Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19

Abstract

The recent pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) calls the whole world into a medical emergency. For tackling Coronavirus Disease 2019 (COVID-19), researchers from around the world are swiftly working on designing and identifying inhibitors against all possible viral key protein targets. One of the attractive drug targets is guanine-N7 methyltransferase which plays the main role in capping the 5'-ends of viral genomic RNA and sub genomic RNAs, to escape the host's innate immunity. We performed homology modeling and molecular dynamic (MD) simulation, in order to understand the molecular architecture of Guanosine-P3-Adenosine-5',5'-Triphosphate (G3A) binding with C-terminal N7-MTase domain of nsp14 from SARS-CoV-2. The residue Asn388 is highly conserved in present both in N7-MTase from SARS-CoV and SARS-CoV-2 and displays a unique function in G3A binding. For an in-depth understanding of these substrate specificities, we tried to screen and identify inhibitors from the Traditional Chinese Medicine (TCM) database. The combination of several computational approaches, including screening, MM/GBSA, MD simulations, and PCA calculations, provides the screened compounds that readily interact with the G3A binding site of homology modeled N7-MTase domain. Compounds from this screening will have strong potency towards inhibiting the substrate-binding and efficiently hinder the viral 5'-end RNA capping mechanism. We strongly believe the final compounds can become COVID-19 therapeutics, with huge international support.[Formula: see text]The focus of this study is to screen for antiviral inhibitors blocking guanine-N7 methyltransferase (N7-MTase), one of the key drug targets involved in the first methylation step of the SARS-CoV-2 RNA capping mechanism. Compounds binding the substrate-binding site can interfere with enzyme catalysis and impede 5'-end cap formation, which is crucial to mimic host RNA and evade host cellular immune responses. Therefore, our study proposes the top hit compounds from the Traditional Chinese Medicine (TCM) database using a combination of several computational approaches.Communicated by Ramaswamy H. Sarma.

Keywords: COVID-19; Methyltransferase; N7-MTase; RNA capping; SARS-CoV-2; TCM; ensemble sampling; molecular dynamics; natural products; nsp14.

Graphical abstract

Figure 1.

Schematic pathway representation of coronaviral (CoV) RNA capping mechanism of showing the target step for proposed antiviral inhibitors against the SARS-CoV-2 N7-MTase resulting in viral RNA degradation by the host immune response and chemical structure of a viral RNA cap-2 formed at the 5’-end of genomic and sub-genomic RNAs.

Figure 2.

Target-template sequence alignment of bifunctional nsp14 containing N-terminal exoribonuclease (ExoN) and C-terminal guanine-N7 methyltransferase domains (shown side-by-side), and lower panel show the domain organization and boundaries of nsp14 protein.

Figure 3.

Overall structures of nsp14 protein displaying N-terminal exoribonuclease (ExoN) and C-terminal guanine-N7 methyltransferase (N7-MTase) domains: (a) template nsp14 structure of SARS-CoV (PDB ID: 5c8s) used for modeling. (b) modeled target nsp14 structure from SARS-CoV-2. (c) Structural superimposition of nsp14 from SARS-CoV with the homology modeled nsp14 from SARS-CoV-2.

Figure 4.

Substrate-binding site of the N7-MTase domain of nsp14 highlighting the bound Guanosine-P3-Adenosine-5’,5’-Triphosphate (G3A) (a) template (PDB ID: 5c8s) from SARS-CoV and (b) modeled structure from SARS-CoV-2, the interacting amino acid residues are shown as sticks.

Figure 5.

Molecular interaction of the top hits of TCM compounds resulted from virtual screening: TCM ligands interacting with the substrate-binding site (a) TCM 57025, (b) TCM 3495, (c) TCM 20111, (d) TCM 31007, and (e) TCM 5376 showing labelled interacting residues obtained from XP docking.

Figure 6.

The RMSD graph for the entire timescale (50 ns) of MD simulation shown for substrate (G3A) and the best TCM compound complex of nsp14 from SARS-CoV-2 for exploring the conformational landscapes, lower panel display the zoomed view of the highlighted region.

Figure 7.

Overall hydrogen-bonding interaction plot of ligand-bound complexes with SARS-CoV-2 substrate-binding site of N7-MTase and its substrate G3A.