ISDA

Deposition Date 2024-09-05

Release Date 2025-01-01

Last Version Date 2025-01-29

Entry Detail

PDB ID:

9DIK

Keywords:

OXIDOREDUCTASE/INHIBITOR

Title:

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM681 (N-cyclopropyl-1,4-dimethyl-5-((6-(trifluoromethyl)pyridin-3-yl)methyl)-1H-pyrazole-3-carboxamide)

Biological Source:

Source Organism:

Plasmodium falciparum 3D7 (Taxon ID: 36329)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.10 Å

R-Value Free:

0.20

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Dihydroorotate dehydrogenase (quinone), mitochondrial
Gene (Uniprot):PFF0160c
Chain IDs:A, B
Chain Length:401
Number of Molecules:2
Biological Source:Plasmodium falciparum 3D7

UniProt ID:Q08210 Pfam ID:PF01180

Ligand Molecules

A1A52

FMN

OG6

Primary Citation

Structure-Based Discovery and Development of Highly Potent Dihydroorotate Dehydrogenase Inhibitors for Malaria Chemoprevention.

Nie, Z, Bonnert, R, Tsien, J, Deng, X, Higgs, C, El Mazouni, F, Zhang, X, Li, R, Ho, N, Feher, V, Paulsen, J, Shackleford, D.M, Katneni, K, Chen, G, Ng, A.C.F, McInerney, M, Wang, W, Saunders, J, Collins, D, Yan, D, Li, P, Campbell, M, Patil, R, Ghoshal, A, Mondal, P, Kundu, A, Chittimalla, R, Mahadeva, M, Kokkonda, S, White, J, Das, R, Mukherjee, P, Angulo-Barturen, I, Jimenez-Diaz, M.B, Malmstrom, R, Lawrenz, M, Rodriguez-Granillo, A, Rathod, P.K, Tomchick, D.R, Palmer, M.J, Laleu, B, Qin, T, Charman, S.A, Phillips, M.A, Liebschner, D, Afonine, P.V, Baker, M.L, Bunkoczi, G, Chen, V.B, Croll, T.I, Hintze, B, Hung, L.W, Jain, S, McCoy, A.J, Moriarty, N.W, Oeffner, R.D, Poon, B.K, Prisant, M.G, Read, R.J, Richardson, J.S, Richardson, D.C, Sammito, M.D, Sobolev, O.V, Stockwell, D.H, Terwilliger, T.C, Urzhumtsev, A.G, Videau, L.L, Williams, C.J, Adams, P.D.Show

J.Med.Chem. 68 590 637 (2025)

PMID: 39710971 DOI: 10.1021/acs.jmedchem.4c02394

Abstact

Malaria remains a serious global health challenge, yet treatment and control programs are threatened by drug resistance. Dihydroorotate dehydrogenase (DHODH) was clinically validated as a target for treatment and prevention of malaria through human studies with DSM265, but currently no drugs against this target are in clinical use. We used structure-based computational tools including free energy perturbation (FEP+) to discover highly ligand efficient, potent, and selective pyrazole-based Plasmodium DHODH inhibitors through a scaffold hop from a pyrrole-based series. Optimized pyrazole-based compounds were identified with low nM-to-pM Plasmodium falciparum cell potency and oral activity in a humanized SCID mouse malaria infection model. The lead compound DSM1465 is more potent and has improved absorption, distribution, metabolism and excretion/pharmacokinetic (ADME/PK) properties compared to DSM265 that support the potential for once-monthly chemoprevention at a low dose. This compound meets the objective of identifying compounds with potential to be used for monthly chemoprevention in Africa to support malaria elimination efforts.

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Primary Citation of related structures