hence, in this study, a quantitative structure-activity relationship (QSAR) model was developed using 43 DNA gyrase inhibitors, and 700 natural compounds were screened for their antibacterial properties. Based on molecular docking and absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies, the top three leads viz., apigenin-4'-glucoside, 8-deoxygartanin, and cryptodorine were selected and structurally optimized using density functional theory (DFT) studies. The optimized structures were redocked, and molecular dynamic (MD) simulations were performed. Binding energies were calculated by molecular mechanics/Poisson-Boltzmann surface area solvation (MM-PBSA). Based on the above studies, apigenin-4'-glucoside was identified as a potent antibacterial lead. Further in vitro confirmation studies were performed using the plant Lawsonia inermis containing apigenin-4'-glucoside to confirm the antibacterial activity. METHODS For QSAR modeling, 2D descriptors were calculated by PaDEL-Descriptors v2.21 software, and the model was developed using the DTClab QSAR tool. Docking was performed using PyRx v0.8 software. ORCA v5.0.1 computational package was used to optimize the structures. The job type used in optimization was equilibrium structure search using the DFT hybrid functional ORCA method B3LYP. The basis set was 6-311G (3df, 3pd) plus four polarization functions for all atoms. Accurate docking was performed for optimized leads using the iGEMDOCK v2.1 tool with a genetic algorithm by 10 solutions each of 80 generations. Molecular dynamic simulations were performed using GROMACS 2020.04 software with CHARMM36 all-atom force field.
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Affiliation(s)
- Manoharan Harini
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Kuppuswamy Kavitha
- PG & Research Department of Microbiology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Vadivel Prabakaran
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Anandan Krithika
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Shanmugam Dinesh
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Arumugam Rajalakshmi
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Gopal Suresh
- PG & Research Department of Microbiology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Rengarajulu Puvanakrishnan
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India
| | - Balasubramanian Ramesh
- PG & Research Department of Biotechnology, Sri Sankara Arts and Science College, University of Madras, Enathur, Kanchipuram, Tamil Nadu, -631561, India.
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