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

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 the 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 (M^pro) of SARS-CoV-2 demonstrated that the lead drug can be discovered through this strategy. First, the M^pro-peptidyl substrate complex structure was predicted using AF2 based on the amino acid sequences of M^pro 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 M^pro exhibited enhanced affinity for the peptidyl substrate, with a ΔG_bind of -103.8 kcal mol^-1. 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 M^pro activity determination. Ultimately, Goserelin was identified as a lead compound against M^pro, 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 M^pro inhibitors (X77, MCULE-5948770040, and ML188). This work provided a feasible drug discovery strategy in response to the Disease X.