9M4O

Crystal structure of human DHODH in complex with Lapachol

This is a non-PDB format compatible entry.

Summary for 9M4O

• Entry DOI: 10.2210/pdb9m4o/pdb
• Descriptor: Dihydroorotate dehydrogenase (quinone), mitochondrial, FLAVIN MONONUCLEOTIDE, OROTIC ACID, ... (7 entities in total)
• Functional Keywords: oxidoreductase, pyrimidine biosynthesis
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 40853.25

Authors

Pemba, M.C.,Sakurai, Y.,Kurosaki, Y.,Amalia, E.,Inaoka, D.K.,Davey, A.R.,Shiba, T.,Kita, K.,Yasuda, J. (deposition date: 2025-03-04, release date: 2026-03-04, Last modification date: 2026-04-29)

Primary citation

Pemba, C.M.,Sakurai, Y.,Kurosaki, Y.,Patten, J.J.,Amalia, E.,Inaoka, D.K.,Davey, R.A.,Shiba, T.,Kita, K.,Yasuda, J.
Antiviral activities of ascofuranone and naphthoquinone derivatives against Ebola virus.
Antiviral Res., 249:106400-106400, 2026

PubMed Abstract: Ebola virus (EBOV) has emerged as a cause of a severe and life-threatening disease since its discovery. Currently, only two monoclonal antibody drugs have been approved by the US Food and Drug Administration for EBOV infection treatment. In this study, we screened 87 human dihydroorotate dehydrogenase (HsDHODH) inhibitors using the transcription and replication-competent virus-like particle (trVLP) system. Two compounds, 280-12 and 511-12, ascofuranone and naphthoquinone derivatives, respectively, were identified. Both compounds inhibited the Ebola trVLP infection in a dose-dependent manner in vitro and strongly inhibited the EBOV minigenome expression. Their antiviral effects against authentic infectious EBOV were also confirmed, with half-maximal inhibitory concentrations of 0.5 and 0.1 μM, respectively. Structural analysis of 511-12 and lapachol, a naphthoquinone derivative with a short isoprene chain, in complex with HsDHODH revealed that these compounds bind to the N-terminal hydrophobic cavity related to the ubiquinone-binding site. Supplementation of nucleosides and metabolites involved in the biosynthesis of pyrimidine nucleotides supported that the antiviral activities of the identified compounds were mainly based on the intracellular pyrimidine pool depletion, specifically at the level of mitochondrial DHODH. Overall, these results suggest 280-12 and 511-12 as promising lead compound candidates for the development of novel drugs for the treatment of EBOV infection.

PubMed: 41933619
DOI: 10.1016/j.antiviral.2026.106400

Experimental method

X-RAY DIFFRACTION (1.75 Å)