Rational Design of a β-Lactamase Inhibitor Achieved via Stabilization of the trans-Enamine Intermediate:  1.28 Å Crystal Structure of wt SHV-1 Complex with a Penam Sulfone

• Published in: Journal of the American Chemical Society 2006-10, Vol.128 (40), p.13235-13242
• Main Authors: Padayatti, Pius S, Sheri, Anjaneyulu, Totir, Monica A, Helfand, Marion S, Carey, Marianne P, Anderson, Vernon E, Carey, Paul R, Bethel, Christopher R, Bonomo, Robert A, Buynak, John D, van den Akker, Focco
• Format: Article
• Language: English
• Subjects: Amines - chemistry; beta-Lactamase Inhibitors; beta-Lactamases - chemistry; Binding Sites; Chemistry; Crystallography, X-Ray; Drug Design; Drug Stability; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; Exact sciences and technology; General and physical chemistry; Heterocyclic compounds; Heterocyclic compounds with n hetero atom and also o and/or s, se, te hetero atoms; Heterocyclic compounds with only one n hetero atom and condensed derivatives; Kinetics; Kinetics and mechanisms; Models, Molecular; Organic chemistry; Penicillanic Acid - analogs & derivatives; Penicillanic Acid - chemistry; Penicillanic Acid - pharmacology; Preparations and properties; Protein Conformation; Reactivity and mechanisms; Sulfones - chemical synthesis; Sulfones - chemistry; Sulfones - pharmacology; Tazobactam
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja063715w

β-Lactamases are one of the major causes of antibiotic resistance in Gram negative bacteria. The continuing evolution of β-lactamases that are capable of hydrolyzing our most potent β-lactams presents a vexing clinical problem, in particular since a number of them are resistant to inhibitors. The efficient inhibition of these enzymes is therefore of great clinical importance. Building upon our previous structural studies that examined tazobactam trapped as a trans-enamine intermediate in a deacylation deficient SHV variant, we designed a novel penam sulfone derivative that forms a more stable trans-enamine intermediate. We report here the 1.28 Å resolution crystal structure of wt SHV-1 in complex with a rationally designed penam sulfone, SA2-13. The compound is covalently bound to the active site of wt SHV-1 similar to tazobactam yet forms an additional salt-bridge with K234 and hydrogen bonds with S130 and T235 to stabilize the trans-enamine intermediate. Kinetic measurements show that SA2-13, once reacted with SHV-1 β-lactamase, is about 10-fold slower at being released from the enzyme compared to tazobactam. Stabilizing the trans-enamine intermediate represents a novel strategy for the rational design of mechanism-based class A β-lactamase inhibitors.