Repurposing potential of posaconazole and grazoprevir as inhibitors of SARS-CoV-2 helicase

Abstract

As the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic engulfs millions worldwide, the quest for vaccines or drugs against the virus continues. The helicase protein of SARS-CoV-2 represents an attractive target for drug discovery since inhibition of helicase activity can suppress viral replication. Using in silico approaches, we have identified drugs that interact with SARS-CoV-2 helicase based on the presence of amino acid arrangements matching binding sites of drugs in previously annotated protein structures. The drugs exhibiting an RMSD of ≤ 3.0 Å were further analyzed using molecular docking, molecular dynamics (MD) simulation, and post-MD analyses. Using these approaches, we found 12 drugs that showed strong interactions with SARS-CoV-2 helicase amino acids. The analyses were performed using the recently available SARS-CoV-2 helicase structure (PDB ID: 5RL6). Based on the MM-GBSA approach, out of the 12 drugs, two drugs, namely posaconazole and grazoprevir, showed the most favorable binding energy, - 54.8 and - 49.1 kcal/mol, respectively. Furthermore, of the amino acids found conserved among all human coronaviruses, 10/11 and 10/12 were targeted by, respectively, grazoprevir and posaconazole. These residues are part of the crucial DEAD-like helicase C and DEXXQc_Upf1-like/ DEAD-like helicase domains. Strong interactions of posaconazole and grazoprevir with conserved amino acids indicate that the drugs can be potent against SARS-CoV-2. Since the amino acids are conserved among the human coronaviruses, the virus is unlikely to develop resistance mutations against these drugs. Since these drugs are already in use, they may be immediately repurposed for SARS-CoV-2 therapy.

Figure 1

Protein and domain classification. Conserved domains in the SARS-CoV-2 structure were mapped using the NCBI Conserved Domain Search (CDD) tool v3.19. The SARS-CoV-2 helicase was found to be a DNA2 superfamily helicase with two significant domains: DEAD-like helicase C (spanning amino acids 323–592) and DEXXQc_Upf1-like (spanning amino acids 272–443), containing Walker A motif (GTGKSH) at N-terminus that is involved in ATP binding. Two additional functional domains ZBD_cv_Nsp13-like (spanning amino acids 1–95) and 1B_cv_Nsp13-like (spanning amino acids 150–228) were also found in the sequence. (note: the figure is an original image generated by CDD v3.19 tool).

Figure 2

Validation of structure and docking strategy: (A) Structure of SARS-CoV-2 helicase used in the study, (B) Ramachandran plots for SARS-CoV-2 helicase structure (PDB ID: 5RL6) used in the study, and (C) Docking strategy was validated by re-docking a previously published inhibitor ITMN-3479 on its receptor. Poses of ligand bound to the receptor generated after docking in our study (left, ligand, and protein are shown in red and dark grey, respectively) and retrieved from PDB (right; ligand and protein are shown in pink and green, respectively) are shown, while the bottom panel shows amino acid interactions reported for each ligand and observed in our study.

Figure 3

2D representations of the predicted binding modes and scores of the investigated twelve drugs inside the active site of the SARS-CoV-2 helicase.

Figure 4

Calculated MM-GBSA binding energies for the investigated drugs as SARS-CoV-2 helicase inhibitors.

Figure 5

Evaluated MM-GBSA binding energy per frame for posaconazole (in black) and grazoprevir (in red) towards SARS-CoV-2 helicase throughout 100 ns MD simulation.

Figure 6

Root mean square deviation (RMSD) of the backbone atoms from the initial structure for posaconazole (in black) and grazoprevir (in red) with the SARS-CoV-2 helicase over 100 ns MD simulations.

Figure 7

Sequence alignment of known human coronaviruses sharing helicase domain architecture: Multiple sequence alignment (ranging from amino acid 3–596, numbered according to their position in the helicase protein) was performed employing ‘Clustal W’. Conserved residues/sites are highlighted in black color, residues conserved in two or more sequences are shown in black font, while differences are shown in grey font. Publication quality alignment was prepared using the ENDscript server.