Sequence and Structure at Play in Designing Allosteric Drugs and Alleviating the Drug Resistance
Wei-Ven Tee, Raechell Raechell, Enrico Guarnera, Igor N. Berezovsky · Journal of Molecular Biology · 2025
The advantages of allosteric drugs in targeting selected members of highly conserved protein families are well established. However, the discovery of allosteric effectors remains largely serendipitous, calling for a rational approach to account for their unique mechanisms and specificity towards protein targets. We show that the high-throughput quantification of allosteric signalling on a single-residue resolution allows one to delineate structural and sequence determinants of allosteric communication that are specific to individual members of a structurally conserved protein family. We demonstrate work of the approach using the matrix metalloproteinases (MMPs), a family of proteases also known to be "undruggable" because of their sequence/structural traits. Specifically, latent allosteric sites and effectors were identified and fine-tuned for precise functional modulation of MMP-7, MMP-12 and MMP-13. We also explored the allosteric effects of mutations in driving pathogenesis and emergence of the drug resistance, arguing that they should be considered in diagnostics and drug design frameworks. The multiplicity of allosteric sites and alternative effectors allow, for example, to rescue the therapeutic actions of orthosteric or allosteric drugs in cases of emerged resistance, because of mutations at the drug binding sites or other distal locations. To conclude, using the matrix metalloproteinases as an example of undruggable targets, we highlighted here advantages of the allosteric paradigm in drug design and illuminated a utility of our directed design protocol for the rational design of allosteric drugs.