Rational design of a beta-lactamase inhibitor achieved via stabilization of the trans-enamine intermediate: 1.28 A crystal structure of wt SHV-1 complex with a penam sulfone

J Am Chem Soc. 2006 Oct 11;128(40):13235-42. doi: 10.1021/ja063715w.

Abstract

beta-Lactamases are one of the major causes of antibiotic resistance in Gram negative bacteria. The continuing evolution of beta-lactamases that are capable of hydrolyzing our most potent beta-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 A 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 beta-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 beta-lactamase inhibitors.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amines / chemistry
  • Binding Sites
  • Crystallography, X-Ray
  • Drug Design
  • Drug Stability
  • Enzyme Inhibitors / chemistry*
  • Enzyme Inhibitors / pharmacology
  • Kinetics
  • Models, Molecular
  • Penicillanic Acid / analogs & derivatives*
  • Penicillanic Acid / chemistry
  • Penicillanic Acid / pharmacology
  • Protein Conformation
  • Sulfones / chemical synthesis
  • Sulfones / chemistry*
  • Sulfones / pharmacology
  • Tazobactam
  • beta-Lactamase Inhibitors*
  • beta-Lactamases / chemistry

Substances

  • Amines
  • Enzyme Inhibitors
  • SA2-13 compound
  • Sulfones
  • beta-Lactamase Inhibitors
  • Penicillanic Acid
  • beta-lactamase PIT-2
  • beta-Lactamases
  • Tazobactam