3DGA

Wild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with RJF01302, NADPH, and dUMP

Summary for 3DGA

• Entry DOI: 10.2210/pdb3dga/pdb
• Related: 1J3I 1J3J 1J3K 3DG8
• Descriptor: Bifunctional dihydrofolate reductase-thymidylate synthase, N-[2-chloro-5-(trifluoromethyl)phenyl]imidodicarbonimidic diamide, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... (6 entities in total)
• Functional Keywords: alpha-beta, methyltransferase, oxidoreductase, transferase
• Biological source: Plasmodium falciparum; More
• Total number of polymer chains: 4
• Total formula weight: 146358.76

Authors

Dasgupta, T.,Chitnumsub, P.,Maneeruttanarungroj, C.,Kamchonwongpaisan, S.,Nichols, S.,Lyons, T.M.,Tirado-Rives, J.,Jorgensen, W.L.,Yuthavong, Y.,Anderson, K.S. (deposition date: 2008-06-13, release date: 2009-01-27, Last modification date: 2023-08-30)

Primary citation

Dasgupta, T.,Chitnumsub, P.,Kamchonwongpaisan, S.,Maneeruttanarungroj, C.,Nichols, S.E.,Lyons, T.M.,Tirado-Rives, J.,Jorgensen, W.L.,Yuthavong, Y.,Anderson, K.S.
Exploiting structural analysis, in silico screening, and serendipity to identify novel inhibitors of drug-resistant falciparum malaria.
Acs Chem.Biol., 4:29-40, 2009

PubMed Abstract: Plasmodium falciparum thymidylate synthase-dihydrofolate reductase (TS-DHFR) is an essential enzyme in folate biosynthesis and a major malarial drug target. This bifunctional enzyme thus presents different design approaches for developing novel inhibitors against drug-resistant mutants. We performed a high-throughput in silico screen of a database of diverse, drug-like molecules against a non-active-site pocket of TS-DHFR. The top compounds from this virtual screen were evaluated by in vitro enzymatic and cellular culture studies. Three compounds active to 20 microM IC(50)'s in both wildtype and antifolate-resistant P. falciparum parasites were identified; moreover, no inhibition of human DHFR enzyme was observed, indicating that the inhibitory effects appeared to be parasite-specific. Notably, all three compounds had a biguanide scaffold. However, relative free energy of binding calculations suggested that the compounds might preferentially interact with the active site over the screened non-active-site region. To resolve the two possible modes of binding, co-crystallization studies of the compounds complexed with TS-DHFR enzyme were performed. Surprisingly, the structural analysis revealed that these novel, biguanide compounds do indeed bind at the active site of DHFR and additionally revealed the molecular basis by which they overcome drug resistance. To our knowledge, these are the first co-crystal structures of novel, biguanide, non-WR99210 compounds that are active against folate-resistant malaria parasites in cell culture.

PubMed: 19146480
DOI: 10.1021/cb8002804

Experimental method

X-RAY DIFFRACTION (2.7 Å)