Chemical Space Exploration Around Thieno[3,2- d]pyrimidin-4(3 H)-one Scaffold Led to a Novel Class of Highly Active Clostridium difficile Inhibitors

J Med Chem. 2019 Nov 14;62(21):9772-9791. doi: 10.1021/acs.jmedchem.9b01198. Epub 2019 Oct 21.


Clostridium difficile infection (CDI) is the leading cause of healthcare-associated infection in the United States. Therefore, development of novel treatments for CDI is a high priority. Toward this goal, we began in vitro screening of a structurally diverse in-house library of 67 compounds against two pathogenic C. difficile strains (ATCC BAA 1870 and ATCC 43255), which yielded a hit compound, 2-methyl-8-nitroquinazolin-4(3H)-one (2) with moderate potency (MIC = 312/156 μM). Optimization of 2 gave lead compound 6a (2-methyl-7-nitrothieno[3,2-d]pyrimidin-4(3H)-one) with improved potency (MIC = 19/38 μM), selectivity over normal gut microflora, CC50s > 606 μM against mammalian cell lines, and acceptable stability in simulated gastric and intestinal fluid. Further optimization of 6a at C2-, N3-, C4-, and C7-positions resulted in a library of >50 compounds with MICs ranging from 3 to 800 μM against clinical isolates of C. difficile. Compound 8f (MIC = 3/6 μM) was identified as a promising lead for further optimization.

Publication types

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

MeSH terms

  • Animals
  • Anti-Bacterial Agents / chemistry*
  • Anti-Bacterial Agents / pharmacology*
  • Anti-Bacterial Agents / toxicity
  • Caco-2 Cells
  • Chlorocebus aethiops
  • Clostridium difficile / drug effects*
  • Drug Design
  • Humans
  • Microbial Sensitivity Tests
  • Models, Molecular
  • Molecular Conformation
  • Pyrimidines / chemistry*
  • Pyrimidines / pharmacology*
  • Pyrimidines / toxicity
  • Stereoisomerism
  • Structure-Activity Relationship
  • Vero Cells


  • Anti-Bacterial Agents
  • Pyrimidines