{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T14:56:18Z","timestamp":1790780178711,"version":"4.1.0"},"reference-count":82,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"vor","delay-in-days":29,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Designing target-relevant molecules is particularly difficult when only limited bioactivity data are available. We present MMP2Mol, a ligand-based generative framework that combines matched molecular pair (MMP) analysis with a pretrained chemical language model (CLM). MMP2Mol extracts target-specific structure\u2013activity transformations from available ligands, applies the prioritized transformations to construct a virtual focused library, and fine-tunes the CLM toward target-relevant chemical space. The framework was evaluated across ten therapeutic targets and compared with direct CLM fine-tuning, Seq2Seq, and Reinvent 4. In repeated experiments on F2, BRD4, and PARP1, MMP2Mol achieved 92.8%\u201395.3% validity and 99.5%\u201399.7% uniqueness. When both methods were evaluated against the same original active-compound reference, molecular novelty increased from 57.8%\u201364.0% for the CLM baseline to 79.8%\u201382.0% for MMP2Mol, while internal diversity remained broadly comparable. The gains were most evident for F2 and BRD4, whereas performance varied across the smaller target datasets. These findings indicate that MMP-derived chemical knowledge can improve the focus and reproducibility of ligand-based molecular generation under limited-data conditions. MMP2Mol therefore provides a practical strategy for computational candidate generation and prioritization in early-stage drug discovery.<\/jats:p>","DOI":"10.1093\/bib\/bbag548","type":"journal-article","created":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T18:23:20Z","timestamp":1789755800000},"source":"Crossref","is-referenced-by-count":0,"title":["MMP2Mol: a matched molecular pairs-based framework for ligand-based\n                    <i>de novo<\/i>\n                    drug design"],"prefix":"10.1093","volume":"27","author":[{"given":"Dekun","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Pharmacy, Xiangya Hospital, Central South University , No. 87 Xiangya Road, Kaifu District, Changsha, Hunan 410008 ,","place":["China"]},{"name":"Clinical Pharmacology Research Center of Hunan, Xiangya Hospital, Central South University , No. 87 Xiangya Road, Kaifu District, Changsha, Hunan 410008 ,","place":["China"]},{"name":"National Clinical Research Center for Geriatric Disorders, Xiangya Hospital , Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, Hunan 410008 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Li","sequence":"additional","affiliation":[{"name":"Xiangya School of Pharmaceutical Sciences, Central South University , No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410013 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianwang","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Xiangya Hospital, Central South University , No. 87 Xiangya Road, Kaifu District, Changsha, Hunan 410008 ,","place":["China"]},{"name":"Clinical Pharmacology Research Center of Hunan, Xiangya Hospital, Central South University , No. 87 Xiangya Road, Kaifu District, Changsha, Hunan 410008 ,","place":["China"]},{"name":"National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University , No. 87 Xiangya Road, Kaifu District, Changsha, Hunan 410008 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yueping","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Xiangya Hospital, Central South University , No. 87 Xiangya Road, Kaifu District, Changsha, Hunan 410008 ,","place":["China"]},{"name":"Clinical Pharmacology Research Center of Hunan, Xiangya Hospital, Central South University , No. 87 Xiangya Road, Kaifu District, Changsha, Hunan 410008 ,","place":["China"]},{"name":"National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University , No. 87 Xiangya Road, Kaifu District, Changsha, Hunan 410008 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3604-3785","authenticated-orcid":false,"given":"Dongsheng","family":"Cao","sequence":"additional","affiliation":[{"name":"Xiangya School 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