Comparative evolutionary pharmacogenomics of human prostaglandin-endoperoxide synthase paralogs identifies population-structured coding variation and protein-contextual candidates in N-terminal leader-sequence and catalytic-channel regions.

Human PTGS1 and PTGS2 encode cyclooxygenase paralogs that regulate prostaglandin biosynthesis and are major targets of nonsteroidal anti-inflammatory drugs (NSAIDs). Interpreting population-differentiated PTGS variation requires integration of allele-frequency structure with transcript consequence, protein topology, splice-prediction evidence and structural context. This study integrated allele-resolved population differentiation, transcript-aware consequence annotation, splice-prediction boundary checks, protein-domain mapping, direct leader-sequence property calculations and controlled structural analyses. Candidate classes distinguished high-FST synonymous contextual markers, N-terminal PTGS1 leader-sequence missense variants, splice-region candidates and PTGS2 p.Val511Ala. Web-based SpliceAI/Pangolin evaluation of seven splice-relevant or comparator variants provided limited support for splice alteration. A retrospective comparison of 31 missense candidates showed that Val511Ala was not the most differentiated missense variant overall, but ranked first by allele frequency, allele-frequency range and maximum pairwise FST within four channel-context candidates; FST was used only to describe population differentiation. Canonical Val511 mapped to 5KIR Val525, a second-shell position adjacent to the rofecoxib-contact network. Controlled docking-score, contact and direct-frame pose analyses detected no systematic variant-associated shift under the tested conditions. PTGS1 p.Trp8Arg and p.Pro17Leu produced distinct directly calculated changes in net-charge proxy, hydrophobic-residue count, mean Kyte-Doolittle hydropathy, aromatic-residue count and proline count across the 23-residue leader sequence and descriptive H-region. No signal-peptide predictor output was used, and effects on SRP recognition, ER targeting, translocation, cleavage, membrane insertion, maturation, abundance, localization, enzyme activity or drug response were not demonstrated. These results support a calibrated prioritisation framework in which population differentiation identifies structured variation, while transcript consequence, protein context and reproducible quantitative analyses define experimentally testable candidates.