Bioinformatics and immunoinformatics assisted multiepitope vaccine construct against Burkholderia anthina

Maha A Alshiekheid; Ali M Dou; Mohammad Algahtani; Wafa Abdullah I Al-Megrin; Yaseer Ali Alhawday; Arwa Essa Alradhi; Khulud Bukhari; Basmah F Alharbi; Ahmed N Algefary; Basmah Awwadh Alhunayhani; Khaled S Allemailem

doi:10.1016/j.jsps.2023.101917

Bioinformatics and immunoinformatics assisted multiepitope vaccine construct against Burkholderia anthina

Saudi Pharm J. 2024 Jan;32(1):101917. doi: 10.1016/j.jsps.2023.101917. Epub 2023 Dec 13.

Affiliations

¹ Department of Botany & Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
² Department of Medical Laboratories, Riyadh Security Forces Hospital, Ministry of Interior, Riyadh 11481, Saudi Arabia.
³ Department of Laboratory & Blood Bank, Security Forces Hospital, P.O. Box 14799, Mecca 21955, Saudi Arabia.
⁴ Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
⁵ Department of Medical Microbiology, Qassim University Medical City , Qassim University, Buraydah 51452, Saudi Arabia.
⁶ Regional Laboratory and Central Blood Bank, Hafr Al Batin 39513, Saudi Arabia.
⁷ Department of Microbiology and Parasitology, College of Veterinary Medicine, P. O. Box 1757, Hofuf 36388, Al-Ahsa, King Faisal University, Saudi Arabia.
⁸ Department of Basic Health Science, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia.
⁹ Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia.

Abstract

Burkholderia anthina is a pathogenic bacterial species belonging to the Burkholderiaceae family and it is mainly considered the etiological agent of chronic obstructive pulmonary diseases associated with cystic fibrosis, due to being intrinsic antibiotic resistant making it difficult to treat pulmonary infections. Hence increased rate of antibiotic-resistant bacterial species vaccine development is the priority to tackle this problem. In research work, we designed a multi-epitope-based vaccine construct against B. anthina using reverse vaccinology immunoinformatics and biophysical approaches. Based on the subtractive proteomic screening of core proteins we identified 3 probable antigenic proteins and good vaccine targets namely, type VI secretion system tube protein hcp Burkholderia, fimbria/pilus periplasmic chaperone and fimbrial biogenesis outer membrane usher protein. The selected 3 proteins were used for B and B cells B-derived T-cell epitopes prediction. In epitopes prediction, different epitopes were predicted with various lengths and percentile scores and subjected to further immunoinformatics analysis. In immunoinformatics screening a total number of 06, IDDGNANAL, KTVKPDPRY, SEVESGSAP, YGGDLTVEV, SVSHDTNGR, and GSKADGYQR epitopes were considered good vaccine target candidates and shortlisted for vaccine construct designing. The vaccine construct was designed by joining selected epitopes with the help of a GPGPG linker and additionally linked with cholera toxin b subunit adjuvant to increase the efficacy of the vaccine construct the sequence of the said adjuvant were retrieved from protein data bank through its (PDB ID: 5ELD). The designed vaccine construct was evaluated for its physiochemical properties analysis in which we reported that the vaccine construct comprises 216 amino acids with a molecular weight of 22.37499 kilo Dalton, 15.55 instability index (II) is computed, and this classifies that the vaccine construct is properly stable. VaxiJen v2.0 web server predicted that the vaccine construct is probable antigenic in nature with 0.6320 predicted value. Furthermore AllerTOP v. 2.0 tool predicted that the designed vaccine construct is non allergic in nature. Molecular docking analysis was done for analysis of the binding affinity of the vaccine construct with TLR-2 (PDB ID: 6NIG), the docking results predicted 799.2 kcal/mol binding energy score that represents the vaccine construct has a good binding ability with TLR-2. Moreover, molecular dynamic simulation analysis results revealed that the vaccine construct and immune cell receptor has proper binding stability over various environmental condition, i.e. change in pressure range, temperature, and motion. After each analysis, we observed that the vaccine construct is safe stable, and probably antigenic and could generate an immune response against the target pathogen but in the future, experimental analysis is still needed to verify in silico base results.

Keywords: Binding energies estimation; Burkholderia anthina; Epitopes base vaccine; Immunoinformatics; Molecular docking; Molecular dynamic simulation.