Accelerating drug discovery for Disease X via AlphaFold2 driven drug repositioning strategy

Abstract

With global concerns about possible outbreaks of Disease X similar to COVID-19 in the future, it is crucial to develop and refine effective drug discovery strategies. Here, we reported a drug discovery strategy for Disease X combined with FDA-approved drug database, AlphaFold (AF) predicted structures, and virtual screening of integrated our developed molecular docking method (MDCC). A case study of revisiting the main protease (Mpro) of SARS-CoV-2 demonstrated that the lead drug can be discovered through this strategy. First, the Mpro-peptidyl substrate complex structure was predicted using AF2 based on the amino acid sequences of Mpro and its peptidyl substrate. Then, the AF2 predicted structure was optimized through molecular dynamics simulations employing a peptidyl substrate-induced binding pocket approach. Binding free energy analysis revealed that the optimized Mpro exhibited enhanced affinity for the peptidyl substrate, with a ΔGbind of -103.8 kcal/mol. Subsequently, this optimized complex structure was used to perform MDCC-based virtual screening of 2005 FDA-approved drugs, from which six drug candidates were selected for Mpro activity determination. Ultimately, Goserelin was identified as a lead compound against Mpro, demonstrating a 75% inhibition rate. Further IC50 determination yielded values of 3.79 μM (pH = 7.5) and 2.05 μM (pH = 6.6), comparable to several reported noncovalent Mpro inhibitors (X77, MCULE-5948770040, and ML188). This work provides a feasible drug discovery strategy in response to the Disease X.