PDBsum entry 4dp3

Oxidoreductase, transferase/inhibitor

PDB id: 4dp3

Contents

Protein chains

545 a.a.

Ligands

MMV ×2

NDP ×2

PO4 ×2

Waters ×441

PDB id:

4dp3

Name:

Oxidoreductase, transferase/inhibitor

Title:

Quadruple mutant (n51i+c59r+s108n+i164l) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (pfdhfr-ts) complexed with p218 and NADPH

Structure:

Bifunctional dihydrofolate reductase-thymidylate synthase. Chain: a, b. Engineered: yes

Source:

Plasmodium falciparum. Organism_taxid: 478864. Strain: v1/s. Gene: dhfr-ts, v1/s. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.205 R-free: 0.239

Authors:

Y.Yuthavong,T.Vilaivan,S.Kamchonwongpaisan,S.A.Charman,D.N.Mclennan, K.L.White,L.Vivas,E.Bongard,P.Chitnumsub,B.Tarnchompoo, C.Thongphanchang,S.Taweechai,J.Vanichtanakul,U.Arwon,P.Fantauzzi, J.Yuvaniyama,W.N.Charman,D.Matthews

Key ref:

Y.Yuthavong et al. (2012). Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target. Proc Natl Acad Sci U S A, 109, 16823-16828. PubMed id: 23035243

Date:

13-Feb-12 Release date: 14-Nov-12

Protein chains

D9N170  (D9N170_PLAFA) -  Bifunctional dihydrofolate reductase-thymidylate synthase from Plasmodium falciparum

Seq: 608 a.a.

Struc: 545 a.a.

Enzyme reactions

• Enzyme class 2: E.C.1.5.1.3 - dihydrofolate reductase.
• Pathway: Folate Coenzymes
• Reaction: (6S)-5,6,7,8-tetrahydrofolate + NADP⁺ = 7,8-dihydrofolate + NADPH + H⁺

(6S)-5,6,7,8-tetrahydrofolate + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = 7,8-dihydrofolate + NADPH + H(+)

• Enzyme class 3: E.C.2.1.1.45 - thymidylate synthase.

Pathway:

• Reaction: dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate = 7,8-dihydrofolate + dTMP

dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate = 7,8-dihydrofolate + dTMP (Bound ligand (Het Group name = NDP) matches with 40.82% similarity)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Proc Natl Acad Sci U S A 109:16823-16828 (2012)

PubMed id: 23035243

Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target.

Y.Yuthavong, B.Tarnchompoo, T.Vilaivan, P.Chitnumsub, S.Kamchonwongpaisan, S.A.Charman, D.N.McLennan, K.L.White, L.Vivas, E.Bongard, C.Thongphanchang, S.Taweechai, J.Vanichtanankul, R.Rattanajak, U.Arwon, P.Fantauzzi, J.Yuvaniyama, W.N.Charman, D.Matthews.

ABSTRACT

Malarial dihydrofolate reductase (DHFR) is the target of antifolate antimalarial drugs such as pyrimethamine and cycloguanil, the clinical efficacy of which have been compromised by resistance arising through mutations at various sites on the enzyme. Here, we describe the use of cocrystal structures with inhibitors and substrates, along with efficacy and pharmacokinetic profiling for the design, characterization, and preclinical development of a selective, highly efficacious, and orally available antimalarial drug candidate that potently inhibits both wild-type and clinically relevant mutated forms of Plasmodium falciparum (Pf) DHFR. Important structural characteristics of P218 include pyrimidine side-chain flexibility and a carboxylate group that makes charge-mediated hydrogen bonds with conserved Arg122 (PfDHFR-TS amino acid numbering). An analogous interaction of P218 with human DHFR is disfavored because of three species-dependent amino acid substitutions in the vicinity of the conserved Arg. Thus, P218 binds to the active site of PfDHFR in a substantially different fashion from the human enzyme, which is the basis for its high selectivity. Unlike pyrimethamine, P218 binds both wild-type and mutant PfDHFR in a slow-on/slow-off tight-binding mode, which prolongs the target residence time. P218, when bound to PfDHFR-TS, resides almost entirely within the envelope mapped out by the dihydrofolate substrate, which may make it less susceptible to resistance mutations. The high in vivo efficacy in a SCID mouse model of P. falciparum malaria, good oral bioavailability, favorable enzyme selectivity, and good safety characteristics of P218 make it a potential candidate for further development.