Proteomics-Guided Identification of Novel Drug Targets in Plasmodium falciparum Artemisinin-Resistant Strains Circulating in the Lake Chad Basin, North East Nigeria

Artemisinin resistance in Plasmodium falciparum, driven primarily by mutations in the Kelch13 propeller domain, has been documented in East Africa and is now a concern for West African malaria control programmes. The Lake Chad Basin region of North East Nigeria, encompassing Borno and Yobe States, presents a unique ecological transmission zone where parasite population genomics remain undercharacterised. This study conducted a proteomics-guided investigation of artemisinin-resistant P. falciparum strains isolated from clinical malaria patients in Maiduguri and Damaturu to identify novel drug target proteins. Clinical isolates were established in ex vivo ring-stage survival assays and phenotypically classified for artemisinin partial resistance. Two-dimensional differential gel electrophoresis combined with MALDI-TOF/TOF mass spectrometry was used to compare protein expression profiles between susceptible and resistant strains. Differentially expressed proteins were subjected to pathway enrichment analysis and protein-protein interaction network analysis. Kelch13 C580Y and M476I mutations were identified in phenotypically resistant isolates. Proteomic analysis identified 47 differentially expressed proteins, including significant upregulation of stress response proteins PfHSP70-1, PfHSP90, and proteasome subunit PfRPN11 in resistant strains. PfRPN11, a deubiquitinase, was identified as a high-confidence novel drug target based on network centrality, human non-homology, and druggability screening. Virtual screening against a 100,000-compound library identified three candidate PfRPN11 inhibitors with predicted binding energies below negative 9 kcal/mol. This study delivers original proteomic target discovery data directly relevant to antimalarial drug development for the Lake Chad Basin resistance context. Keywords: proteomics, Plasmodium falciparum, artemisinin resistance, drug target, Lake Chad Basin.