Invited
Efficient discovery of potent enzyme inhibitors

Drug discovery is being pursued through computer-aided design, synthesis, biological assaying, and crystallography.^1-4 Lead identification features de novo design with the ligand growing program BOMB or virtual screening. Emphasis is placed on optimization of the resultant hits to yield potent, drug-like inhibitors. Monte Carlo/free-energy perturbation (FEP) simulations are executed to identify the most promising choices for heterocycles, substituents on rings, and linking groups. The illustrated applications center on the design of inhibitors targeting HIV-1 reverse transcriptase, macrophage migration inhibitory factor (MIF), and JAK2 kinase. Micromolar leads have been rapidly advanced to low nanomolar inhibitors, and numerous crystal structures for protein-inhibitor complexes have been obtained. Development and use of fluorescence polarization (FP) assays provide direct binding data. Key computational issues are considered including force fields, computation of absolute free energies of binding, and unbinding pathways from metadynamics.

Figure 1. Rendering from an X-ray crystal structure (6B1C) of a designed inhibitor bound to human MIF. The compound yields a K_i of 75 nM in an enzyme inhibition assay and a K_d of 111 nM in an FP assay.

References

(1) Computer-Aided Discovery of Anti-HIV Agents. Jorgensen, W. L. Bioorg. Med. Chem. 2016, 24, 4768-4788.

(2) Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: from design to protein crystallography. Chan, A. H.; Lee, W.-G.; Spasov, K. A.; Cisneros, J. A.; Kudalkar, S. N.; Petrova, Z. O.; Buckingham, A. B.; Anderson, K. S.; Jorgensen, W. L. Proc. Nat. Acad. Sci. USA. 2017, 114, 9725-9730.

(3) JAK2-JH2 Fluorescence Polarization Assay and Crystal Structures for Complexes with Three Small Molecules. Newton, A. S.; Deiana, L.; Puleo, D.; Cisneros, J. A; Cutrona, K. J.; Schlessinger, J.; Jorgensen, W. L. ACS Med. Chem. Lett. 2017, 8, 614-617.

(4) Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding. Cabeza de Vaca, I.; Qian, Y.; Vilseck, J. Z.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Theory Comput. 2018, 14, 3279-3288.