In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain)

Abstract

The N terminal domain (NTD) of Nucleocapsid protein (N protein) of coronavirus (CoV) binds to the viral (+) sense RNA and results in CoV ribonucleoprotien (CoV RNP) complex, essential for the virus replication. In this study, the RNA-binding N terminal domain (NTD) of the N protein was targeted for the identification of possible inhibitors of RNA binding. Two NTD structures of N proteins were selected (2OFZ and 1SSK, 92% homology) for virtual screening of 56,079 compounds from Asinex and Maybridge library to identify top 15 hits for each of the targets based on 'docking score'. These top-hits were further screened for MM-GBSA binding free energy, pharmacokinetic properties (QikProp) and drug-likeness (SwissADME) and subjected to molecular dynamics (MD) studies. Two suitable binders (ZINC00003118440 and ZINC0000146942) against the target 2OFZ were identified. ZINC00003118440 is a theophylline derivative under the drug class 'bronchodilators' and further screening with approved bronchodilators was also studied to identify their ability to bind to the RNA binding region on the N protein. The other identified top hit is ZINC0000146942, which is a 3,4dihydropyrimidone class molecule. Hence this study suggests two important class of compounds, theophylline and pyrimidone derivaties as possible inhibitors of RNA binding to the N terminal domain of N protein of coronavirus, thus opening new avenues for in vitro validations. Communicated by Ramaswamy H. Sarma.

Keywords: 2019 novel corona virus; 2019-nCoV; N terminal domain; Nucleocapsid protein; RNA binding; SARS-CoV-2; drug design.

Figure 1.

Sitemap derived binding pockets of 2OFZ (a) and 1SSK (b) at distinct regions with the hydrophobic region (blue bubbles), electrostatic regions (red bubbles) and lipophilic points (yellow bubble).

Figure 2.

Potential energy surface structure with an elaborate display of binding sites of 1SSK (a) and 2OFZ (b) with in place docked poses of AMP (cyan) and UMP (yellow). The position of the interacting ligands can be noticed with faded regions indicating the non-polar clefts of CoV N protein NTD.

Figure 3.

MD simulation interaction diagrams of 100 ns trajectory showing RMSD; Root mean square fluctuation of essential residue with viable ligand contacts; Residue-ligand interaction profile and interaction strength of the ligand in the binding cavity for SARS-CoV N protein RNA binding domain (2OFZ) with top hits ZINC00003118440 (a, c, e, g) and ZINC0000146942 (b, d, f, h), respectively in order.

Figure 4.

In place docking poses of most potent hits ZINC00003118440 (a) and ZINC0000146942 (b) with SARS-CoV N protein NTD (2OFZ).

Figure 5.

Structure of the two identified hits.