State-of-the-art tools to identify druggable protein ligand of SARS-CoV-2

Abstract

Introduction: The SARS-CoV-2 (previously 2019-nCoV) outbreak in Wuhan, China and other parts of the world affects people and spreads coronavirus disease 2019 (COVID-19) through human-to-human contact, with a mortality rate of > 2%. There are no approved drugs or vaccines yet available against SARS-CoV-2.

Material and methods: State-of-the-art tools based on in-silico methods are a cost-effective initial approach for identifying appropriate ligands against SARS-CoV-2. The present study developed the 3D structure of the envelope and nucleocapsid phosphoprotein of SARS-CoV-2, and molecular docking analysis was done against various ligands.

Results: The highest log octanol/water partition coefficient, high number of hydrogen bond donors and acceptors, lowest non-bonded interaction energy between the receptor and the ligand, and high binding affinity were considered for the best ligand for the envelope (mycophenolic acid: log P = 3.00; DG = -10.2567 kcal/mol; pKi = 7.713 µM) and nucleocapsid phosphoprotein (1-[(2,4-dichlorophenyl)methyl]pyrazole-3,5-dicarboxylic acid: log P = 2.901; DG = -12.2112 kcal/mol; pKi = 7.885 µM) of SARS-CoV-2.

Conclusions: The study identifies the most potent compounds against the SARS-CoV-2 envelope and nucleocapsid phosphoprotein through state-of-the-art tools based on an in-silico approach. A combination of these two ligands could be the best option to consider for further detailed studies to develop a drug for treating patients infected with SARS-CoV-2, COVID-19.

Keywords: COVID-19; SARS-CoV-2; druggable protein; envelope protein; ligand; molecular docking; nucleocapsid phosphoprotein; phylogenetic tree.

Figure 1

A, B – Ramachandran plot from RAMPAGE of Wuhan coronavirus, SARS-CoV-2 protein. A – Envelope protein. B – Nucleocapsid phosphoprotein. The phi (φ) values of amino acid residues are on the x-axis. The psi (ψ) values are on the y-axis. C, D – 3D structure of envelope protein (C) and nucleocapsid phosphoprotein (D) after homology modelling

Figure 2

Significant druggable protein ligand complex of envelope protein and nucleocapsid phosphoprotein of SARS-CoV-2. E2 ligand has five hydrogen bonds: one with Asn_64, two with lys_63, one with val_49, and one with ILE_46. N2 has two hydrogen bonds: one with Thr 49, and the other with Tyr112, in addition to one arene-arene interaction with Tyr 109

Figure 3

2D and 3D protein-ligand interaction of envelope protein and nucleocapsid phosphoprotein of SARS-CoV-2

Figure 4

Phylogenetic analysis of the nucleocapsid phosphoprotein of SARS-CoV-2 by Maximum Likelihood method. “The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [11]. The bootstrap consensus tree inferred from 500 replicates [10] is taken to represent the evolutionary history of the taxa analysed [10]. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. Initial tree(s) for the heuristic search were obtained automatically by applying neighbour-joining and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The analysis involved 78 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 43 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 [9].” Nucleocapsid phosphoprotein sequence used for constructing the phylogenetic tree: MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETALPQRQKKQQTVTLLPAADLDDFSKQLQQSMSSADSTQA

Figure 5

Representative of the multiple protein sequence alignment of envelope protein (A) and nucleocapsid phosphoprotein (B) of Wuhan novel coronavirus, SARS-CoV-2. Envelope protein and nucleocapsid phosphoprotein sequence used for the sequence alignment are available in Figures 4 and 6, respectively

Figure 6

Phylogenetic analysis of the envelope protein of Wuhan coronavirus, SARS-CoV-2 by Maximum Likelihood method. “The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [11]. The bootstrap consensus tree inferred from 500 replicates [10] is taken to represent the evolutionary history of the taxa analysed [10]. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. Initial tree(s) for the heuristic search were obtained automatically by applying neighbour-joining and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The analysis involved 78 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 43 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 [9].” Envelope protein sequence used for constructing the phylogenetic tree: MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRVPDLLV