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BioTechnologia
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1/2022
vol. 103
 
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abstract:
RESEARCH PAPERS

Drummondin E and Flinderole B are potential inhibitors of RNA-dependent RNA polymerase of SARS-CoV-2: an in silico study

Nahid Akhtar
1
,
Himanshu Verma
2
,
O.M. Silkari
2
,
Atul K. Upadhyay
3
,
Vikas Kaushik
1
,
M. Amin-ul Mannan
1

  1. Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi, Punjab, India
  2. Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
  3. Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
BioTechnologia vol. 103(1) ∙ pp. 53–70 ∙ 2022
DOI: https://doi.org/10.5114/bta.2022.113915
Online publish date: 2022/03/24
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Coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected 235.6 million people worldwide. In the present study, RNA-dependent RNA polymerase (RdRp) (PDB Id: 6M71) of SARS-CoV-2, an essential enzyme needed for subgenomic replication and amplification of RNA, was selected. Similar to other RdRps, it is a conserved protein and a popular target for antiviral drug therapy. Based on a computational approach, potential RdRp inhibitors were identified. The absorption, distribution, metabolism, excretion, and toxicity (ADMET) of selected molecules were determined using computation tools. The potential inhibitors were docked to the RdRp and later confirmed by Molecular Dynamics (MD) using the “Flare” module of Cresset software. Drummondin E and Flinderole B had higher drug similarity scores among the compounds selected in this study. Both these compounds are noncarcinogenic, nonirritant, nontumorigenic, and nonmutagenic. Molecular docking studies showed that both compounds can bind to RdRp. The best ligand interaction patterns were validated by MD using the “Flare” module. MD was performed for the period of 100 ns with the time step of 1 fs. The simulation results suggest that Thr-680, Arg-624, Lys-676, and Val-557 are key interacting partners in the Drummondin E-RdRp complex, while Asp-618, Asp-760, Asp-623, Arg-624, and Asp-761 are the interacting partners in the Flinderole B-RdRp complex. Based on the in silico drug-likeness score; ADMET properties; and molecular simulation result, we surmise that Flinderole B and Drummondin E could impede SARS-CoV-2 genome replication and transcription by targeting the RdRp protein.
keywords:

RNA polymerase, SARS-CoV-2, RNA-dependent, Drummondin E, Flinderole B


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