Structural deviation and identification of novel inhibitor of SARS-CoV-2 spike protein through molecular docking; an insilico study

Purpose: Pandemic Novel Coronavirus (SARS-CoV-2) has emerger centered from wuhan, China. Structurally homologous spike protein of SARS-CoV-2 receptor is taxonomically homologous with SARS-Cov and SARS associated bat coronavirus. Still now scientists are trying to find out proper vaccine and treatments for this disease. Methods: Systematically we modeled and compared the structure of SARS-CoV-2 spike protein along with Bat Cov, Bat SARS Cov and SARS Cov Urbani. S1 and S2 unit of the coronavirus (SARS-CoV-2) are attached with ACE2 and furin, here we docked 5 Ca+ chelating drugs with these two proteins. Results: Structural comparison with all these spike proteins revealed that less significant but not negligible difference exists among them. Inserted stable nucleotide sequences and corresponding surface exposed peptidal region may be considered as epitope. Docking result with Toxicokinetics and half life of Penicillamine can effectly inhibit the attachment site of spike protein of coronavirus (SARS-CoV-2). Conclusions: Docking summery and the pharmacokinetics with toxicokinetics index recommend that Penicillamine can able to inhibit the infection of SARS-CoV-2.


Introduction
The recent pandemic novel coronavirus (2019-nCoV), caused by severe acute respiratory syndrome corona virus2 (SARS-CoV-2; first identified on December 12th, 2019) was initially detected in Wuhan, Hubei Province, China [1]. Coronaviruses infect many mammalian and avian species cause severe acute respiratory syndrome coronavirus (SARS-CoV) [2,3]. Coronaviruses having a single-stranded enveloped RNA viruses and the envelope-anchored spike protein with S1 and S2 units [4,5] recognize the host receptor angiotensin-converting enzyme 2 (ACE2) and polybasic cleavage site furin. By regulating furin-mediated substrate cleavage results a crucial role in pathogen infection, neurologic disease and cancer, already several drugs are already explore based on furin cleavage-targeted mechanism [6,7]. The genome of SARS-CoV-2 has been sequenced (Lu R et al., 2020) and it was reported that the structure of spike proteins of SARS-CoV-2 and SARS-CoV have a high degree of homology [8]. In our study, we perform in-silico sequence analyses and model structural homology of corona virus (2019-nCoV) and related four SARS-CoV viruses and calculate RMSD. As furin is calcium-dependent proteases, we have retrieved five selected calcium chelating drug from published literature based upon their therapeutic ability which may control the structural alteration in the spike protein that allows the viral entry process into host cells [9,10,11,12]. The selected drugs have been evaluated against ACE2 and Furin both by molecular docking. Based on our observation, we hypothesize the strategies for pharmacological intervention by targeting ACE2 and furin to combat corona virus (2019-nCoV) infection in human.

Result
Insertion of new RNA sequence was already identified by Andersen KG., et al and he reported that 12 number of newly evolved nucleotides adopted by SARS-CoV-2 [15].

Figure 1. Sequence comparison and structural deviation of the spike glyco-protein of SARS-CoV-2 binds.
Newly inserted Nucleotides highlighted as yellow and green colour, the corresponding amino acids are in Red colour. The structures of spike glyco-proteins are modelled and structural deviation (RMSD) are presented.
This newly inserted nucleotide sequences which is highly GC rich (CTCCTCGGCGGGCA) and the corresponding amino acids (PRRA), expressed on the surface of spike protein of SARS-CoV-2. The exposed peptidal region of the spike protein may help to screen epitope for the development of new vaccine to combat SARS-CoV-2 infection (Fig 1).

Figure 2. Docking analysis of the molecular interactions and the binding mode conformation of the calcium chelating compounds with ACE2 and Furin target proteins.
Molecular docking result showed that Deforexamine and Edetate calcium disodium display highest number of interaction with furin and ACE2 both. All though based on binding energy of Penicillamine and Dimercaprol displayed stable interaction with ACE2 and furin. Out of the five drugs, Penicillamine and Dimercaprol were potential drug candidates represented highest dock scores and strong interactions with catalytic active residues of Furin and ACE2 both (Fig 2). Although the toxicokinetics and half life are very different when compare Penicillamine with Dimercaprol. Penicillamine has less toxicological effect and has a much longer half-life up to 4-6 days, in case of long-term therapy.

Conclusion
The disease severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is spreading rapidly throughout the world. The gene of the SARS-CoV-2 spike protein adopt 12 stable nucleotides and the corresponding peptidal region of S2 region of the spike protein may reveal a screened set of epitopes that can guide to design an experimental effort towards the development of vaccines against SARS-CoV-2. Molecular docking resulted that Penicillamine and Dimercaprol compounds showed good inhibitory activity against Furin and ACE2. We therefore speculate that based on pharmacokinetics and toxicokinetics index, Penicillamine can be more effective to inhibit two receptor proteins of the host where the spike glyco-protein of SARS-CoV-2 binds.