{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T13:52:58Z","timestamp":1791553978569,"version":"4.3.4"},"reference-count":57,"publisher":"American Chemical Society (ACS)","issue":"10","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Neisseria gonorrhoeae causes \u223c82.4 million infections annually and is rapidly approaching an untreatable status. The pathogen has developed resistance to every antibiotic class introduced since the sulfonamide era. Ceftriaxone, the last WHO- and CDC-recommended empirical therapy, is now compromised by high-level resistance in extensively drug-resistant lineages reported across multiple continents. No licensed vaccine exists, and no antibiotic with a novel mechanism has been introduced for this pathogen in over 40 years. Conventional drug discovery is too slow and insufficiently resistance-aware to address this escalating threat. In this review, we examine in silico proteome-wide target fishing as a rapid, systematic approach. The approach applies six biologically informed filters to the N. gonorrhoeae core proteome: core-genome definition, host-homology exclusion, essentiality screening, metabolic chokepoint identification, subcellular localization, and resistance-aware prioritization. Across data sets spanning 12\u201369 clinical strains, this pipeline reduces 2000\u201312,300 protein-coding sequences to 12\u201330 high-confidence targets. An integrated artificial intelligence (AI)\/machine learning (ML) scoring layer further ranks candidates using sequence features, AlphaFold2 structures, protein\u2013protein interaction networks, and genotype\u2013phenotype data from \u223c20,000 clinical isolates. Five targets showed consistent cross-study prioritization: LpxC, MurA, FabI, DapD, and NGFG_RS03485. Of these, only LpxC has experimental inhibitor validation against multidrug-resistant gonococci; the remaining candidates are supported computationally but lack biochemical confirmation. Bridging this validation gap remains the critical bottleneck. However, advances in pan-genome analysis, structural prediction, and generative AI for compound design provide a more tractable route to novel therapeutics than previously available.<\/jats:p>","DOI":"10.1021\/acsinfecdis.6c00521","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T11:02:02Z","timestamp":1788951722000},"page":"3296-3308","source":"Crossref","is-referenced-by-count":0,"title":["Artificial Intelligence-Integrated Proteome-Wide Target\nPrioritization for Drug Discovery against Multidrug-Resistant\n                    <i>Neisseria gonorrhoeae<\/i>"],"prefix":"10.1021","volume":"12","author":[{"given":"Ravi","family":"Kant","sequence":"first","affiliation":[{"name":"Shoolini University , , , ,","place":["Solan, Himachal Pradesh, India, 173229"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saurabh","family":"Mazumdar","sequence":"additional","affiliation":[{"name":"Shoolini University , , , ,","place":["Solan, Himachal Pradesh, India, 173229"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ananya","family":"Mahajan","sequence":"additional","affiliation":[{"name":"Shoolini University , , , ,","place":["Solan, Himachal Pradesh, India, 173229"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9663-4731","authenticated-orcid":true,"given":"Myron","family":"Christodoulides","sequence":"additional","affiliation":[{"name":"University of Southampton Faculty of Medicine, Southampton General Hospital , , ,","place":["Southampton, U.K., SO16 6YD"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"issue":"3","key":"2026100909103121300_cit1","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1128\/CMR.00010-14","article-title":"Antimicrobial resistance in Neisseria gonorrhoeae in the 21st century: past, evolution, and future","volume":"27","author":"Unemo","year":"2014","journal-title":"Clin. Microbiol. Rev."},{"key":"2026100909103121300_cit2","unstructured":"World Health Organisation.\n          . Multi-drug resistant gonorrhoea2025https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/multi-drug-resistant-gonorrhoea."},{"issue":"12 Suppl 2","key":"2026100909103121300_cit3","doi-asserted-by":"publisher","first-page":"S56","DOI":"10.1093\/infdis\/jiab227","article-title":"Gonococcal\nPelvic Inflammatory Disease: Placing Mechanistic\nInsights Into the Context of Clinical and Epidemiological Observations","volume":"224","author":"Xu","year":"2021","journal-title":"J. Infect. Dis."},{"issue":"12 Suppl 2","key":"2026100909103121300_cit4","doi-asserted-by":"publisher","first-page":"S39","DOI":"10.1093\/infdis\/jiab031","article-title":"Pelvic Inflammatory\nDisease Due to Neisseria gonorrhoeae and Chlamydia trachomatis: Immune Evasion Mechanisms and Pathogenic\nDisease Pathways","volume":"224","author":"Darville","year":"2021","journal-title":"J. Infect. Dis."},{"issue":"1","key":"2026100909103121300_cit5","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1097\/QCO.0000000000001170","article-title":"Combatting\nantimicrobial-resistant Neisseria gonorrhoeae: new\nantibiotics and the pipeline\nof antigonococcal therapeutics","volume":"39","author":"Ram","year":"2025","journal-title":"Curr. Opin.\nInfect. Dis."},{"issue":"1","key":"2026100909103121300_cit6","doi-asserted-by":"publisher","DOI":"10.3201\/eid1701.100397","article-title":"Ceftriaxone-Resistant Neisseria gonorrhoeae, Japan","volume":"17","author":"Ohnishi","year":"2011","journal-title":"Emerging Infect.\nDis."},{"issue":"37","key":"2026100909103121300_cit7","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2023.28.37.2300456","article-title":"Two cases\nof extensively drug-resistant (XDR) Neisseria gonorrhoeae infection combining ceftriaxone-resistance and high-level azithromycin\nresistance, France, November 2022 and May 2023","volume":"28","author":"Maubaret","year":"2023","journal-title":"Eurosurveillance"},{"issue":"3","key":"2026100909103121300_cit8","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S1473-3099(20)30055-4","article-title":"Lessons learnt from\nceftriaxone-resistant gonorrhoea in the UK and Australia","volume":"20","author":"Fifer","year":"2020","journal-title":"Lancet Infect. Dis."},{"key":"2026100909103121300_cit9","doi-asserted-by":"publisher","DOI":"10.3389\/fphar.2024.1284665","article-title":"Global trends\nof antimicrobial resistance rates in Neisseria gonorrhoeae: a systematic review and meta-analysis","volume":"15","author":"Hooshiar","year":"2024","journal-title":"Front.\nPharmacol."},{"issue":"2","key":"2026100909103121300_cit10","doi-asserted-by":"publisher","DOI":"10.1093\/jacamr\/dlae053","article-title":"High prevalence\nof ceftriaxone-resistant and XDR Neisseria gonorrhoeae in several cities of Cambodia, 2022-23: WHO Enhanced Gonococcal\nAntimicrobial Surveillance Programme (EGASP)","volume":"6","author":"Ouk","year":"2024","journal-title":"JAC-Antimicrob. Resist."},{"issue":"8","key":"2026100909103121300_cit11","doi-asserted-by":"publisher","first-page":"1885","DOI":"10.1093\/jac\/dkae176","article-title":"The novel\n2024 WHO Neisseria gonorrhoeae reference strains\nfor global quality assurance of laboratory investigations and superseded\nWHO N. gonorrhoeae reference strains\u2500phenotypic, genetic and\nreference genome characterization","volume":"79","author":"Unemo","year":"2024","journal-title":"J. Antimicrob.\nChemother."},{"key":"2026100909103121300_cit12","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.02417","article-title":"Progress Toward a Gonococcal Vaccine:\nThe Way Forward","volume":"10","author":"Russell","year":"2019","journal-title":"Front. Immunol."},{"key":"2026100909103121300_cit13","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.881392","article-title":"Recent\nProgress Towards a Gonococcal Vaccine","volume":"12","author":"Maurakis","year":"2022","journal-title":"Front.\nCell. Infect. 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Immunol."},{"issue":"1","key":"2026100909103121300_cit17","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1111\/nyas.14549","article-title":"Machine\nlearning models for Neisseria gonorrhoeae antimicrobial\nsusceptibility tests","volume":"1520","author":"Martin","year":"2023","journal-title":"Ann. N. Y. Acad. Sci."},{"issue":"1","key":"2026100909103121300_cit18","doi-asserted-by":"publisher","DOI":"10.3390\/ijms27010496","article-title":"Gyrase and\nTopoisomerase IV as Antibacterial Targets for Gepotidacin and Zoliflodacin:\nTeaching Old Enzymes New Tricks","volume":"27","author":"Osheroff","year":"2026","journal-title":"Int. J. Mol.\nSci."},{"key":"2026100909103121300_cit19","doi-asserted-by":"publisher","DOI":"10.1016\/j.nmni.2026.101747","article-title":"Antimicrobial resistance crisis in\nSTIs: Gonorrhea and M. genitalium on the brink of\nuntreatability","volume":"71","author":"Ghodsi","year":"2026","journal-title":"New Microbes New Infect."},{"issue":"4","key":"2026100909103121300_cit20","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1080\/14787210.2026.2667361","article-title":"Efficacy\nand safety of gepotidacin\nversus standard of-care antibiotics for the treatment of uncomplicated\nurogenital infections in adults and adolescents: a systematic review\nand meta-analysis","volume":"24","author":"Reddy","year":"2026","journal-title":"Expert Rev. Anti-Infect.\nTher."},{"key":"2026100909103121300_cit21","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1017315","article-title":"Computer-aided\ngenomic\ndata analysis of drug-resistant Neisseria gonorrhoeae for the Identification of alternative therapeutic targets","volume":"13","author":"Qasim","year":"2023","journal-title":"Front. Cell. Infect. Microbiol."},{"issue":"9","key":"2026100909103121300_cit22","doi-asserted-by":"publisher","first-page":"1271","DOI":"10.2174\/0113892010295441240515074348","article-title":"Computational Strategies\nin Drug Discovery: Leveraging Subtractive Genomic Analysis for Target\nIdentification","volume":"26","author":"Patil","year":"2025","journal-title":"Curr. Pharm. 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Dis."},{"issue":"5","key":"2026100909103121300_cit26","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.01991-22","article-title":"Canary\nin the Coal Mine: How Resistance Surveillance\nin Commensals Could Help Curb the Spread of AMR in Pathogenic Neisseria","volume":"13","author":"Goytia","year":"2022","journal-title":"mBio"},{"key":"2026100909103121300_cit27","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1093\/infdis\/jiag197","article-title":"Evidence-Based\nAssessment of the\nRole of Pharyngeal Gonorrhea and Commensal Neisseria Species in the\nEmergence of Antimicrobial Resistance in Neisseria Gonorrhoeae: Data Gaps and Future Research","volume":"233","author":"Kimble","year":"2026","journal-title":"J. Infect.\nDis."},{"key":"2026100909103121300_cit28","doi-asserted-by":"publisher","DOI":"10.1016\/j.jtbi.2020.110172","article-title":"Identification\nof potential therapeutic targets in Neisseria gonorrhoeae by an in-silico approach","volume":"490","author":"Tanwer","year":"2020","journal-title":"J. Theor. Biol."},{"issue":"1","key":"2026100909103121300_cit29","doi-asserted-by":"publisher","DOI":"10.5808\/gi.22066","article-title":"Antibiotic resistance\nin Neisseria gonorrhoeae: broad-spectrum drug target\nidentification using subtractive genomics","volume":"21","author":"Omeershffudin","year":"2023","journal-title":"Genomics\nInf."},{"issue":"W1","key":"2026100909103121300_cit30","doi-asserted-by":"publisher","first-page":"W185","DOI":"10.1093\/nar\/gkab341","article-title":"EDGAR3.0: comparative\ngenomics and phylogenomics on a scalable infrastructure","volume":"49","author":"Dieckmann","year":"2021","journal-title":"Nucleic Acids Res."},{"issue":"22","key":"2026100909103121300_cit31","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale\nprokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"issue":"23","key":"2026100909103121300_cit32","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated\nfor clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"2026100909103121300_cit33","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1534659","article-title":"Subtractive genomics and drug repurposing\nstrategies\nfor targeting Streptococcus pneumoniae: insights from molecular docking\nand dynamics simulations","volume":"16","author":"Gohain","year":"2025","journal-title":"Front. Microbiol."},{"key":"2026100909103121300_cit34","doi-asserted-by":"publisher","first-page":"D271","DOI":"10.1093\/nar\/gkh024","article-title":"DEG: a\ndatabase of essential genes","volume":"32","author":"Zhang","year":"2004","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"2026100909103121300_cit35","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.157","article-title":"Recent advances in the characterization\nof essential genes and development of a database of essential genes","volume":"3","author":"Liang","year":"2024","journal-title":"Imeta"},{"key":"2026100909103121300_cit36","doi-asserted-by":"publisher","first-page":"W182","DOI":"10.1093\/nar\/gkm321","article-title":"KAAS: an automatic genome annotation and pathway reconstruction\nserver","volume":"35","author":"Moriya","year":"2007","journal-title":"Nuc Acids Res."},{"key":"2026100909103121300_cit37","first-page":"41","article-title":"Choke point analysis of the metabolic\npathways of Acinetobacter baylyi: A genomics approach to assess potential\ndrug targets","volume":"1","author":"Singh","year":"2009","journal-title":"J. Bioinf. Sequence Anal."},{"issue":"13","key":"2026100909103121300_cit38","doi-asserted-by":"publisher","first-page":"1608","DOI":"10.1093\/bioinformatics\/btq249","article-title":"PSORTb\n3.0: improved protein subcellular localization\nprediction with refined localization subcategories and predictive\ncapabilities for all prokaryotes","volume":"26","author":"Yu","year":"2010","journal-title":"Bioinformatics"},{"issue":"1","key":"2026100909103121300_cit39","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-021-00858-2","article-title":"A community-driven\nresource for genomic epidemiology and antimicrobial resistance prediction\nof Neisseria gonorrhoeae at Pathogenwatch","volume":"13","author":"Sa\u0301nchez-Buso\u0301","year":"2021","journal-title":"Genome Med."},{"issue":"7873","key":"2026100909103121300_cit40","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein\nstructure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2026100909103121300_cit41","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2022.102526","article-title":"AlphaFold2 protein structure prediction: Implications\nfor drug discovery","volume":"78","author":"Borkakoti","year":"2023","journal-title":"Curr. Opin. Struct. Biol."},{"issue":"3","key":"2026100909103121300_cit42","doi-asserted-by":"publisher","DOI":"10.1038\/s41397-025-00367-0","article-title":"Similarity\nof drug targets to human microbiome metaproteome promotes pharmacological\npromiscuity","volume":"25","author":"Beaudoin","year":"2025","journal-title":"Pharmacogen. J."},{"issue":"14","key":"2026100909103121300_cit43","doi-asserted-by":"publisher","DOI":"10.3390\/healthcare13141643","article-title":"AI-Prediction of Neisseria\ngonorrhoeae Resistance at\nthe Point of Care from Genomic and Epidemiologic Data","volume":"13","author":"Kolluru","year":"2025","journal-title":"Healthcare"},{"issue":"D1","key":"2026100909103121300_cit44","doi-asserted-by":"publisher","first-page":"D368","DOI":"10.1093\/nar\/gkad1011","article-title":"AlphaFold Protein Structure Database\nin 2024: providing structure coverage for over 214 million protein\nsequences","volume":"52","author":"Varadi","year":"2024","journal-title":"Nucleic Acids Res."},{"issue":"6637","key":"2026100909103121300_cit45","doi-asserted-by":"publisher","first-page":"1123","DOI":"10.1126\/science.ade2574","article-title":"Evolutionary-scale prediction of atomic-level protein structure with\na language model","volume":"379","author":"Lin","year":"2023","journal-title":"Science"},{"issue":"21","key":"2026100909103121300_cit46","doi-asserted-by":"publisher","first-page":"5962","DOI":"10.1016\/j.cell.2025.07.033","article-title":"A generative deep learning approach to de novo antibiotic\ndesign","volume":"188","author":"Krishnan","year":"2025","journal-title":"Cell"},{"issue":"1","key":"2026100909103121300_cit47","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-54655-z","article-title":"AI is a viable\nalternative to high throughput screening: a 318-target study","volume":"14","author":"Atomwise AIMS Program.","year":"2024","journal-title":"Sci. Rep."},{"issue":"1","key":"2026100909103121300_cit48","doi-asserted-by":"publisher","DOI":"10.1186\/s40659-024-00543-9","article-title":"Antimicrobial\nactivity of compounds identified by artificial intelligence discovery\nengine targeting enzymes involved in Neisseria gonorrhoeae peptidoglycan metabolism","volume":"57","author":"Kant","year":"2024","journal-title":"Biol. Res."},{"key":"2026100909103121300_cit49","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1146\/annurev.biochem.71.110601.135414","article-title":"Lipopolysaccharide Endotoxins","volume":"71","author":"Raetz","year":"2002","journal-title":"Ann. Rev. Biochem."},{"issue":"2","key":"2026100909103121300_cit50","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02543-25","article-title":"Biology of novel\nLpxC inhibitors for Neisseria gonorrhoeae informs\nstrategy for therapeutic innovation","volume":"14","author":"Otala","year":"2026","journal-title":"Microbiol.\nSpectr."},{"issue":"2","key":"2026100909103121300_cit51","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1128\/jb.124.2.713-717.1975","article-title":"Phospholipids and fatty acids of Neisseria gonorrhoeae","volume":"124","author":"Sud","year":"1975","journal-title":"J. Bacteriol."},{"issue":"6","key":"2026100909103121300_cit52","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1007\/s00253-001-0918-z","article-title":"Inhibitors of fatty acid synthesis\nas antimicrobial chemotherapeutics","volume":"58","author":"Heath","year":"2002","journal-title":"Appl. Microbiol.\nBiotechnol."},{"issue":"7654","key":"2026100909103121300_cit53","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/nature22308","article-title":"Predictive\ncompound accumulation\nrules yield a broad-spectrum antibiotic","volume":"545","author":"Richter","year":"2017","journal-title":"Nature"},{"issue":"1","key":"2026100909103121300_cit54","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1111\/nyas.14134","article-title":"Permeability barriers of Gram-negative pathogens","volume":"1459","author":"Zgurskaya","year":"2020","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"2026100909103121300_cit55","doi-asserted-by":"publisher","DOI":"10.3390\/biology14091272","article-title":"Investigating\nthe Antimicrobial Efficacy of Cannabinoids and Their Derivatives Against Neisseria Gonorrhoeae by Computational Analysis","volume":"14","author":"Mohd Omeershffudin","year":"2025","journal-title":"Biology"},{"issue":"4","key":"2026100909103121300_cit56","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1128\/MMBR.67.4.593-656.2003","article-title":"Molecular\nBasis of Bacterial Outer Membrane Permeability Revisited","volume":"67","author":"Nikaido","year":"2003","journal-title":"Microbiol. Mol. Biol. 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