ReLink-PyB: an adapted REINVENT-based framework for non-DSM PfDHODH inhibitor discovery

ReLink-PyB, an integrated computational framework that synergistically combines reinforcement learning (RL), molecular dynamics (MD) simulations, and quantum-level analyses, was developed to discover next-generation Plasmodium falciparum dihydroorotate dehydrogenase ( Pf DHODH) inhibitors. This study proposes a new series of non-DSM compounds the PyB Series having Pyrazole-benzene core, generated by this approach. PyB-318, a novel lead molecule from this series, shows compelling in silico evidence of drug-like behavior and target engagement, and proposes it as a promising antimalarial candidate against drug-resistant parasites. The lack of effective PfDHODH inhibitors, particularly the clinical trial failure of triazolopyrimidine-based (DSM) scaffolds, highlights the urgent need for novel antimalarial drug discovery. Using the REINVENT 4.0 platform and its LinkINVENT model, two rationally selected warheads, pyrazole and benzene, were employed to guide scaffold innovation, generating a user-defined library of 20,000 compounds. Following Rigorous RDKit-based cheminformatics filtering integrating synthetic accessibility (SynA), quantitative drug-likeness (QED ≥ 0.7), and lipophilicity (logP: −1 to 4) yielded 625 drug-like candidates. Molecular docking against Pf DHODH (PDB ID: 6I4B) identified 264 compounds with binding affinities ranging from − 8.7 to − 8.5 kcal/mol, significantly exceeding the co-crystallized ligand E2N (− 7.8 kcal/mol). The top four docked complexes underwent rigorous 100-nanosecond molecular dynamics simulations, revealing PyB-318 as the optimal lead compound with exceptional stability (ligand RMSD: 2.5 Å, RMSF: 0.5 Å plateau by 10 ns) and superior conformational compactness (radius of gyration: 0.48 Å). MM-GBSA binding free energy calculations confirmed PyB-318’s thermodynamic superiority (ΔG_bind = − 52.3 kcal/mol), representing a 10.2 kcal/mol advantage over E2N and demonstrating remarkable resistance to single-point mutations through distributed secondary interactions. Quantum theory of atoms in molecules (QTAIM) analysis with DFT (6-31G (d, p)) affirmed binding interactions via bond critical point (BCP) evaluation, identifying five high-electron-density BCPs (ρ > 0.1 au) distributed across diverse residue pairs, further validating the superior thermodynamic and electronic landscape. PyB-318 exhibits exceptional drug-like properties with a QED of 0.71, optimal logP of 3.54, and most favourable synthetic accessibility (SynA: 2.51) superior to DSM265 and the reference ligand positioning it as a readily synthesizable lead candidate. ReLink-PyB thus establishes a systematic, transferable paradigm for accelerated de novo antimalarial drug discovery against drug-resistant parasites while providing a generalizable template for neglected-disease therapeutic development.