{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T23:42:18Z","timestamp":1791848538769,"version":"4.3.4"},"reference-count":79,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"King Saud University, Riyadh, Saudi Arabia","award":["RSP-2021\/301"],"award-info":[{"award-number":["RSP-2021\/301"]}]},{"name":"King Saud University, Riyadh, Saudi Arabia","award":["RSP-2021\/301"],"award-info":[{"award-number":["RSP-2021\/301"]}]},{"name":"King Saud University, Riyadh, Saudi Arabia","award":["RSP-2021\/301"],"award-info":[{"award-number":["RSP-2021\/301"]}]},{"name":"King Saud University, Riyadh, Saudi Arabia","award":["RSP-2021\/301"],"award-info":[{"award-number":["RSP-2021\/301"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Bioengineering"],"abstract":"<jats:p>Brucella suis, one of the causative agents of brucellosis, is Gram-negative intracellular bacteria that may be found all over the globe and it is a significant facultative zoonotic pathogen found in livestock. It may adapt to a phagocytic environment, reproduce, and develop resistance to harmful environments inside host cells, which is a crucial part of the Brucella life cycle making it a worldwide menace. The molecular underpinnings of Brucella pathogenicity have been substantially elucidated due to comprehensive methods such as proteomics. Therefore, we aim to explore the complete Brucella suis proteome to prioritize the novel proteins as drug targets via subtractive proteo-genomics analysis, an effort to conjecture the existence of distinct pathways in the development of brucellosis. Consequently, 38 unique metabolic pathways having 503 proteins were observed while among these 503 proteins, the non-homologs (n = 421), essential (n = 350), drug-like (n = 114), virulence (n = 45), resistance (n = 42), and unique to pathogen proteins were retrieved from Brucella suis. The applied subsequent hierarchical shortlisting resulted in a protein, i.e., isocitrate lyase, that may act as potential drug target, which was finalized after the extensive literature survey. The interacting partners for these shortlisted drug targets were identified through the STRING database. Moreover, structure-based studies were also performed on isocitrate lyase to further analyze its function. For that purpose, ~18,000 ZINC compounds were screened to identify new potent drug candidates against isocitrate lyase for brucellosis. It resulted in the shortlisting of six compounds, i.e., ZINC95543764, ZINC02688148, ZINC20115475, ZINC04232055, ZINC04231816, and ZINC04259566 that potentially inhibit isocitrate lyase. However, the ADMET profiling showed that all compounds fulfill ADMET properties except for ZINC20115475 showing positive Ames activity; whereas, ZINC02688148, ZINC04259566, ZINC04232055, and ZINC04231816 showed hepatoxicity while all compounds were observed to have no skin sensitization. In light of these parameters, we recommend ZINC95543764 compound for further experimental studies. According to the present research, which uses subtractive genomics, proteins that might serve as therapeutic targets and potential lead options for eradicating brucellosis have been narrowed down.<\/jats:p>","DOI":"10.3390\/bioengineering9110633","type":"journal-article","created":{"date-parts":[[2022,11,2]],"date-time":"2022-11-02T03:36:44Z","timestamp":1667360204000},"page":"633","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Integrated Bioinformatics-Based Subtractive Genomics Approach to Decipher the Therapeutic Drug Target and Its Possible Intervention against Brucellosis"],"prefix":"10.3390","volume":"9","author":[{"given":"Kanwal","family":"Khan","sequence":"first","affiliation":[{"name":"Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi City 75270, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Munirah Sulaiman Othman","family":"Alhar","sequence":"additional","affiliation":[{"name":"Department of Chemistry, College of Science, University of Ha\u2019il, Ha\u2019il 81451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Naseer","family":"Abbas","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Kohat University of Science and Technology, Kohat 26000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3774-9907","authenticated-orcid":false,"given":"Syed Qamar","family":"Abbas","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Sarhad University of Science and Technology, Peshawar 25000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5611-0378","authenticated-orcid":false,"given":"Mohsin","family":"Kazi","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutics, College of Pharmacy, P.O. Box-2457, King Saud University, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5606-2719","authenticated-orcid":false,"given":"Saeed Ahmad","family":"Khan","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Kohat University of Science and Technology, Kohat 26000, Pakistan"},{"name":"Division of Molecular Pharmaceutics and Drug Delivery, The University of Texas at Austin, 2409 University Ave., Austin, TX 78712, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0154-7863","authenticated-orcid":false,"given":"Abdul","family":"Sadiq","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Faculty of Biological Sciences, University of Malakand, Chakdara 18000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5188-6540","authenticated-orcid":false,"given":"Syed Shams ul","family":"Hassan","sequence":"additional","affiliation":[{"name":"Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China"},{"name":"Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3236-1292","authenticated-orcid":false,"given":"Simona","family":"Bungau","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1556-615X","authenticated-orcid":false,"given":"Khurshid","family":"Jalal","sequence":"additional","affiliation":[{"name":"HEJ Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi City 75270, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,11,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/S0378-1135(02)00210-9","article-title":"Brucella evolution and taxonomy","volume":"90","author":"Moreno","year":"2002","journal-title":"Vet. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1111\/j.1462-5822.2012.01771.x","article-title":"BmaC, a novel autotransporter of Brucella suis, is involved in bacterial adhesion to host cells","volume":"14","author":"Posadas","year":"2012","journal-title":"Cell. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1177\/104063871102300127","article-title":"Detection of Brucella canis\u2013induced reproductive diseases in a kennel","volume":"23","author":"Gyuranecz","year":"2011","journal-title":"J. Vet. Diagn. Investig."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"27","DOI":"10.2174\/1574891X11308010006","article-title":"Brucella as a potential agent of bioterrorism","volume":"8","author":"Doganay","year":"2013","journal-title":"Recent Pat. Anti-Infect. Drug Discov."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2201034","DOI":"10.1002\/advs.202201034","article-title":"Gestational Leucylation Suppresses Embryonic T-Box Transcription Factor 5 Signal and Causes Congenital Heart Disease","volume":"9","author":"Zhang","year":"2022","journal-title":"Adv. Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1016\/j.vetmic.2009.06.021","article-title":"Brucellosis: A re-emerging zoonosis","volume":"140","author":"Seleem","year":"2010","journal-title":"Vet. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/j.prevetmed.2003.08.004","article-title":"Brucellosis and Q-fever seroprevalences of nomadic pastoralists and their livestock in Chad","volume":"61","author":"Schelling","year":"2003","journal-title":"Prev. Vet. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1038\/s41392-020-00411-4","article-title":"Ketogenic diets inhibit mitochondrial biogenesis and induce cardiac fibrosis","volume":"6","author":"Xu","year":"2021","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Akinyemi, K.O., Fakorede, C.O., Amisu, K.O., and Wareth, G. (2022). Human and Animal Brucellosis in Nigeria: A Systemic Review and Meta-Analysis in the Last Twenty-One Years (2001\u20132021). Vet. Sci., 9.","DOI":"10.3390\/vetsci9080384"},{"key":"ref_10","first-page":"1500846","article-title":"Comparisons of brucellosis between human and veterinary medicine","volume":"8","author":"Hull","year":"2018","journal-title":"Infect. Ecol. Epidemiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.mib.2004.12.003","article-title":"Brucella lipopolysaccharide acts as a virulence factor","volume":"8","author":"Lapaque","year":"2005","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Martirosyan, A., P\u00e9rez-Gutierrez, C., Banchereau, R., Dutartre, H., Lecine, P., Dullaers, M., Mello, M., Salcedo, S.P., Muller, A., and Leserman, L. (2012). Brucella \u03b2 1, 2 cyclic glucan is an activator of human and mouse dendritic cells. PLoS Pathog., 8.","DOI":"10.1371\/journal.ppat.1002983"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"287","DOI":"10.4142\/jvs.2012.13.3.287","article-title":"Protective effects of recombinant Brucella abortus Omp28 against infection with a virulent strain of Brucella abortus 544 in mice","volume":"13","author":"Lim","year":"2012","journal-title":"J. Vet. Sci."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3428","DOI":"10.1038\/s41467-021-23827-0","article-title":"Low chorionic villous succinate accumulation associates with recurrent spontaneous abortion risk","volume":"12","author":"Wang","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1128\/JB.01336-12","article-title":"Brucella melitensis MucR, an Orthologue of Sinorhizobium meliloti MucR, Is Involved in Resistance to Oxidative, Detergent, and Saline Stresses and Cell Envelope Modifications","volume":"195","author":"Mirabella","year":"2013","journal-title":"J. Bacteriol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"151","DOI":"10.21307\/pjm-2018-029","article-title":"Brucella\u2013virulence factors, pathogenesis and treatment","volume":"67","author":"Naylor","year":"2018","journal-title":"Pol. J. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"72","DOI":"10.3389\/fcimb.2015.00072","article-title":"Type IV secretion system of Brucella spp. and its effectors","volume":"5","author":"Ke","year":"2015","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"988326","DOI":"10.3389\/fimmu.2022.988326","article-title":"Gut microbiota on admission as predictive biomarker for acute necrotizing pancreatitis","volume":"13","author":"Zou","year":"2022","journal-title":"Front. Immunol."},{"key":"ref_19","first-page":"702784","article-title":"Proteins of Bartonella bacilliformis: Candidates for vaccine development","volume":"2015","author":"Ventosilla","year":"2015","journal-title":"Int. J. Pept."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.meegid.2019.03.003","article-title":"Vaccinomics strategy for developing a unique multi-epitope monovalent vaccine against Marburg marburgvirus","volume":"70","author":"Hasan","year":"2019","journal-title":"Infect. Genet. Evol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.compbiolchem.2018.02.017","article-title":"Prioritization of potential drug targets against P. aeruginosa by core proteomic analysis using computational subtractive genomics and Protein-Protein interaction network","volume":"74","author":"Uddin","year":"2018","journal-title":"Comput. Biol. Chem."},{"key":"ref_22","first-page":"255","article-title":"Subtractive genomics approach for in silico identification and characterization of novel drug targets in Neisseria meningitides Serogroup B","volume":"2","author":"Sarangi","year":"2009","journal-title":"J. Comput. Sci. Syst. Biol."},{"key":"ref_23","first-page":"49","article-title":"Identification of potential drug targets by subtractive genome analysis of Escherichia coli O157: H7: An in silico approach","volume":"8","author":"Mondal","year":"2015","journal-title":"Adv. Appl. Bioinform. Chem. AABC"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2502","DOI":"10.1038\/s41467-019-10375-x","article-title":"APC\/CCDH1 synchronizes ribose-5-phosphate levels and DNA synthesis to cell cycle progression","volume":"10","author":"Li","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.ajps.2020.05.003","article-title":"Alginate-based complex fibers with the Janus morphology for controlled release of co-delivered drugs","volume":"16","author":"Lai","year":"2021","journal-title":"Asian J. Pharm. Sci."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1089\/107999000312379","article-title":"Localization and post-Golgi trafficking of tumor necrosis factor-alpha in macrophages","volume":"20","author":"Shurety","year":"2000","journal-title":"J. Interferon Cytokine Res."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Scott, M.S., Calafell, S.J., Thomas, D.Y., and Hallett, M.T. (2005). Refining protein subcellular localization. PLoS Comput. Biol., 1.","DOI":"10.1371\/journal.pcbi.0010066"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/S1672-0229(04)02027-3","article-title":"Predicting protein subcellular localization: Past, present, and future","volume":"2","year":"2004","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"796363","DOI":"10.3389\/fmicb.2021.796363","article-title":"Comparative Metabolic Pathways Analysis and Subtractive Genomics Profiling to Prioritize Potential Drug Targets against Streptococcus pneumoniae","volume":"12","author":"Khan","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Duan, C., Jiang, Q., Jiang, X., Zeng, H., Wu, Q., Yu, Y., and Yang, X. (2022). Discovery of a Novel Inhibitor Structure of Mycobacterium tuberculosis Isocitrate Lyase. Molecules, 27.","DOI":"10.3390\/molecules27082447"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"17666","DOI":"10.1021\/jacs.1c07970","article-title":"Mechanism-Based Inactivation of Mycobacterium tuberculosis Isocitrate Lyase 1 by (2 R, 3 S)-2-Hydroxy-3-(nitromethyl) succinic acid","volume":"143","author":"Mellott","year":"2021","journal-title":"J. Am. Chem. Soc."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Hwang, J.-Y., Chung, B., Kwon, O.-S., Park, S.C., Cho, E., Oh, D.-C., Shin, J., and Oh, K.-B. (2021). Inhibitory Effects of Epipolythiodioxopiperazine Fungal Metabolites on Isocitrate Lyase in the Glyoxylate Cycle of Candida albicans. Mar. Drugs, 19.","DOI":"10.3390\/md19060295"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.2217\/fmb-2019-0166","article-title":"Identification of a new antifungal compound against isocitrate lyase of Paracoccidioides brasiliensis","volume":"14","author":"Barbosa","year":"2019","journal-title":"Future Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Kwofie, S.K., Dankwa, B., Odame, E.A., Agamah, F.E., Doe, L.P., Teye, J., Agyapong, O., Miller III, W.A., Mosi, L., and Wilson, M.D. (2018). In silico screening of isocitrate lyase for novel anti-buruli ulcer natural products originating from Africa. Molecules, 23.","DOI":"10.3390\/molecules23071550"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1478","DOI":"10.1002\/pmic.201100563","article-title":"History of protein\u2013protein interactions: From egg-white to complex networks","volume":"12","author":"Braun","year":"2012","journal-title":"Proteomics"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1751-0473-5-8","article-title":"Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information","volume":"5","author":"Pedamallu","year":"2010","journal-title":"Source Code Biol. Med."},{"key":"ref_37","first-page":"5129","article-title":"Flexible nets: The roles of intrinsic disorder in protein interaction networks","volume":"272","author":"Dunker","year":"2005","journal-title":"Fed. Eur. Biochem. Soc. J."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Zhang, A. (2009). Protein Interaction Networks: Computational Analysis, Cambridge University Press.","DOI":"10.1017\/CBO9780511626593"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Hassan, S.S.u., Abbas, S.Q., Ali, F., Ishaq, M., Bano, I., Hassan, M., Jin, H.-Z., and Bungau, S.G. (2022). A Comprehensive in silico exploration of pharmacological properties, bioactivities, molecular docking, and anticancer potential of vieloplain F from Xylopia vielana Targeting B-Raf Kinase. Molecules, 27.","DOI":"10.3390\/molecules27030917"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1550","DOI":"10.2174\/092986710790979944","article-title":"In silico prediction of binding sites on proteins","volume":"17","author":"Leis","year":"2010","journal-title":"Curr. Med. Chem."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1016\/S1367-5931(99)00007-1","article-title":"Evolution of protein function, from a structural perspective","volume":"3","author":"Todd","year":"1999","journal-title":"Curr. Opin. Chem. Biol."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Ghufran, M., Khan, H.A., Ullah, M., Ghufran, S., Ayaz, M., Siddiq, M., Hassan, S.S.u., and Bungau, S. (2022). In Silico Strategies for Designing of Peptide Inhibitors of Oncogenic K-Ras G12V Mutant: Inhibiting Cancer Growth and Proliferation. Cancers, 14.","DOI":"10.3390\/cancers14194884"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Shahinozzaman, M., Taira, N., Ishii, T., Halim, M.A., Hossain, M.A., and Tawata, S. (2018). Anti-inflammatory, anti-diabetic, and anti-Alzheimer\u2019s effects of prenylated flavonoids from Okinawa propolis: An investigation by experimental and computational studies. Molecules, 23.","DOI":"10.3390\/molecules23102479"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Hassan, S.S.u., Muhammad, I., Abbas, S.Q., Hassan, M., Majid, M., Jin, H.-Z., and Bungau, S. (2021). Stress driven discovery of natural products from actinobacteria with anti-oxidant and cytotoxic activities including docking and admet properties. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222111432"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"100385","DOI":"10.1016\/j.imu.2020.100385","article-title":"Subtractive genomics approach towards the identification of novel therapeutic targets against human Bartonella bacilliformis","volume":"20","author":"Khan","year":"2020","journal-title":"Inform. Med. Unlocked"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1007\/s00044-016-1501-6","article-title":"Computational identification of potential drug targets against Mycobacterium leprae","volume":"25","author":"Uddin","year":"2016","journal-title":"Med. Chem. Res."},{"key":"ref_47","first-page":"536","article-title":"Complete genomes in WWW Entrez: Data representation and analysis","volume":"15","author":"Tatusova","year":"1999","journal-title":"Bioinform. (Oxf. Engl.)"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.gene.2015.08.044","article-title":"Identification of putative drug targets in Vancomycin-resistant Staphylococcus aureus (VRSA) using computer aided protein data analysis","volume":"575","author":"Hasan","year":"2016","journal-title":"Gene"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"D545","DOI":"10.1093\/nar\/gkaa970","article-title":"KEGG: Integrating viruses and cellular organisms","volume":"49","author":"Kanehisa","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"D677","DOI":"10.1093\/nar\/gkaa917","article-title":"DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools","volume":"49","author":"Luo","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"D1074","DOI":"10.1093\/nar\/gkx1037","article-title":"DrugBank 5.0: A major update to the DrugBank database for 2018","volume":"46","author":"Wishart","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"D687","DOI":"10.1093\/nar\/gky1080","article-title":"VFDB 2019: A comparative pathogenomic platform with an interactive web interface","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1128\/AAC.01310-13","article-title":"ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes","volume":"58","author":"Gupta","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1093\/bioinformatics\/btq249","article-title":"PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes","volume":"26","author":"Yu","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1402","DOI":"10.1110\/ps.03479604","article-title":"Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions","volume":"13","author":"Yu","year":"2004","journal-title":"Protein Sci."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"D607","DOI":"10.1093\/nar\/gky1131","article-title":"STRING v11: Protein\u2013protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets","volume":"47","author":"Szklarczyk","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"D437","DOI":"10.1093\/nar\/gkaa1038","article-title":"RCSB Protein Data Bank: Powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences","volume":"49","author":"Burley","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"Kelley","year":"2015","journal-title":"Nat. Protoc."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK\u2014A program to check the stereochemical quality of protein structures","volume":"26","author":"Laskowski","year":"1993","journal-title":"J. Appl. Crystallogr."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nsb0295-171","article-title":"A method to predict functional residues in proteins","volume":"2","author":"Casari","year":"1995","journal-title":"Nat. Struct. Biol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"W299","DOI":"10.1093\/nar\/gki370","article-title":"ConSurf 2005: The projection of evolutionary conservation scores of residues on protein structures","volume":"33","author":"Landau","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"2445","DOI":"10.1093\/bioinformatics\/btn474","article-title":"INTREPID\u2014INformation-theoretic TREe traversal for Protein functional site IDentification","volume":"24","author":"Sankararaman","year":"2008","journal-title":"Bioinformatics"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1006\/jmbi.1996.0077","article-title":"The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria","volume":"256","author":"Peters","year":"1996","journal-title":"J. Mol. Biol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1110\/ps.073213608","article-title":"Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines","volume":"17","author":"Tong","year":"2008","journal-title":"Protein Sci."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.pbiomolbio.2017.02.005","article-title":"ProBiS tools (algorithm, database, and web servers) for predicting and modeling of biologically interesting proteins","volume":"128","author":"Konc","year":"2017","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1002\/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B","article-title":"Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function","volume":"19","author":"Morris","year":"1998","journal-title":"J. Comput. Chem."},{"key":"ref_67","first-page":"33","article-title":"Open babel","volume":"3","author":"Banck","year":"2013","journal-title":"J. Cheminform."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"731","DOI":"10.2174\/1871520621666211013115500","article-title":"Computational Exploration of Anti-Cancer Potential of GUAIANE Dimers from Xylopia vielana by Targeting B-Raf Kinase Using Chemo-Informatics, Molecular Docking, and MD Simulation Studies","volume":"22","author":"Abbas","year":"2022","journal-title":"Anti-Cancer Agents Med. Chem."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"42717","DOI":"10.1038\/srep42717","article-title":"SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules","volume":"7","author":"Daina","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Franc, K., Krecek, R., H\u00e4sler, B., and Arenas-Gamboa, A. (2018). Brucellosis remains a neglected disease in the developing world: A call for interdisciplinary action. BMC Public Health, 18.","DOI":"10.1186\/s12889-017-5016-y"},{"key":"ref_71","first-page":"1","article-title":"Brucella suis and farm biosecurity: Assessing risk in pigs raised outdoors in New York State","volume":"1","author":"Havas","year":"2022","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1111\/zph.12359","article-title":"Identification of Brucella spp. in feral swine (Sus scrofa) at abattoirs in Texas, USA","volume":"64","author":"Pedersen","year":"2017","journal-title":"Zoonoses Public Health"},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Ashraf, B., Atiq, N., Khan, K., Wadood, A., and Uddin, R. (2022). Subtractive genomics profiling for potential drug targets identification against Moraxella catarrhalis. PLoS ONE, 17.","DOI":"10.1371\/journal.pone.0273252"},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Khan, K., Basharat, Z., Jalal, K., Mashraqi, M.M., Alzamami, A., Alshamrani, S., and Uddin, R. (2022). Identification of Therapeutic Targets in an Emerging Gastrointestinal Pathogen Campylobacter ureolyticus and Possible Intervention through Natural Products. Antibiotics, 11.","DOI":"10.3390\/antibiotics11050680"},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Jalal, K., Khan, K., Ahmad, D., Hayat, A., Basharat, Z., Abbas, M.N., Alghamdi, S., Almehmadi, M., and Sahibzada, M.U.K. (2021). Pan-genome reverse vaccinology approach for the design of multi-epitope vaccine construct against Escherichia albertii. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222312814"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"104608","DOI":"10.1016\/j.micpath.2020.104608","article-title":"Identification of novel non-homologous drug targets against Acinetobacter baumannii using subtractive genomics and comparative metabolic pathway analysis","volume":"152","author":"Kaur","year":"2021","journal-title":"Microb. Pathog."},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Jaiswal, A.K., Tiwari, S., Jamal, S.B., Oliveira, L.d.C., Sales-Campos, H., Andrade-Silva, L.E., Oliveira, C.J.F., Ghosh, P., Barh, D., and Azevedo, V. (2021). Reverse vaccinology and subtractive genomics approaches for identifying common therapeutics against Mycobacterium leprae and Mycobacterium lepromatosis. J. Venom. Anim. Toxins Incl. Trop. Dis., 27.","DOI":"10.1590\/1678-9199-jvatitd-2020-0027"},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Kwon, S., Chun, H.L., Ha, H.J., Lee, S.Y., and Park, H.H. (2021). Heterogeneous multimeric structure of isocitrate lyase in complex with succinate and itaconate provides novel insights into its inhibitory mechanism. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0251067"},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Chung, B., Hwang, J.-Y., Park, S.C., Kwon, O.-S., Cho, E., Lee, J., Lee, H.-S., Oh, D.-C., Shin, J., and Oh, K.-B. (2022). Inhibitory Effects of Nitrogenous Metabolites from a Marine-Derived Streptomyces bacillaris on Isocitrate Lyase of Candida albicans. Mar. Drugs, 20.","DOI":"10.3390\/md20020138"}],"container-title":["Bioengineering"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-5354\/9\/11\/633\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:08:59Z","timestamp":1760144939000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-5354\/9\/11\/633"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,1]]},"references-count":79,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11]]}},"alternative-id":["bioengineering9110633"],"URL":"https:\/\/doi.org\/10.3390\/bioengineering9110633","relation":{},"ISSN":["2306-5354"],"issn-type":[{"value":"2306-5354","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,1]]}}}