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However, few inhibitors that target this potential anticancer target have been discovered. Quantitative characterization of the interactions between SHMT2 and its known inhibitors should benefit future discovery of novel inhibitors. In this study, we employed a recently developed alanine-scanning-interaction-entropy method to quantitatively calculate the residue-specific binding free energy of 28 different SHMT2 inhibitors that originate from the same skeleton. Major contributing residues from SHMT2 and chemical groups from the inhibitors were identified, and the binding energy of each residue was quantitatively determined, revealing essential features of the protein-inhibitor interaction. The most important contributing residue is Y105 of the B chain followed by L166 of the A chain. The calculated protein\u2013ligand binding free energies are in good agreement with the experimental results and showed better correlation and smaller errors compared with those obtained using the conventional MM\/GBSA with the normal mode method. These results may aid the rational design of more effective SHMT2 inhibitors.<\/jats:p>","DOI":"10.1021\/acs.jcim.9b00370","type":"journal-article","created":{"date-parts":[[2019,8,23]],"date-time":"2019-08-23T16:52:29Z","timestamp":1566579149000},"page":"3871-3878","source":"Crossref","is-referenced-by-count":31,"title":["Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational\nAlanine Scanning"],"prefix":"10.1021","volume":"59","author":[{"given":"Liping","family":"He","sequence":"first","affiliation":[{"name":"East China Normal University , , ,","place":["Shanghai, China, 200062"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingxiao","family":"Bao","sequence":"additional","affiliation":[{"name":"East China Normal University , , ,","place":["Shanghai, China, 200062"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunpeng","family":"Yang","sequence":"additional","affiliation":[{"name":"East China Normal University , , ,","place":["Shanghai, China, 200062"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suzhen","family":"Dong","sequence":"additional","affiliation":[{"name":"East China Normal University , , ,","place":["Shanghai, China, 200062"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lujia","family":"Zhang","sequence":"additional","affiliation":[{"name":"East China Normal University , , ,","place":["Shanghai, China, 200062"]},{"name":"NYU-ECNU Center for Computational Chemistry at NYU Shanghai , ,","place":["Shanghai, China, 200062"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2853-7910","authenticated-orcid":true,"given":"Yifei","family":"Qi","sequence":"additional","affiliation":[{"name":"East China Normal University , , ,","place":["Shanghai, China, 200062"]},{"name":"NYU-ECNU Center for Computational Chemistry at NYU Shanghai , ,","place":["Shanghai, China, 200062"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4612-1863","authenticated-orcid":true,"given":"John Z. H.","family":"Zhang","sequence":"additional","affiliation":[{"name":"East China Normal University , , ,","place":["Shanghai, China, 200062"]},{"name":"NYU-ECNU Center for Computational Chemistry at NYU Shanghai , ,","place":["Shanghai, China, 200062"]},{"name":"New York University , , , ,","place":["New York, New York, United States, 10003"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2019,8,23]]},"reference":[{"key":"2026081805133562300_cit1","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1038\/nrc3557","article-title":"Serine, glycine and one-carbon units:\ncancer metabolism in full circle","volume":"13","author":"Locasale","year":"2013","journal-title":"Nat. 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Drug Discovery Des."},{"key":"2026081805133562300_cit48","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1002\/prot.20033","article-title":"Exploring\nprotein native states and large-scale conformational changes with\na modified generalized born model","volume":"55","author":"Onufriev","year":"2004","journal-title":"Proteins:\nStruct., Funct., Genet."},{"issue":"7","key":"2026081805133562300_cit49","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004276","article-title":"Predicting binding free energy change caused by point\nmutations with knowledge-modified MM\/PBSA method","volume":"11","author":"Petukh","year":"2015","journal-title":"PLoS Comput. 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