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In Silico Functional and Structural Characterization of Streptococcus pneumoniae Atypical Rib Domain-Containing

Stephen Kyle C Arcan¹, Gyraldin Marietony D Gan¹, Debrah Jannsen N Almazan¹

¹Department of Biology, College of Science, Pamantasan Ng Lungsod Ng Maynila (University of the City of Manila), Manila, Metro Manila, Philippines.

|January 22, 2026

Abstract:

Streptococcus pneumoniae is a high-mortality pathogen exhibiting broad-spectrum antibiotic resistance, necessitating the development of alternative therapies, such as antigenic protein-based vaccines, which have recently gained interest due to their novelty. Here, we characterized antigenic hypothetical proteins (HPs) of S. pneumoniae and determined their potential as vaccine construct targets. Subcellular localization reported 10 extracellular proteins, six of which were antigenic and nonallergenic, thus making them ideal vaccine construct targets. Functional annotation through conserved protein domain and motif prediction identified a unique, atypical Rib (aRib) domain from WP_001166178.1, widely distributed on bacterial cell surface proteins. A comparison with a canonical Rib domain showed domain atrophy, highlighting the lack of structural core elements. Further analysis revealed non-covalent interactions of Thr47, Ala48, Val41, and Phe38 interacting with an alpha-d-mannopyranose ligand, triggering S. pneumoniae colonization and capsule synthesis mechanism, with highly dynamic and flexible residues present on the ligand binding site. A strong immune response was observed from a computational immune response simulation, likely attributed to the presence of predicted 4 cytotoxic T lymphocyte (CTL), 10 helper T lymphocyte (HTL), and 5 B-cell lymphocyte (BCL) epitopes. Therefore, the study presents a novel protein for designing a vaccine construct against S. pneumoniae , thus offering a new target for future vaccinology studies. Future studies should confirm protective efficacy of this candidate in vitro and in vivo through immunological assays.

Keywords:

Streptococcus pneumoniae atypical rib domain epitope protein domain vaccinology

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