{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,28]],"date-time":"2025-09-28T11:05:01Z","timestamp":1759057501536,"version":"3.37.3"},"reference-count":70,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T00:00:00Z","timestamp":1619481600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T00:00:00Z","timestamp":1619481600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["21775060"],"award-info":[{"award-number":["21775060"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2021,5]]},"DOI":"10.1007\/s10822-021-00386-6","type":"journal-article","created":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T07:18:25Z","timestamp":1619507905000},"page":"679-694","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Discovery of novel IDO1 inhibitors via structure-based virtual screening and biological assays"],"prefix":"10.1007","volume":"35","author":[{"given":"Huizhen","family":"Ge","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Longfei","family":"Mao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuwei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danfeng","family":"Shi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xing","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaorui","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huanxiang","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6972-2971","authenticated-orcid":false,"given":"Xiaojun","family":"Yao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,4,27]]},"reference":[{"issue":"4","key":"386_CR1","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1080\/13543776.2018.1441290","volume":"28","author":"JE Cheong","year":"2018","unstructured":"Cheong JE, Ekkati A, Sun L (2018) A patent review of IDO1 inhibitors for cancer. Expert Opin Ther Pat 28(4):317\u2013330. https:\/\/doi.org\/10.1080\/13543776.2018.1441290","journal-title":"Expert Opin Ther Pat"},{"key":"386_CR2","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1016\/bs.acc.2019.08.005","volume":"95","author":"S Comai","year":"2020","unstructured":"Comai S, Bertazzo A, Brughera M, Crotti S (2020) Tryptophan in health and disease. Adv Clin Chem 95:165\u2013218. https:\/\/doi.org\/10.1016\/bs.acc.2019.08.005","journal-title":"Adv Clin Chem"},{"issue":"5","key":"386_CR3","doi-asserted-by":"publisher","first-page":"1195","DOI":"10.1007\/s00726-010-0752-7","volume":"41","author":"N Le Floc'h","year":"2011","unstructured":"Le Floc\u2019h N, Otten W, Merlot E (2011) Tryptophan metabolism, from nutrition to potential therapeutic applications. Amino Acids 41(5):1195\u20131205. https:\/\/doi.org\/10.1007\/s00726-010-0752-7","journal-title":"Amino Acids"},{"issue":"1","key":"386_CR4","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.bbrc.2005.09.032","volume":"338","author":"O Takikawa","year":"2005","unstructured":"Takikawa O (2005) Biochemical and medical aspects of the indoleamine 2,3-dioxygenase-initiated L-tryptophan metabolism. Biochem Biophys Res Commun 338(1):12\u201319. https:\/\/doi.org\/10.1016\/j.bbrc.2005.09.032","journal-title":"Biochem Biophys Res Commun"},{"issue":"17","key":"386_CR5","doi-asserted-by":"publisher","first-page":"4886","DOI":"10.1016\/j.bmc.2018.08.028","volume":"26","author":"R Yang","year":"2018","unstructured":"Yang R, Chen Y, Pan L, Yang Y, Zheng Q, Hu Y, Wang Y, Zhang L, Sun Y, Li Z, Meng X (2018) Design, synthesis and structure-activity relationship study of novel naphthoindolizine and indolizinoquinoline-5,12-dione derivatives as IDO1 inhibitors. Bioorg Med Chem 26(17):4886\u20134897. https:\/\/doi.org\/10.1016\/j.bmc.2018.08.028","journal-title":"Bioorg Med Chem"},{"issue":"10","key":"386_CR6","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1021\/ml500247w","volume":"5","author":"S Tojo","year":"2014","unstructured":"Tojo S, Kohno T, Tanaka T, Kamioka S, Ota Y, Ishii T, Kamimoto K, Asano S, Isobe Y (2014) Crystal structures and structure-activity relationships of imidazothiazole derivatives as IDO1 inhibitors. ACS Med Chem Lett 5(10):1119\u20131123. https:\/\/doi.org\/10.1021\/ml500247w","journal-title":"ACS Med Chem Lett"},{"issue":"9","key":"386_CR7","doi-asserted-by":"publisher","first-page":"1230","DOI":"10.1039\/C7MT00105C","volume":"9","author":"D Yan","year":"2017","unstructured":"Yan D, Lin YW, Tan X (2017) Heme-containing enzymes and inhibitors for tryptophan metabolism. Metallomics 9(9):1230\u20131240","journal-title":"Metallomics"},{"issue":"21","key":"386_CR8","doi-asserted-by":"publisher","first-page":"9760","DOI":"10.1021\/acs.jmedchem.6b00718","volume":"59","author":"A Coluccia","year":"2016","unstructured":"Coluccia A, Passacantilli S, Famiglini V, Sabatino M, Patsilinakos A, Ragno R, Mazzoccoli C, Sisinni L, Okuno A, Takikawa O, Silvestri R, La Regina G (2016) New Inhibitors of Indoleamine 2,3-Dioxygenase 1: Molecular Modeling Studies, Synthesis, and Biological Evaluation. J Med Chem 59(21):9760\u20139773. https:\/\/doi.org\/10.1021\/acs.jmedchem.6b00718","journal-title":"J Med Chem"},{"issue":"24","key":"386_CR9","doi-asserted-by":"publisher","first-page":"2682","DOI":"10.1002\/cmdc.201600446","volume":"11","author":"Z Shiokawa","year":"2016","unstructured":"Shiokawa Z, Kashiwabara E, Yoshidome D, Fukase K, Inuki S, Fujimoto Y (2016) Discovery of a novel scaffold as an indoleamine 2,3-Dioxygenase 1 (IDO1) inhibitor based on the pyrrolopiperazinone alkaloid. Longamide B ChemMedChem 11(24):2682\u20132689. https:\/\/doi.org\/10.1002\/cmdc.201600446","journal-title":"Longamide B ChemMedChem"},{"key":"386_CR10","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.ejca.2017.01.011","volume":"76","author":"L Brochez","year":"2017","unstructured":"Brochez L, Chevolet I, Kruse V (2017) The rationale of indoleamine 2,3-dioxygenase inhibition for cancer therapy. Eur J Cancer 76:167\u2013182. https:\/\/doi.org\/10.1016\/j.ejca.2017.01.011","journal-title":"Eur J Cancer"},{"issue":"2","key":"386_CR11","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1021\/acsmedchemlett.7b00488","volume":"9","author":"MG Brant","year":"2018","unstructured":"Brant MG, Goodwin-Tindall J, Stover KR, Stafford PM, Wu F, Meek AR, Schiavini P, Wohnig S, Weaver DF (2018) Identification of potent indoleamine 2,3-Dioxygenase 1 (IDO1) inhibitors based on a phenylimidazole scaffold. ACS Med Chem Lett 9(2):131\u2013136. https:\/\/doi.org\/10.1021\/acsmedchemlett.7b00488","journal-title":"ACS Med Chem Lett"},{"issue":"4","key":"386_CR12","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1021\/acsmedchemlett.7b00487","volume":"9","author":"K Fang","year":"2018","unstructured":"Fang K, Dong G, Li Y, He S, Wu Y, Wu S, Wang W, Sheng C (2018) Discovery of novel indoleamine 2,3-Dioxygenase 1 (IDO1) and histone deacetylase (HDAC) dual inhibitors. ACS Med Chem Lett 9(4):312\u2013317. https:\/\/doi.org\/10.1021\/acsmedchemlett.7b00487","journal-title":"ACS Med Chem Lett"},{"key":"386_CR13","doi-asserted-by":"publisher","first-page":"151","DOI":"10.3389\/fimmu.2018.00151","volume":"9","author":"L Hornyak","year":"2018","unstructured":"Hornyak L, Dobos N, Koncz G, Karanyi Z, Pall D, Szabo Z, Halmos G, Szekvolgyi L (2018) The role of indoleamine-2,3-Dioxygenase in cancer development, diagnostics, and therapy. Front Immunol 9:151. https:\/\/doi.org\/10.3389\/fimmu.2018.00151","journal-title":"Front Immunol"},{"issue":"1","key":"386_CR14","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1002\/cmdc.201700666","volume":"13","author":"K Fang","year":"2018","unstructured":"Fang K, Dong G, Wang H, He S, Wu S, Wang W, Sheng C (2018) Improving the potency of cancer immunotherapy by dual targeting of IDO1 and DNA. Chem Med Chem 13(1):30\u201336. https:\/\/doi.org\/10.1002\/cmdc.201700666","journal-title":"Chem Med Chem"},{"key":"386_CR15","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1016\/j.intimp.2017.10.008","volume":"54","author":"R Hong","year":"2018","unstructured":"Hong R, Zhou Y, Tian X, Wang L, Wu X (2018) Selective inhibition of IDO1, D-1-methyl-tryptophan (D-1MT), effectively increased EpCAM\/CD3-bispecific BiTE antibody MT110 efficacy against IDO1(hi)breast cancer via enhancing immune cells activity. Int Immunopharmacol 54:118\u2013124. https:\/\/doi.org\/10.1016\/j.intimp.2017.10.008","journal-title":"Int Immunopharmacol"},{"issue":"9","key":"386_CR16","doi-asserted-by":"publisher","first-page":"1216","DOI":"10.1097\/PAS.0000000000001099","volume":"42","author":"A Volaric","year":"2018","unstructured":"Volaric A, Gentzler R, Hall R, Mehaffey JH, Stelow EB, Bullock TN, Martin LW, Mills AM (2018) Indoleamine-2,3-Dioxygenase in non-small cell lung cancer: a targetable mechanism of immune resistance frequently coexpressed with PD-L1. Am J Surg Pathol 42(9):1216\u20131223. https:\/\/doi.org\/10.1097\/PAS.0000000000001099","journal-title":"Am J Surg Pathol"},{"issue":"6","key":"386_CR17","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1007\/s00432-018-2620-x","volume":"144","author":"SJ Lee","year":"2018","unstructured":"Lee SJ, Jun S-Y, Lee IH, Kang BW, Park SY, Kim HJ, Park JS, Choi G-S, Yoon G, Kim JG (2018) CD274, LAG3, and IDO1 expressions in tumor-infiltrating immune cells as prognostic biomarker for patients with MSI-high colon cancer. J Cancer Res Clin Oncol 144(6):1005\u20131014. https:\/\/doi.org\/10.1007\/s00432-018-2620-x","journal-title":"J Cancer Res Clin Oncol"},{"key":"386_CR18","doi-asserted-by":"publisher","first-page":"8169724","DOI":"10.1155\/2016\/8169724","volume":"2016","author":"IC Chen","year":"2016","unstructured":"Chen IC, Lee KH, Hsu YH, Wang WR, Chen CM, Cheng YW (2016) Expression pattern and clinicopathological relevance of the indoleamine 2,3-Dioxygenase 1\/Tryptophan 2,3-Dioxygenase protein in colorectal cancer. Dis Markers 2016:8169724. https:\/\/doi.org\/10.1155\/2016\/8169724","journal-title":"Dis Markers"},{"issue":"16","key":"386_CR19","doi-asserted-by":"publisher","first-page":"4671","DOI":"10.1158\/0008-5472.can-17-3752","volume":"78","author":"K Kolijn","year":"2018","unstructured":"Kolijn K, Verhoef EI, Smid M, B\u00f6ttcher R, Jenster GW, Debets R, van Leenders GJLH (2018) Epithelial-mesenchymal transition in human prostate cancer demonstrates enhanced immune evasion marked by IDO1 expression. Cancer Res 78(16):4671\u20134679. https:\/\/doi.org\/10.1158\/0008-5472.can-17-3752","journal-title":"Cancer Res"},{"issue":"3","key":"386_CR20","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1016\/j.tranon.2018.11.012","volume":"12","author":"W Zhang","year":"2018","unstructured":"Zhang W, Zhang J, Zhang Z, Guo Y, Wu Y, Wang R, Wang L, Mao S, Yao X (2018) Overexpression of indoleamine 2,3-Dioxygenase 1 promotes epithelial-mesenchymal transition by activation of the IL-6\/STAT3\/PD-L1 pathway in bladder cancer. Transl Oncol 12(3):485\u2013492. https:\/\/doi.org\/10.1016\/j.tranon.2018.11.012","journal-title":"Transl Oncol"},{"issue":"12","key":"386_CR21","doi-asserted-by":"publisher","first-page":"1930","DOI":"10.4161\/cc.8.12.8745","volume":"8","author":"JR Brody","year":"2009","unstructured":"Brody JR, Costantino CL, Berger AC, Sato T, Lisanti MP, Yeo CJ, Emmons RV, Witkiewicz AK (2009) Expression of indoleamine 2,3-dioxygenase in metastatic malignant melanoma recruits regulatory T cells to avoid immune detection and affects survival. Cell Cycle 8(12):1930\u20131934. https:\/\/doi.org\/10.4161\/cc.8.12.8745","journal-title":"Cell Cycle"},{"issue":"1","key":"386_CR22","doi-asserted-by":"publisher","first-page":"1777625","DOI":"10.1080\/2162402X.2020.1777625","volume":"9","author":"J Le Naour","year":"2020","unstructured":"Le Naour J, Galluzzi L, Zitvogel L, Kroemer G, Vacchelli E (2020) Trial watch: IDO inhibitors in cancer therapy. Oncoimmunology 9(1):1777625. https:\/\/doi.org\/10.1080\/2162402X.2020.1777625","journal-title":"Oncoimmunology"},{"issue":"2","key":"386_CR23","doi-asserted-by":"publisher","first-page":"185","DOI":"10.4155\/fmc.14.151","volume":"7","author":"T Jiang","year":"2015","unstructured":"Jiang T, Sun Y (2015) Research progress of indoleamine 2,3-dioxygenase inhibitors. Future Med Chem 7(2):185\u2013201. https:\/\/doi.org\/10.4155\/fmc.14.151","journal-title":"Future Med Chem"},{"key":"386_CR24","doi-asserted-by":"publisher","first-page":"423","DOI":"10.3389\/fonc.2018.00423","volume":"8","author":"T Komiya","year":"2018","unstructured":"Komiya T, Huang CH (2018) Updates in the clinical development of epacadostat and other indoleamine 2,3-Dioxygenase 1 inhibitors (IDO1) for human cancers. Front Oncol 8:423. https:\/\/doi.org\/10.3389\/fonc.2018.00423","journal-title":"Front Oncol"},{"issue":"2","key":"386_CR25","doi-asserted-by":"publisher","first-page":"792","DOI":"10.1158\/0008-5472.CAN-06-2925","volume":"67","author":"DY Hou","year":"2007","unstructured":"Hou DY, Muller AJ, Sharma MD, DuHadaway J, Banerjee T, Johnson M, Mellor AL, Prendergast GC, Munn DH (2007) Inhibition of indoleamine 2,3-dioxygenase in dendritic cells by stereoisomers of 1-methyl-tryptophan correlates with antitumor responses. Cancer Res 67(2):792\u2013801. https:\/\/doi.org\/10.1158\/0008-5472.CAN-06-2925","journal-title":"Cancer Res"},{"issue":"23","key":"386_CR26","doi-asserted-by":"publisher","first-page":"7364","DOI":"10.1021\/jm900518f","volume":"52","author":"EW Yue","year":"2009","unstructured":"Yue EW, Douty B, Wayland B, Bower M, Liu X, Leffet L, Wang Q, Bowman KJ, Hansbury MJ, Liu C, Wei M, Li Y, Wynn R, Burn TC, Koblish HK, Fridman JS, Metcalf B, Scherle PA, Combs AP (2009) Discovery of potent competitive inhibitors of indoleamine 2,3-dioxygenase with in vivo pharmacodynamic activity and efficacy in a mouse melanoma model. J Med Chem 52(23):7364\u20137367. https:\/\/doi.org\/10.1021\/jm900518f","journal-title":"J Med Chem"},{"issue":"5","key":"386_CR27","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1021\/acsmedchemlett.6b00391","volume":"8","author":"EW Yue","year":"2017","unstructured":"Yue EW, Sparks R, Polam P, Modi D, Douty B, Wayland B, Glass B, Takvorian A, Glenn J, Zhu W, Bower M, Liu X, Leffet L, Wang Q, Bowman KJ, Hansbury MJ, Wei M, Li Y, Wynn R, Burn TC, Koblish HK, Fridman JS, Emm T, Scherle PA, Metcalf B, Combs AP (2017) INCB24360 (Epacadostat), a Highly Potent and Selective Indoleamine-2,3-dioxygenase 1 (IDO1) Inhibitor for Immuno-oncology. ACS Med Chem Lett 8(5):486\u2013491. https:\/\/doi.org\/10.1021\/acsmedchemlett.6b00391","journal-title":"ACS Med Chem Lett"},{"issue":"1","key":"386_CR28","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1021\/acs.jmedchem.5b01390","volume":"59","author":"YH Peng","year":"2016","unstructured":"Peng YH, Ueng SH, Tseng CT, Hung MS, Song JS, Wu JS, Liao FY, Fan YS, Wu MH, Hsiao WC, Hsueh CC, Lin SY, Cheng CY, Tu CH, Lee LC, Cheng MF, Shia KS, Shih C, Wu SY (2016) Important Hydrogen Bond Networks in Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitor Design Revealed by Crystal Structures of Imidazoleisoindole Derivatives with IDO1. J Med Chem 59(1):282\u2013293. https:\/\/doi.org\/10.1021\/acs.jmedchem.5b01390","journal-title":"J Med Chem"},{"issue":"1","key":"386_CR29","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1186\/s40425-018-0351-9","volume":"6","author":"A Nayak-Kapoor","year":"2018","unstructured":"Nayak-Kapoor A, Hao Z, Sadek R, Dobbins R, Marshall L, Vahanian NN, Jay Ramsey W, Kennedy E, Mautino MR, Link CJ, Lin RS, Royer-Joo S, Liang X, Salphati L, Morrissey KM, Mahrus S, McCall B, Pirzkall A, Munn DH, Janik JE, Khleif SN (2018) Phase Ia study of the indoleamine 2,3-dioxygenase 1 (IDO1) inhibitor navoximod (GDC-0919) in patients with recurrent advanced solid tumors. J Immunother Cancer 6(1):61. https:\/\/doi.org\/10.1186\/s40425-018-0351-9","journal-title":"J Immunother Cancer"},{"issue":"7","key":"386_CR30","doi-asserted-by":"publisher","first-page":"724","DOI":"10.1080\/1061186X.2018.1523416","volume":"27","author":"Y Zhao","year":"2018","unstructured":"Zhao Y, Wang B, Liu J, Sun P, Liu H (2018) An overview on the methods of determining the activity of indoleamine 2, 3-dioxygenase 1. J Drug Target 27(7):724\u2013731. https:\/\/doi.org\/10.1080\/1061186X.2018.1523416","journal-title":"J Drug Target"},{"issue":"9","key":"386_CR31","doi-asserted-by":"publisher","first-page":"3737","DOI":"10.1021\/jm401908w","volume":"57","author":"L Xu","year":"2014","unstructured":"Xu L, Zhang Y, Zheng L, Qiao C, Li Y, Li D, Zhen X, Hou T (2014) Discovery of novel inhibitors targeting the macrophage migration inhibitory factor via structure-based virtual screening and bioassays. J Med Chem 57(9):3737\u20133745. https:\/\/doi.org\/10.1021\/jm401908w","journal-title":"J Med Chem"},{"key":"386_CR32","doi-asserted-by":"publisher","first-page":"16749","DOI":"10.1038\/srep16749","volume":"5","author":"M Shen","year":"2015","unstructured":"Shen M, Tian S, Pan P, Sun H, Li D, Li Y, Zhou H, Li C, Lee SM, Hou T (2015) Discovery of novel ROCK1 inhibitors via integrated virtual screening strategy and bioassays. Sci Rep 5:16749. https:\/\/doi.org\/10.1038\/srep16749","journal-title":"Sci Rep"},{"key":"386_CR33","doi-asserted-by":"publisher","first-page":"277","DOI":"10.3389\/fphar.2018.00277","volume":"9","author":"G Zhang","year":"2018","unstructured":"Zhang G, Xing J, Wang Y, Wang L, Ye Y, Lu D, Zhao J, Luo X, Zheng M, Yan S (2018) Discovery of novel inhibitors of indoleamine 2,3-Dioxygenase 1 through structure-based virtual screening. Front Pharmacol 9:277. https:\/\/doi.org\/10.3389\/fphar.2018.00277","journal-title":"Front Pharmacol"},{"issue":"9","key":"386_CR34","doi-asserted-by":"publisher","first-page":"2713","DOI":"10.1039\/c6mb00343e","volume":"12","author":"CM Chong","year":"2016","unstructured":"Chong CM, Kou MT, Pan P, Zhou H, Ai N, Li C, Zhong HJ, Leung CH, Hou T, Lee SM (2016) Discovery of a novel ROCK2 inhibitor with anti-migration effects via docking and high-content drug screening. Mol Biosyst 12(9):2713\u20132721. https:\/\/doi.org\/10.1039\/c6mb00343e","journal-title":"Mol Biosyst"},{"issue":"6","key":"386_CR35","doi-asserted-by":"publisher","first-page":"1474","DOI":"10.1021\/acs.jcim.7b00188","volume":"57","author":"S Tian","year":"2017","unstructured":"Tian S, Wang X, Li L, Zhang X, Li Y, Zhu F, Hou T, Zhen X (2017) Discovery of novel and selective adenosine A2A receptor antagonists for treating parkinson\u2019s disease through comparative structure-based virtual screening. J Chem Inf Model 57(6):1474\u20131487. https:\/\/doi.org\/10.1021\/acs.jcim.7b00188","journal-title":"J Chem Inf Model"},{"key":"386_CR36","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1016\/j.ejmech.2016.12.029","volume":"126","author":"P Tomek","year":"2017","unstructured":"Tomek P, Palmer BD, Flanagan JU, Sun C, Raven EL, Ching LM (2017) Discovery and evaluation of inhibitors to the immunosuppressive enzyme indoleamine 2,3-dioxygenase 1 (IDO1): Probing the active site-inhibitor interactions. Eur J Med Chem 126:983\u2013996. https:\/\/doi.org\/10.1016\/j.ejmech.2016.12.029","journal-title":"Eur J Med Chem"},{"issue":"45","key":"386_CR37","doi-asserted-by":"publisher","first-page":"25276","DOI":"10.1039\/C9CP04290C","volume":"21","author":"H Zhong","year":"2019","unstructured":"Zhong H, Wang Z, Wang X, Liu H, Li D, Liu H, Yao X, Hou T (2019) Importance of a crystalline water network in docking-based virtual screening: a case study of BRD4. Phys Chem Chem Phys 21(45):25276\u201325289. https:\/\/doi.org\/10.1039\/C9CP04290C","journal-title":"Phys Chem Chem Phys"},{"issue":"6","key":"386_CR38","doi-asserted-by":"publisher","first-page":"3149","DOI":"10.1039\/c9cp06303j","volume":"22","author":"Z Wang","year":"2020","unstructured":"Wang Z, Sun H, Shen C, Hu X, Gao J, Li D, Cao D, Hou T (2020) Combined strategies in structure-based virtual screening. Phys Chem Chem Phys 22(6):3149\u20133159. https:\/\/doi.org\/10.1039\/c9cp06303j","journal-title":"Phys Chem Chem Phys"},{"key":"386_CR39","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1016\/j.ejmech.2017.03.021","volume":"131","author":"Y Zou","year":"2017","unstructured":"Zou Y, Wang F, Wang Y, Guo W, Zhang Y, Xu Q, Lai Y (2017) Systematic study of imidazoles inhibiting IDO1 via the integration of molecular mechanics and quantum mechanics calculations. Eur J Med Chem 131:152\u2013170. https:\/\/doi.org\/10.1016\/j.ejmech.2017.03.021","journal-title":"Eur J Med Chem"},{"key":"386_CR40","doi-asserted-by":"crossref","unstructured":"Schr\u00f6dinger, version 10.1; Schr\u00f6dinger, LLC: New York (2015).","DOI":"10.1063\/pt.5.031026"},{"issue":"28","key":"386_CR41","doi-asserted-by":"publisher","first-page":"6474","DOI":"10.1021\/jp003919d","volume":"105","author":"GA Kaminski","year":"2001","unstructured":"Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem 105(28):6474\u20136487. https:\/\/doi.org\/10.1021\/jp003919d","journal-title":"J Phys Chem"},{"issue":"4","key":"386_CR42","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.ddtec.2004.11.007","volume":"1","author":"CA Lipinski","year":"2004","unstructured":"Lipinski CA (2004) Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today Technol 1(4):337\u2013341. https:\/\/doi.org\/10.1016\/j.ddtec.2004.11.007","journal-title":"Drug Discov Today Technol"},{"issue":"24","key":"386_CR43","doi-asserted-by":"publisher","first-page":"7595","DOI":"10.1016\/j.bmc.2013.10.037","volume":"21","author":"SP Fung","year":"2013","unstructured":"Fung SP, Wang H, Tomek P, Squire CJ, Flanagan JU, Palmer BD, Bridewell DJ, Tijono SM, Jamie JF, Ching LM (2013) Discovery and characterisation of hydrazines as inhibitors of the immune suppressive enzyme, indoleamine 2,3-dioxygenase 1 (IDO1). Bioorg Med Chem 21(24):7595\u20137603. https:\/\/doi.org\/10.1016\/j.bmc.2013.10.037","journal-title":"Bioorg Med Chem"},{"issue":"56","key":"386_CR44","doi-asserted-by":"publisher","first-page":"30814","DOI":"10.18632\/oncotarget.25720","volume":"9","author":"T Richards","year":"2018","unstructured":"Richards T, Brin E (2018) Cell based functional assays for IDO1 inhibitor screening and characterization. Oncotarget 9(56):30814\u201330820. https:\/\/doi.org\/10.18632\/oncotarget.25720","journal-title":"Oncotarget"},{"issue":"4","key":"386_CR45","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1021\/acs.jcim.5b00674","volume":"56","author":"P Li","year":"2016","unstructured":"Li P, Merz KM Jr (2016) MCPBpy: a python based metal center parameter builder. J Chem Inf Model 56(4):599\u2013604. https:\/\/doi.org\/10.1021\/acs.jcim.5b00674","journal-title":"J Chem Inf Model"},{"issue":"8","key":"386_CR46","doi-asserted-by":"publisher","first-page":"818","DOI":"10.1002\/jcc.20221","volume":"26","author":"A Oda","year":"2005","unstructured":"Oda A, Yamaotsu N, Hirono S (2005) New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models. J Comput Chem 26(8):818\u2013826. https:\/\/doi.org\/10.1002\/jcc.20221","journal-title":"J Comput Chem"},{"key":"386_CR47","volume-title":"Gaussian 09","author":"MJ Frisch","year":"2009","unstructured":"Frisch MJ, Schlegel HB, Scuseria GE, Robb MA, Scalmani G, Barone V, Mennucci B, Petersson GA, Caricato HN, Li X, Hratchian HP, Izmaylov AF, Zheng G, Sonnenberg JL, Hada M, Ehara M, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Nakai H, Vreven T, Montgomery JA, Peralta JE, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Kobayashi R, Normand J, Raghavachari K, Burant JC, Iyengar SS, Tomasi J, Cossi M, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Cammi R, Pomelli C, Ochterski JW, Martin RL, Zakrzewski VG, Voth GA, Salvador P, Dapprich S, Daniels AD, Farkas O, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09. Gaussian Inc, Wallingford"},{"issue":"9","key":"386_CR48","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1002\/jcc.20035","volume":"25","author":"W Junmei","year":"2004","unstructured":"Junmei W, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25(9):1157\u20131174. https:\/\/doi.org\/10.1002\/jcc.20035","journal-title":"J Comput Chem"},{"issue":"8","key":"386_CR49","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","volume":"11","author":"JA Maier","year":"2015","unstructured":"Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. J Chem Theory Comput 11(8):3696\u20133713. https:\/\/doi.org\/10.1021\/acs.jctc.5b00255","journal-title":"J Chem Theory Comput"},{"issue":"16","key":"386_CR50","doi-asserted-by":"publisher","first-page":"1668","DOI":"10.1002\/jcc.20290","volume":"26","author":"DA Case","year":"2005","unstructured":"Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem 26(16):1668\u20131688. https:\/\/doi.org\/10.1002\/jcc.20290","journal-title":"J Comput Chem"},{"issue":"28","key":"386_CR51","doi-asserted-by":"publisher","first-page":"8408","DOI":"10.1021\/jp404160y","volume":"117","author":"L Xu","year":"2013","unstructured":"Xu L, Sun H, Li Y, Wang J, Hou T (2013) Assessing the performance of MM\/PBSA and MM\/GBSA methods 3 The impact of force fields and ligand charge models. J Phys Chem B 117(28):8408\u20138421. https:\/\/doi.org\/10.1021\/jp404160y","journal-title":"J Phys Chem B"},{"issue":"31","key":"386_CR52","doi-asserted-by":"publisher","first-page":"16719","DOI":"10.1039\/c4cp01388c","volume":"16","author":"H Sun","year":"2014","unstructured":"Sun H, Li Y, Tian S, Xu L, Hou T (2014) Assessing the performance of MM\/PBSA and MM\/GBSA methods 4 Accuracies of MM\/PBSA and MM\/GBSA methodologies evaluated by various simulation protocols using PDBbind data set. Phys Chem Chem Phys 16(31):16719\u201316729. https:\/\/doi.org\/10.1039\/c4cp01388c","journal-title":"Phys Chem Chem Phys"},{"issue":"1","key":"386_CR53","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1021\/ci100275a","volume":"51","author":"T Hou","year":"2011","unstructured":"Hou T, Wang J, Li Y, Wang W (2011) Assessing the performance of the MM\/PBSA and MM\/GBSA methods 1 the accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model 51(1):69\u201382. https:\/\/doi.org\/10.1021\/ci100275a","journal-title":"J Chem Inf Model"},{"issue":"40","key":"386_CR54","doi-asserted-by":"publisher","first-page":"22035","DOI":"10.1039\/C4CP03179B","volume":"16","author":"H Sun","year":"2014","unstructured":"Sun H, Li Y, Shen M, Tian S, Xu L, Pan P, Guan Y, Hou T (2014) Assessing the performance of MM\/PBSA and MM\/GBSA methods 5 Improved docking performance using high solute dielectric constant MM\/GBSA and MM\/PBSA rescoring. Phys Chem Chem Phys 16(40):22035\u201322045. https:\/\/doi.org\/10.1039\/C4CP03179B","journal-title":"Phys Chem Chem Phys"},{"issue":"9","key":"386_CR55","doi-asserted-by":"publisher","first-page":"3314","DOI":"10.1021\/ct300418h","volume":"8","author":"BR Miller 3rd","year":"2012","unstructured":"Miller BR 3rd, McGee TD Jr, Swails JM, Homeyer N, Gohlke H, Roitberg AE (2012) MMPBSApy: An Efficient Program for End-State Free Energy Calculations. J Chem Theory Comput 8(9):3314\u20133321. https:\/\/doi.org\/10.1021\/ct300418h","journal-title":"J Chem Theory Comput"},{"issue":"7","key":"386_CR56","doi-asserted-by":"publisher","first-page":"1978","DOI":"10.1021\/j100058a043","volume":"98","author":"D Sitkoff","year":"1994","unstructured":"Sitkoff D, Sharp KA, Honig B (1994) Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 98(7):1978\u20131988. https:\/\/doi.org\/10.1021\/j100058a043","journal-title":"J Phys Chem"},{"issue":"3","key":"386_CR57","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1006\/jmbi.1995.0252","volume":"248","author":"DA Pearlman","year":"1995","unstructured":"Pearlman DA, Connelly PR (1995) Determination of the differential effects of hydrogen bonding and water release on the binding of FK506 to native and Tyr82\u2013>Phe82 FKBP-12 proteins using free energy simulations. J Mol Biol 248(3):696\u2013717","journal-title":"J Mol Biol"},{"issue":"4","key":"386_CR58","doi-asserted-by":"publisher","first-page":"1421","DOI":"10.1007\/s00894-011-1159-4","volume":"18","author":"J Guo","year":"2012","unstructured":"Guo J, Wang X, Sun H, Liu H, Yao X (2012) The molecular basis of IGF-II\/IGF2R recognition: a combined molecular dynamics simulation, free-energy calculation and computational alanine scanning study. J Mol Model 18(4):1421\u20131430. https:\/\/doi.org\/10.1007\/s00894-011-1159-4","journal-title":"J Mol Model"},{"issue":"8","key":"386_CR59","doi-asserted-by":"publisher","first-page":"2106","DOI":"10.1039\/c2mb25042j","volume":"8","author":"Y Yang","year":"2012","unstructured":"Yang Y, Liu H, Yao X (2012) Understanding the molecular basis of MK2-p38alpha signaling complex assembly: insights into protein-protein interaction by molecular dynamics and free energy studies. Mol Biosyst 8(8):2106\u20132118. https:\/\/doi.org\/10.1039\/c2mb25042j","journal-title":"Mol Biosyst"},{"key":"386_CR60","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/j.chemolab.2016.03.015","volume":"154","author":"D Pan","year":"2016","unstructured":"Pan D, Niu Y, Xue W, Bai Q, Liu H, Yao X (2016) Computational study on the drug resistance mechanism of hepatitis C virus NS5B RNA-dependent RNA polymerase mutants to BMS-791325 by molecular dynamics simulation and binding free energy calculations. Chemometer Intell Lab Syst 154:185\u2013193. https:\/\/doi.org\/10.1016\/j.chemolab.2016.03.015","journal-title":"Chemometer Intell Lab Syst"},{"issue":"12","key":"386_CR61","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.1007\/s10822-017-0086-6","volume":"31","author":"L Li","year":"2017","unstructured":"Li L, Wei W, Jia WJ, Zhu Y, Zhang Y, Chen JH, Tian J, Liu H, He YX, Yao X (2017) Discovery of small molecules binding to the normal conformation of prion by combining virtual screening and multiple biological activity evaluation methods. J Comput Aided Mol Des 31(12):1053\u20131062. https:\/\/doi.org\/10.1007\/s10822-017-0086-6","journal-title":"J Comput Aided Mol Des"},{"key":"386_CR62","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/j.bbagen.2017.11.022","volume":"3","author":"D Shi","year":"1862","unstructured":"Shi D, Zhou S, Liu X, Zhao C, Liu H (1862) Yao X (2018) Understanding the structural and energetic basis of PD-1 and monoclonal antibodies bound to PD-L1: A molecular modeling perspective. Biochim Biophys Acta Gen Subj 3:576\u2013588. https:\/\/doi.org\/10.1016\/j.bbagen.2017.11.022","journal-title":"Biochim Biophys Acta Gen Subj"},{"issue":"1","key":"386_CR63","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1021\/mp90013p","volume":"7","author":"H Liu","year":"2010","unstructured":"Liu H, Yao X (2010) Molecular basis of the interaction for an essential subunit PA-PB1 in influenza virus RNA polymerase: insights from molecular dynamics simulation and free energy calculation. Mol Pharm 7(1):75\u201385. https:\/\/doi.org\/10.1021\/mp90013p","journal-title":"Mol Pharm"},{"issue":"33","key":"386_CR64","doi-asserted-by":"publisher","first-page":"4323","DOI":"10.1021\/acs.biochem.7b00586","volume":"56","author":"UF Rohrig","year":"2017","unstructured":"Rohrig UF, Zoete V, Michielin O (2017) The binding mode of N-Hydroxyamidines to indoleamine 2,3-Dioxygenase 1 (IDO1). Biochemistry 56(33):4323\u20134325. https:\/\/doi.org\/10.1021\/acs.biochem.7b00586","journal-title":"Biochemistry"},{"issue":"3","key":"386_CR65","doi-asserted-by":"publisher","first-page":"1172","DOI":"10.1021\/jm9014718","volume":"53","author":"UF RoHrig","year":"2010","unstructured":"RoHrig UF, Loay A, Aur\u00e9lien G, Pierre L, Vincent S, Didier C, Vincenzo C, Simpson AJG, Pierre V, Eynde BTJ, Den V (2010) Rational design of indoleamine 2,3-dioxygenase inhibitors. J Med Chem 53(3):1172\u20131189. https:\/\/doi.org\/10.1021\/jm9014718","journal-title":"J Med Chem"},{"issue":"8\u20139","key":"386_CR66","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1002\/minf.201501038","volume":"35","author":"FA Greco","year":"2016","unstructured":"Greco FA, Bournique A, Coletti A, Custodi C, Dolciami D, Carotti A, Macchiarulo A (2016) Docking studies and molecular dynamic simulations reveal different features of IDO1 structure. Mol Inform 35(8\u20139):449\u2013459. https:\/\/doi.org\/10.1002\/minf.201501038","journal-title":"Mol Inform"},{"issue":"11","key":"386_CR67","doi-asserted-by":"publisher","first-page":"5270","DOI":"10.1021\/jm300260v","volume":"55","author":"UF Rohrig","year":"2012","unstructured":"Rohrig UF, Majjigapu SR, Grosdidier A, Bron S, Stroobant V, Pilotte L, Colau D, Vogel P, Van den Eynde BJ, Zoete V, Michielin O (2012) Rational design of 4-aryl-1,2,3-triazoles for indoleamine 2,3-dioxygenase 1 inhibition. J Med Chem 55(11):5270\u20135290. https:\/\/doi.org\/10.1021\/jm300260v","journal-title":"J Med Chem"},{"issue":"5","key":"386_CR68","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1002\/jcc.22885","volume":"33","author":"T Lu","year":"2012","unstructured":"Lu T, Chen F (2012) Multiwfn: a multifunctional wavefunction analyzer. J Comput Chem 33(5):580\u2013592. https:\/\/doi.org\/10.1002\/jcc.22885","journal-title":"J Comput Chem"},{"issue":"1","key":"386_CR69","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"W Humphrey","year":"1996","unstructured":"Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33\u201338. https:\/\/doi.org\/10.1016\/0263-7855(96)00018-5","journal-title":"J Mol Graph"},{"issue":"2","key":"386_CR70","doi-asserted-by":"publisher","first-page":"684","DOI":"10.1021\/jm0508888","volume":"49","author":"P Gaspari","year":"2006","unstructured":"Gaspari P, Banerjee T, Malachowski WP, Muller AJ, Prendergast GC, DuHadaway J, Bennett S, Donovan AM (2006) Structure\u2212activity study of brassinin derivatives as indoleamine 2,3-dioxygenase inhibitors. J Med Chem 49(2):684\u2013692. https:\/\/doi.org\/10.1021\/jm0508888","journal-title":"J Med Chem"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-021-00386-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10822-021-00386-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-021-00386-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,29]],"date-time":"2024-08-29T14:21:08Z","timestamp":1724941268000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10822-021-00386-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,4,27]]},"references-count":70,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2021,5]]}},"alternative-id":["386"],"URL":"https:\/\/doi.org\/10.1007\/s10822-021-00386-6","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"type":"print","value":"0920-654X"},{"type":"electronic","value":"1573-4951"}],"subject":[],"published":{"date-parts":[[2021,4,27]]},"assertion":[{"value":"27 September 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 April 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 April 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}