The conformation of an inhibitor bound to the gastric proton pump

Abstract Substituted imidazo[1,2- a ]pyridines are pharmaceutically important small molecule inhibitors of the gastric H + /K + -ATPase, the membrane-bound therapeutic target for peptic ulcer disease. A non-perturbing analytical technique, rotational resonance NMR spectroscopy, was used to measure a precise (to ±0.2 A) distance between atomic sites in a substituted imidazo[1,2- a ]pyridine, TMPIP, bound to H + /K + -ATPase at its high-affinity site in the intact, native membrane. The structural analysis of the enzyme–inhibitor complex revealed that the flexible moiety of TMPIP adopts a ` syn -type' conformation at its site of action. Hence, the conformation of an inhibitor has been resolved directly under near-physiological conditions, providing a sound experimental basis for rational design of many active compounds of pharmaceutical interest. Chemically restraining the flexible moiety of compounds like TMPIP in the syn -type binding conformation was found to increase activity by over 2 orders of magnitude. Such information is normally only available after extensive synthesis of related compounds and multiple screening approaches.