Structural basis for the function and inhibition of dihydroorotate dehydrogenase from Schistosoma mansoni

Abstract

Schistosomiasis is a serious public health problem, prevalent in tropical and subtropical areas, especially in poor communities without access to safe drinking water and adequate sanitation. Transmission has been reported in 78 countries, and its control depends on a single drug, praziquantel, which has been used over the past 30 years. Our work is focused on exploiting target‐based drug discovery strategies to develop new therapeutics to treat schistosomiasis. In particular, we are interested in evaluating the enzyme dihydroorotate dehydrogenase (DHODH) as a drug target. DHODH is a flavoenzyme that catalyzes the stereospecific oxidation of (S)‐dihydroorotate (DHO) to orotate during the fourth and only redox step of the de novo pyrimidine nucleotide biosynthetic pathway. Previously, we identified atovaquone, used in the treatment of malaria, and its analogues, as potent and selective inhibitors against Schistosoma mansoni DHODH (SmDHODH). In the present article, we report the first crystal structure of SmDHODH in complex with the atovaquone analogue inhibitor 2‐((4‐fluorophenyl)amino)‐3‐hydroxynaphthalene‐1,4‐dione (QLA). We discuss three major findings: (a) the open conformation of the active site loop and the unveiling of a novel transient druggable pocket for class 2 DHODHs; (b) the presence of a protuberant domain, only present in Schistosoma spp DHODHs, that was found to control and modulate the dynamics of the inhibitor binding site; (c) a detailed description of an unexpected binding mode for the atovaquone analogue to SmDHODH. Our findings contribute to the understanding of the catalytic mechanism performed by class 2 DHODHs and provide the molecular basis for structure‐guided design of SmDHODH inhibitors. Database The structural data are available in Protein Data Bank (PDB) database under the accession code number https://www.rcsb.org/structure/6UY4.

In silico Identification of Potential Sesquiterpene Lactones from SistematX Database against <em>Schistosoma mansoni</em>

“…Some metabolites structurally related with structure 1, 9α-linoloyloxy-8β-(2-methylbutyryloxy)-15-hydroxy-14-oxo-acanthospermolide and 9a-linolenoyloxy-15-hydroxy-8b-2-methylbutyryloxy-14oxo-acanthospermolide have been identified as potential antileishmanial and antichagasic SLs, two of the main NTDs that affect the American continent [8,13]. https://mol2net-07.sciforum.net/ Molecular docking calculations were performed to explore the mechanism of action of the five bestranked SLs in the active site of Schistosoma mansoni dihydroorotate dehydrogenase (SmDHODH), a flavoenzyme that catalyzes the stereospecific oxidation of (S)-dihydroorotate (DHO) to orotate during the fourth and only redox step of the de novo pyrimidine nucleotide biosynthetic pathway [2]. The crystal structure of SmDHODH in complex with the inhibitor 2-((4-fluorophenyl)amino)-3hydroxynaphthalene-1,4-dione (QLA) was obtained from the Protein Data Bank (PDB).…”

“…After this modeling set (which was used to build and validate models) is divided additionally into multiple training (80%) and test sets (20%) [8]. In addition, the structure of the Schistosoma mansoni dihydroorotate dehydrogenase, DHODH, (PDB ID: 6UY4) in complex with its respective inhibitor: 2-[(4-fluorophenyl)amino]-3-hydroxynaphthalene-1,4-dione (PDB ID: QLA) was downloaded from PDB [2]. Using Molegro 6.0.1, molecular docking calculations were performed using a grid, with a 15-Å radius and a 0.30-Å resolution, to cover the ligandbinding site for the DHODH structure.…”

“…For 2019, the World Health Organization (WHO) estimated that close to 240 million people required preventive treatment against this disease, mainly poor communities without access to safe drinking water and adequate sanitation [1]. One of the most interesting targets of Schistosoma for the development of new treatments is the dihydroorotate dehydrogenase (DHODH), a flavoenzyme that catalyzes the stereospecific oxidation of (S)-dihydroorotate (DHO) to orotate during the fourth and only redox step of the de novo pyrimidine nucleotide biosynthetic pathway [2]. Atovaquone (an antimalarial treatment) was identified by de Mori et al, as a selective inhibitor against Schistosoma mansoni DHODH [3].…”

In vivo efficacy of combination therapy with albendazole and atovaquone against primary hydatid cysts in mice

“…Additionally, under hypoxia, the efficacy of the treatment in vivo may be enhanced by the synergistic action of ABZ and ATV, as shown in the anaerobic culture assay. ATV inhibits not only complex III but also dihydroorotate The proportion of cysts on the liver surface was a 0.73%, b 6.5%, c 4.0%, d 0.65%, and e 0.29% dehydrogenase (DHODH), which has been annotated in the genome data of E. multilocularis [19] and other parasites [20,21]. DHODH contributes to adaptation to anaerobiosis by regulating fumarate reductase activity and pyrimidine synthesis [22].…”

In vivo efficacy of combination therapy with albendazole and atovaquone against primary hydatid cysts in mice

“…Additionally, under hypoxia, the e cacy of treatment in vivo may be enhanced by the synergistic action of ABZ and ATV, as shown in the anaerobic culture assay. Atovaquone inhibits not only complex III but also dihydroorotate dehydrogenase (DHODH), which has been annotated in the genome data of E. multilocularis [22], and some other parasites [23,24]. DHODH contributes to the adaptation to anaerobiosis through the regulation of fumarate reductase activity and pyrimidine synthesis [25].…”