Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase Inhibitors

Abstract

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has led to significant global morbidity and mortality. A crucial viral protein, the non-structural protein 14 (nsp14), catalyzes the methylation of viral RNA and plays a critical role in viral genome replication and transcription. Due to the low mutation rate in the nsp region among various SARS-CoV-2 variants, nsp14 has emerged as a promising therapeutic target. However, discovering potential inhibitors remains a challenge. In this work, we introduce a computational pipeline for the rapid and efficient identification of potential nsp14 inhibitors by leveraging virtual screening and the NCI open compound collection, which contains 250,000 freely available molecules for researchers worldwide. The introduced pipeline provides a cost-effective and efficient approach for early-stage drug discovery by allowing researchers to evaluate promising molecules without incurring synthesis expenses. Our pipeline successfully identified seven promising candidates after experimentally validating only 40 compounds. Notably, we discovered NSC620333, a compound that exhibits a strong binding affinity to nsp14 with a dissociation constant of 427 ± 84 nM. In addition, we gained new insights into the structure and function of this protein through molecular dynamics simulations. We identified new conformational states of the protein and determined that residues Phe367, Tyr368, and Gln354 within the binding pocket serve as stabilizing residues for novel ligand interactions. We also found that metal coordination complexes are crucial for the overall function of the binding pocket. Lastly, we present the solved crystal structure of the nsp14-MTase complexed with SS148 (PDB:8BWU), a potent inhibitor of methyltransferase activity at the nanomolar level (IC50value of 70 ± 6 nM). Our computational pipeline accurately predicted the binding pose of SS148, demonstrating its effectiveness and potential in accelerating drug discovery efforts against SARS-CoV-2 and other emerging viruses.

New Strategies for Responding to SARS-CoV-2: The Present and Future of Dual-Target Drugs

“…It is speculated that introducing a physically larger substituent at the C7 position may enhance efficacy and selectivity for Nsp14 compared to the nitrile group. 136 The binding mode of SS148 with Nsp16 is similar to SAH (Figure 4C,D). WZ16's additional aminomethyl forming a hydrogen bond with N43 contributes to stabilizing the Nsp16-RNA-WZ16 ternary complex (Figure 4E,F).…”

“…The crystal structure of SS148 and Nsp14 (Figure A,B) reveals a significant space at the C7 position of Nsp14. It is speculated that introducing a physically larger substituent at the C7 position may enhance efficacy and selectivity for Nsp14 compared to the nitrile group . The binding mode of SS148 with Nsp16 is similar to SAH (Figure C,D).…”