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Molecular docking and dynamic simulation of approved drugs targeting against spike protein (6VXX) of 2019-nCoV (novel coronavirus)

ABSTRACT: The 2019-nCoV has triggered a global public health emergency due to its rapid spread, resulting in a pandemic situation. Because of its ability to bind with the host cell receptor ACE-2, the spike protein of the 2019-nCoV is a critical factor in viral infection. The current study aims to investigate the molecular-docking of the spike protein (6VXX) using PyRx for FDA-approved drugs available for the treatment of SARS-1 and MERS, with the hypothesis that these drugs could be suggested for the treatment of 2019-nCoV or not. A phylogenetic analysis of 2019-nCoV in relation to SARS-1 and MERS confirmed the validation. The positive result urged the Multiple Sequence Alignment analysis of the top five affected countries, with China serving as a control, using WHO available reference data to determine the rate of mutant variation. The docking results revealed that the top ten drugs with the highest binding affinity rate are also used for Hepatitis-C virus treatment, and the Molecular Dynamic Simulation was carried out for the drug Paritaprevir, which had the highest binding affinity rate, using Gromacs. The results indicated that the drug Paritaprevir could be used as a potential target against the 2019-nCoV Spike protein. Graphical abstract Image 1

SUBMITTER: Thakur A

PROVIDER: S-EPMC9197568 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:Medicines for the treatment of 2019-novel coronavirus (2019-nCoV) infections are urgently needed. However, drug screening using live 2019-nCoV requires high-level biosafety facilities, which imposes an obstacle for those institutions without such facilities or 2019-nCoV. This study aims to repurpose the clinically approved drugs for the treatment of coronavirus disease 2019 (COVID-19) in a 2019-nCoV-related coronavirus model. METHODS:A 2019-nCoV-related pangolin coronavirus GX_P2V/pangolin/2017/Guangxi was described. Whether GX_P2V uses angiotensin-converting enzyme 2 (ACE2) as the cell receptor was investigated by using small interfering RNA (siRNA)-mediated silencing of ACE2. The pangolin coronavirus model was used to identify drug candidates for treating 2019-nCoV infection. Two libraries of 2406 clinically approved drugs were screened for their ability to inhibit cytopathic effects on Vero E6 cells by GX_P2V infection. The anti-viral activities and anti-viral mechanisms of potential drugs were further investigated. Viral yields of RNAs and infectious particles were quantified by quantitative real-time polymerase chain reaction (qRT-PCR) and plaque assay, respectively. RESULTS:The spike protein of coronavirus GX_P2V shares 92.2% amino acid identity with that of 2019-nCoV isolate Wuhan-hu-1, and uses ACE2 as the receptor for infection just like 2019-nCoV. Three drugs, including cepharanthine (CEP), selamectin, and mefloquine hydrochloride, exhibited complete inhibition of cytopathic effects in cell culture at 10 ?mol/L. CEP demonstrated the most potent inhibition of GX_P2V infection, with a concentration for 50% of maximal effect [EC50] of 0.98 ?mol/L. The viral RNA yield in cells treated with 10 ?mol/L CEP was 15,393-fold lower than in cells without CEP treatment ([6.48?±?0.02]?×?10vs. 1.00?±?0.12, t?=?150.38, P?<?0.001) at 72 h post-infection (p.i.). Plaque assays found no production of live viruses in media containing 10 ?mol/L CEP at 48 h p.i. Furthermore, we found CEP had potent anti-viral activities against both viral entry (0.46?±?0.12, vs.1.00?±?0.37, t?=?2.42, P?<?0.05) and viral replication ([6.18?±?0.95]?×?10vs. 1.00?±?0.43, t?=?3.98, P?<?0.05). CONCLUSIONS:Our pangolin coronavirus GX_P2V is a workable model for 2019-nCoV research. CEP, selamectin, and mefloquine hydrochloride are potential drugs for treating 2019-nCoV infection. Our results strongly suggest that CEP is a wide-spectrum inhibitor of pan-betacoronavirus, and further study of CEP for treatment of 2019-nCoV infection is warranted.

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Molecular docking and dynamic simulation of approved drugs targeting against spike protein (6VXX) of 2019-nCoV (novel coronavirus)

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