Structure-based design of parasitic protease inhibitors

Rongshi Li, Xiaowu Chen, Baoqing Gong, Paul M. Selzer, Zhe Li, Eugene Davidson, Gary Kurzban, Robert E. Miller, Edwin O. Nuzum, James H. McKerrow, Robert J. Fletterick, Sarah A. Gillmor, Charles S. Craik, Irwin D. Kuntz, Fred E. Cohen, George L. Kenyon

Research output: Contribution to journalArticle

113 Scopus citations


To streamline the preclinical phase of pharmaceutical development, we have explored the utility of structural data on the molecular target and synergy between computational and medicinal chemistry. We have concentrated on parasitic infectious diseases with a particular emphasis on the development of specific noncovalent inhibitors of proteases that play a key role in the parasites' life cycles. Frequently, the structure of the enzyme target of pharmaceutical interest is not available. In this setting we have modeled the structure of the relevant enzyme by virtue of its sequence similarity with proteins of known structure. For example, we have constructed a homology-based model of falcipain, the trophozoite cysteine protease, and used the computational ligand identification algorithm DOCK to identify in compound enzyme inhibitors including oxalic bis(2-hydroxy-1-naphthylmethylene)hydrazide (1) [Ring, C.S.; Sun, E.; McKerow, J.K.; Lee, G.; Rosenthal, P.J., Kuntz, I.D.; Cohen, F.E., Proc. Natl Acad. Sci. U.S.A. 1993, 90, 3583]. Compound 1 inhibits falcipain (IC50 6 μM) and the organism in vitro as judged by hypoxanthine. uptake (IC50 7 μM). Following this lead, to date, we have identified potent bis arylacylhydrazides (IC50 150 nM) and chalcones (IC50 200 nM) that are active against both chloroquine-sensitive and chloroquine-resistant strains of malaria. In a second example, cruzain, the crystallographically determined structure of a papain-like cysteine protease, resolved to 2.35 Å, was available. Aided by DOCK, we have identified a family of bis-arylacylhydrazides that are potent inhibitors of cruzain (IC50 600 μM). These compounds represent useful leads for pharmaceutical development over strict enzyme inhibition criteria in a structure-based design program.

Original languageEnglish (US)
Pages (from-to)1421-1427
Number of pages7
JournalBioorganic and Medicinal Chemistry
Issue number9
Publication statusPublished - Jan 1 1996


ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Pharmaceutical Science
  • Drug Discovery
  • Clinical Biochemistry
  • Organic Chemistry

Cite this

Li, R., Chen, X., Gong, B., Selzer, P. M., Li, Z., Davidson, E., ... Kenyon, G. L. (1996). Structure-based design of parasitic protease inhibitors. Bioorganic and Medicinal Chemistry, 4(9), 1421-1427.