Prediction of potential inhibitors for RNA-dependent RNA polymerase of SARS-CoV-2 using comprehensive drug repurposing and molecular docking approach

Md. Sorwer Alam Parveza, Md. Adnan Karim, Mahmudul Hasan, Jomana Jaman, Ziaul Karim, Tohura Tahsin, Md. Nazmul Hasan, Mohammad Jakir Hosen

10.1016/j.ijbiomac.2020.09.098

Research curated

Abstract

The pandemic prevalence of COVID-19 has become a very serious global health issue. Scientists all over the world have been seriously attempting in the discovery of a drug to combat SARS-CoV-2. It has been found that RNA-dependent RNA polymerase (RdRp) plays a crucial role in SARS-CoV-2 replication, and thus could be a potential drug target. Here, comprehensive computational approaches including drug repurposing and molecular docking were employed to predict an effective drug candidate targeting RdRp of SARS-CoV-2. This study revealed that Rifabutin, Rifapentine, Fidaxomicin, 7-methyl-guanosine-5′-triphosphate-5′-guanosine and Ivermectin have a potential inhibitory interaction with RdRp of SARS-CoV-2 and could be effective drugs for COVID-19. In addition, virtual screening of the compounds from ZINC database also allowed the prediction of two compounds (ZINC09128258 and ZINC09883305) with pharmacophore features that interact effectively with RdRp of SARS-CoV-2, indicating their potentiality as effective inhibitors of the enzyme. Furthermore, ADME analysis along with analysis of toxicity was also undertaken to check the pharmacokinetics and drug-likeness properties of the two compounds. Comparative structural analysis of protein-inhibitor complexes revealed that the amino acids Y32, K47, Y122, Y129, H133, N138, D140, T141, S709 and N781 are crucial for drug surface hotspot in the RdRp of SARS-CoV-2.

Source: PubMed

Related molecules

Name	Synonyms	Genes
Fidaxomicin
7-methyl-guanosine-5′-triphosphate-5′-guanosine
RNA dependent RNA polymerase	RDR, viral RNA polymerase, RdRp, nsp12	rep, ORF1a-1b, RdRp
Ivermectin	IVERMECTIN, Ivermectin B1a, Dihydroavermectin B1a, 70288-86-7, 22-23-Dihydroavermectin B1a
Rifabutin
Rifapentine

Related interactions

Target	Drug	Type	Result
RNA dependent RNA polymerase	Rifabutin	Computational	positive
RNA dependent RNA polymerase	Rifapentine	Computational	positive
RNA dependent RNA polymerase	Fidaxomicin	Computational	positive
RNA dependent RNA polymerase	7-methyl-guanosine-5′-triphosphate-5′-guanosine	Computational	positive
RNA dependent RNA polymerase	Ivermectin	Computational	positive