Drug design and optimisation at the dihydroorotate dehydrogenase receptor using the teriflunomide scaffold as a lead

Abstract

Dravet Syndrome is a dangerous form of childhood epilepsy, for which current anti-epileptic treatment is insufficient. Animal studies show that intracerebral dihydroorotate dehydrogenase (DHODH) inhibition is a novel route for the treatment of epilepsy. Teriflunomide has been identified as a potent inhibitor of DHODH, with poor blood brain barrier (BBB) permeation due to its high polarity. The aim of this study was to identify high in silico binding affinity DHODH inhibitors based on the teriflunomide scaffold, which are orally bioavailable and have improved non-polar characteristics, predisposing them to increased intra-cerebral penetration. The virtual screening and de novo drug design methods were applied. PDB crystallographic depositions 1D3H and 3U2O, describing the bound coordinates of the holo DHODH receptor with ligands teriflunomide and its biaryl analogue, respectively, were used to create a consensus pharmacophore. Pharmacophore-based virtual screening was carried out in ZINCPharmer®, with application of the Rule of 3 for lead-likeness. The resultant molecules were filtered in MONA® for drug-likeness, generating a cohort of 299 Lipinski Rule compliant molecules. Ranking of the molecules according to their binding affinity for the protomol, generated in SYBYL-X®, and lipophilicity, lead to the identification of high affinity molecules capable of penetrating the BBB. The ‘pocket’ module of LigBuilder® was used to elucidate the DHODH ligand binding pocket, as delineated around the bioactive conformation of teriflunomide. Structure activity relationship (SAR) data from X-Score® and a 2D topology map of the interactions between teriflunomide and the cognate receptor DHODH, guided the creation of seed structures which sustained molecular growth within the DHODH ligand binding pocket at pre-defined loci. The resultant molecules were filtered for Lipinski Rule compliance and ranked according to binding affinity for the DHODH ligand binding pocket and lipophilicity. Six teriflunomide analogues, with a propensity to oral bioavailability and intracerebral penetration were identified. 2D topology maps describing the molecular interactions they forge with the DHODH receptor were created to determine their binding modalities. The preliminary cohort of molecules produced will be used in iterative rounds of rational drug design, with optimisation carried out to improve their toxicity profile and to further explore the defined pharmacophoric space.