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

Publication date: Sep 22, 2025

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) of SARS-CoV-2 demonstrated that the lead drug can be discovered through this strategy. First, the M-peptidyl substrate complex structure was predicted using AF2 based on the amino acid sequences of M 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 exhibited enhanced affinity for the peptidyl substrate, with a ΔG 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 M activity determination. Ultimately, Goserelin was identified as a lead compound against M, demonstrating a 75% inhibition rate. Further IC determination yielded values of 3. 79 μM (pH = 7. 5) and 2. 05 μM (pH = 6. 6), comparable to several reported noncovalent M inhibitors (X77, MCULE-5948770040, and ML188). This work provided a feasible drug discovery strategy in response to the Disease X.

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