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Integrating bio\/chemical information and artificial intelligence would bring new strategies for antimicrobial drug discovery. Herein, the Human Pathogenic Microorganisms Chemogenomics Knowledgebase (HPM-CKB) is presented as the largest domain-specific resource, consolidating chemical, genetic, and proteomic data on human-transmissible pathogens, together with multiple computational functional modules. The current release covers 7876 pathogenic proteins from 267 microorganisms (including 13,914 protein 3D structures) and 234,287 associated with bioactive molecules. HPM-CKB enables large-scale virtual screening, target identification, and drug repurposing, and integrates a large language model (LLM) for interactive queries. The computational prediction performance of HPM-CKB is corroborated by known inhibitors targeting SARS-CoV-2 replicase polyprotein 1ab. In wet-lab validations, four approved drugs (cefixime, ceftazidime, saquinavir, and rilapladib) identified via virtual screening show binding activity to SARS-CoV-2 nucleoprotein in affinity assays and inhibit SARS-CoV-2 replication in Vero E6 cells, demonstrating HPM-CKB\u2019s potential in drug repurposing. Meanwhile, two anti-Staphylococcus aureus lead compounds with novel scaffolds (CYC-HXL-9124 and CYC-HXL-9126) are identified via deep learning, and the potential target protein, cell division protein FtsZ, is subsequently prioritized using HPM-CKB (http:\/\/cgai.asia\/g\/pathogenDB) and experimentally validated by affinity assays. Collectively, these findings establish HPM-CKB as both a chemogenomic knowledgebase and a systematic drug development platform against EIDs.<\/jats:p>","DOI":"10.1021\/acs.jcim.6c02102","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T10:03:47Z","timestamp":1789466627000},"page":"12179-12195","source":"Crossref","is-referenced-by-count":0,"title":["An AI-Driven Chemogenomics\nKnowledgebase for Human-Transmissible\nPathogens: A Platform for Antimicrobial Drug Discovery"],"prefix":"10.1021","volume":"66","author":[{"given":"Jiaxiong","family":"Kang","sequence":"first","affiliation":[{"name":"Third Military Medical University , , ,","place":["Chongqing, China, 400038"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7870-8469","authenticated-orcid":true,"given":"Lei","family":"Zhu","sequence":"additional","affiliation":[{"name":"Third Military Medical University , , ,","place":["Chongqing, China, 400038"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4014-3770","authenticated-orcid":true,"given":"Haibo","family":"Li","sequence":"additional","affiliation":[{"name":"Third Military Medical University , , ,","place":["Chongqing, China, 400038"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangyu","family":"Xie","sequence":"additional","affiliation":[{"name":"Shenzhen University of Advanced Technology , , , ,","place":["Shenzhen, Guangdong, China, 518107"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cong","family":"Liu","sequence":"additional","affiliation":[{"name":"Shenzhen University of Advanced Technology , , , ,","place":["Shenzhen, Guangdong, China, 518107"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6533-8932","authenticated-orcid":true,"given":"Zhiwei","family":"Feng","sequence":"additional","affiliation":[{"name":"Shenzhen University of Advanced Technology , , , ,","place":["Shenzhen, Guangdong, China, 518107"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Wang","sequence":"additional","affiliation":[{"name":"Third Military Medical University , , ,","place":["Chongqing, China, 400038"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ouyang","family":"Mo","sequence":"additional","affiliation":[{"name":"Shenzhen University of Advanced Technology , , , ,","place":["Shenzhen, Guangdong, China, 518107"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengsu","family":"Wang","sequence":"additional","affiliation":[{"name":"Third Military Medical University , , ,","place":["Chongqing, China, 400038"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinzi","family":"Lin","sequence":"additional","affiliation":[{"name":"Shenzhen University of Advanced Technology , , , ,","place":["Shenzhen, Guangdong, China, 518107"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Xue","sequence":"additional","affiliation":[{"name":"Fudan University , , ,","place":["Shanghai, China, 200032"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haibin","family":"Liu","sequence":"additional","affiliation":[{"name":"Dong\u2019e Ejiao Co., Ltd. , , E\u2019jiao Road 78 , , ,","place":["Dong\u2019e, Liaocheng, China, 252200"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1161-5102","authenticated-orcid":true,"given":"Qin","family":"Ouyang","sequence":"additional","affiliation":[{"name":"Third Military Medical University , , ,","place":["Chongqing, China, 400038"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,15]]},"reference":[{"key":"2026092810072507800_cit1","doi-asserted-by":"publisher","first-page":"990","DOI":"10.1038\/nature06536","article-title":"Global trends in emerging\ninfectious diseases","volume":"451","author":"Jones","year":"2008","journal-title":"Nature"},{"key":"2026092810072507800_cit2","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1093\/milmed\/usz081","article-title":"Emerging Infectious Diseases and\nAntimicrobial Resistance (EIDAR)","volume":"184","author":"Lanteri","year":"2019","journal-title":"Mil. 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