5CPF

Compensation of the effect of isoleucine to alanine mutation by designed inhibition in the InhA enzyme

5CPF の概要

• エントリーDOI: 10.2210/pdb5cpf/pdb
• 関連するPDBエントリー: 5COQ 5CP8
• 分子名称: Enoyl-[acyl-carrier-protein] reductase [NADH], NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 2-(2-methylphenoxy)-5-[(4-phenyl-1H-1,2,3-triazol-1-yl)methyl]phenol (3 entities in total)
• 機能のキーワード: fatty acid biosynthesis inhibition substrate binding loop conformation free energy calculation, oxidoreductase
• 由来する生物種: Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 126819.53

構造登録者

Li, H.-J.,Lai, C.-T.,Pan, P.,Yu, W.,Shah, S.,Bommineni, G.R.,Perrone, V.,Garcia-Diaz, M.,Tonge, P.J.,Simmerling, C. (登録日: 2015-07-21, 公開日: 2015-08-12, 最終更新日: 2023-09-27)

主引用文献

Lai, C.T.,Li, H.J.,Yu, W.,Shah, S.,Bommineni, G.R.,Perrone, V.,Garcia-Diaz, M.,Tonge, P.J.,Simmerling, C.
Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA.
Biochemistry, 54:4683-4691, 2015

PubMed Abstract: Slow-onset enzyme inhibitors are the subject of considerable interest as an approach to increasing the potency of pharmaceutical compounds by extending the residence time of the inhibitor on the target (the lifetime of the drug-receptor complex). However, rational modulation of residence time presents significant challenges because it requires additional mechanistic insight, such as the nature of the transition state for postbinding isomerization. Our previous work, based on X-ray crystallography, enzyme kinetics, and molecular dynamics simulation, suggested that the slow step in inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA involves a change in the conformation of the substrate binding loop from an open state in the initial enzyme-inhibitor complex to a closed state in the final enzyme-inhibitor complex. Here, we use multidimensional free energy landscapes for loop isomerization to obtain a computational model for the transition state. The results suggest that slow-onset inhibitors crowd key side chains on helices that slide past each other during isomerization, resulting in a steric clash. The landscapes become significantly flatter when residues involved in the steric clash are replaced with alanine. Importantly, this lower barrier can be increased by rational inhibitor redesign to restore the steric clash. Crystallographic studies and enzyme kinetics confirm the predicted effects on loop structure and flexibility, as well as inhibitor residence time. These loss and regain of function studies validate our mechanistic hypothesis for interactions controlling substrate binding loop isomerization, providing a platform for the future design of inhibitors with longer residence times and better in vivo potency. Similar opportunities for slow-onset inhibition via the same mechanism are identified in other pathogens.

PubMed: 26147157
DOI: 10.1021/acs.biochem.5b00284

実験手法

X-RAY DIFFRACTION (3.409 Å)