De Novo Molecular Design and Bioactivity Prediction of Novel Hexahydroquinolines as Plasmodium falciparum Calcium-Dependent Protein Kinase 4 (CDPK4) Inhibitors

Abstract

Plasmodium falciparum Calcium-Dependent Protein Kinase 4 (PfCDPK4) is a validated target for malaria transmission-blocking interventions, as its inhibition disrupts male gametocyte exflagellation. Hexahydroquinolines (HHQs) have emerged as promising gametocytocidal agents. This study aimed to design novel HHQs as potential PfCDPK4 inhibitors with good binding affinity, favourable pharmacokinetics, and structural stability. A library of 20,000 novel HHQ analogs was generated using genetic algorithm-driven de novo molecular design in AlvaBuilder and systematically filtered through a pipeline comprising machine-learning-based bioactivity prediction, PAINS removal, pharmacophore modeling, ADMET screening, and structure-based virtual screening. Top-ranking compounds underwent bioisosteric optimization and were evaluated using 300 ns molecular dynamics simulations and density functional theory (DFT) calculations. Comparative in silico validation against known inhibitor Bumped Kinase Inhibitor-1 (BKI-1) and the co-crystallized ligand DXR as controls demonstrated that four HHQ analogs exhibited comparable binding affinities and stable interactions with key residues within the ATP-binding pocket. Favourable ADMET profiles, dynamic stability, and supportive electronic properties further reinforced their inhibition potential. These findings provide biologically meaningful computational evidence supporting HHQ scaffolds as potential PfCDPK4 inhibitors and demonstrate the utility of integrated bioinformatics approaches for malaria transmission-blocking drug discovery. Further experimental validation is required to confirm the inhibitory activities of the identified hexahydroquinoline compounds.