{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T18:21:57Z","timestamp":1774981317946,"version":"3.50.1"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2022,4,9]],"date-time":"2022-04-09T00:00:00Z","timestamp":1649462400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81720108032"],"award-info":[{"award-number":["81720108032"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81930109"],"award-info":[{"award-number":["81930109"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Key Research and Development Programme of China","award":["2021YFA1301300"],"award-info":[{"award-number":["2021YFA1301300"]}]},{"name":"Project of State Key Laboratory of Natural Medicines, China Pharmaceutical University","award":["SKLNMZZ202020"],"award-info":[{"award-number":["SKLNMZZ202020"]}]},{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang Province","doi-asserted-by":"publisher","award":["LQ21H300007"],"award-info":[{"award-number":["LQ21H300007"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2020M671770"],"award-info":[{"award-number":["2020M671770"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Young Elite Scientists Sponsorship Program","award":["131810011"],"award-info":[{"award-number":["131810011"]}]},{"name":"Young Elite Scientists Sponsorship Program","award":["1132010013"],"award-info":[{"award-number":["1132010013"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Drug design targeting protein\u2013protein interactions (PPIs) associated with the development of diseases has been one of the most important therapeutic strategies. Besides interrupting the PPIs with PPI inhibitors\/blockers, increasing evidence shows that stabilizing the interaction between two interacting proteins may also benefit the therapy, such as the development of various types of molecular glues\/stabilizers that mostly work by stabilizing the two interacting proteins to regulate the downstream biological effects. However, characterizing the stabilization effect of a stabilizer is usually hard or too complicated for traditional experiments since it involves ternary interactions [protein\u2013protein\u2013stabilizer (PPS) interaction]. Thus, developing reliable computational strategies will facilitate the discovery\/design of molecular glues or PPI stabilizers. Here, by fully analyzing the energetic features of the binary interactions in the PPS ternary complex, we systematically investigated the performance of molecular mechanics Poisson-Boltzmann surface area (MM\/PBSA) and molecular mechanics generalized Born surface area (MM\/GBSA) methods on characterizing the stabilization effects of stabilizers in 14-3-3 systems. The results show that both MM\/PBSA and MM\/GBSA are powerful tools in distinguishing the stabilizers from the decoys (with area under the curves of 0.90\u20130.93 for all tested cases) and are reasonable for ranking protein\u2013peptide interactions in the presence or absence of stabilizers as well (with the average Pearson correlation coefficient of ~0.6 at a relatively high dielectric constant for both methods). Moreover, to give a detailed picture of the stabilization effects, the stabilization mechanism is also analyzed from the structural and energetic points of view for individual systems containing strong or weak stabilizers. This study demonstrates a potential strategy to accelerate the discovery of PPI stabilizers.<\/jats:p>","DOI":"10.1093\/bib\/bbac127","type":"journal-article","created":{"date-parts":[[2022,3,16]],"date-time":"2022-03-16T20:11:00Z","timestamp":1647461460000},"source":"Crossref","is-referenced-by-count":23,"title":["Characterizing the stabilization effects of stabilizers in protein\u2013protein systems with end-point binding free energy calculations"],"prefix":"10.1093","volume":"23","author":[{"given":"Rongfan","family":"Tang","sequence":"first","affiliation":[{"name":"Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China"}]},{"given":"Pengcheng","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, Taizhou 318000, Zhejiang, P. R. China"}]},{"given":"Zhe","family":"Wang","sequence":"additional","affiliation":[{"name":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China"}]},{"given":"Lingling","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China"}]},{"given":"Haiping","family":"Hao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, 210009 Nanjing, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7227-2580","authenticated-orcid":false,"given":"Tingjun","family":"Hou","sequence":"additional","affiliation":[{"name":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7107-7481","authenticated-orcid":false,"given":"Huiyong","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. 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