Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR

• Published in: Journal of chemical information and modeling Vol. 63; no. 15; pp. 4839 - 4849
• Main Authors: Cetin, Ebru, Guclu, Tandac F., Kantarcioglu, Isik, Gaszek, Ilona K., Toprak, Erdal, Atilgan, Ali Rana, Dedeoglu, Burcu, Atilgan, Canan
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 14.08.2023
• Subjects: Computational Biochemistry; Dihydrofolate reductase; E coli; Energy costs; Enzymes; Free energy; Hydrogen bonds; Inhibitors; Proteins; Reductases; Trimethoprim
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.3c00818

Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model protein for understanding enzyme dynamics. DHFR’s crucial role in folate synthesis renders it an ideal candidate to understand protein function and protein evolution mechanisms. In this study, to understand how a newly proposed DHFR inhibitor, 4′-deoxy methyl trimethoprim (4′-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior performance over that of trimethoprim (TMP). To elucidate the inhibition mechanism of 4′-DTMP, we first confirmed, both computationally and experimentally, that the relative binding free energy cost for the mutation of TMP and 4′-DTMP is the same, pointing the origin of the characteristic differences to be kinetic rather than thermodynamic. We then employed an interaction-based analysis by focusing first on the active site and then on the whole enzyme. We confirmed that the polar modification in 4′-DTMP induces additional local interactions with the enzyme, particularly, the M20 loop. These changes are propagated to the whole enzyme as shifts in the hydrogen bond networks. To shed light on the allosteric interactions, we support our analysis with network-based community analysis and show that segmentation of the loop domain of inhibitor-bound DHFR must be avoided by a successful inhibitor.