{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T09:17:36Z","timestamp":1788167856147,"version":"build-2803163510"},"reference-count":46,"publisher":"American Chemical Society (ACS)","issue":"16","license":[{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82304295"],"award-info":[{"award-number":["82304295"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003995","name":"Natural Science Foundation of Anhui Province","doi-asserted-by":"publisher","award":["2308085QH284"],"award-info":[{"award-number":["2308085QH284"]}],"id":[{"id":"10.13039\/501100003995","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009558","name":"University Natural Science Research Project of Anhui Province","doi-asserted-by":"publisher","award":["2022AH051148"],"award-info":[{"award-number":["2022AH051148"]}],"id":[{"id":"10.13039\/501100009558","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/na","name":"Anhui Province Key Laboratory of Infectious Diseases","doi-asserted-by":"publisher","award":["AHIDL-2402R"],"award-info":[{"award-number":["AHIDL-2402R"]}],"id":[{"id":"10.13039\/na","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The rational design of selective kinase inhibitors is hampered by the conserved ATP-binding pockets. Vps34-IN-3, a potent VPS34 inhibitor developed by Genentech, Inc., showed \u223c95-fold selectivity over the closely related PI3K\u03b1, yet the atomic-level mechanism underlying this selectivity remains unclear. Here, we combined supervised molecular dynamics (SuMD) and potential of mean force (PMF) analysis to reconstruct the complete binding and unbinding pathways of Vps34-IN-3 to both targets. Our calculations revealed that selectivity arose primarily from a dramatically higher dissociation barrier for VPS34, leading to a prolonged residence time on the intended target. In VPS34, a persistent hydrogen bond with Ile685 and a hydrophobic socket beneath the P-loop acted as a structural latch, raising the unbinding barrier to 6.37 kcal\/mol. In contrast, the more open PI3K\u03b1 pocket presented a lower barrier of 3.71 kcal\/mol. The computed residence-time ratio (\u223c80-fold) was strongly consistent with the experimentally measured selectivity (\u223c95-fold based on IC50 values), suggesting that the selectivity of Vps34-IN-3 is primarily kinetic in origin. Our integrated SuMD\/PMF framework thus established a kinetic basis for inhibitor selectivity and provided a quantitative, transferable approach for predicting residence time in drug discovery.<\/jats:p>","DOI":"10.1021\/acs.jcim.6c01571","type":"journal-article","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T08:02:04Z","timestamp":1786608124000},"page":"10242-10254","source":"Crossref","is-referenced-by-count":0,"title":["A Kinetic Origin\nof Vps34-IN-3 Selectivity\nfor VPS34 over PI3K\u03b1 Revealed by Supervised Molecular Dynamics\nand Potential of Mean Force Analysis"],"prefix":"10.1021","volume":"66","author":[{"given":"Liang","family":"Yu","sequence":"first","affiliation":[{"name":"The First Affiliated Hospital of Anhui Medical University , , ,","place":["Hefei, China, 230022"]},{"name":"The First Affiliated Hospital of Anhui Medical University , , ,","place":["Hefei, China, 230022"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianqian","family":"Dong","sequence":"additional","affiliation":[{"name":"Anhui Medical University , , ,","place":["Hefei, China, 230032"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiqi","family":"Han","sequence":"additional","affiliation":[{"name":"Anhui Medical University , , ,","place":["Hefei, China, 230032"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Si","family":"Dong","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital of Anhui Medical University , , ,","place":["Hefei, China, 230022"]},{"name":"The First Affiliated Hospital of Anhui Medical University , , ,","place":["Hefei, China, 230022"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoshuai","family":"Cheng","sequence":"additional","affiliation":[{"name":"Anhui Medical University , , ,","place":["Hefei, China, 230032"]},{"name":"The Second Affiliated Hospital, Anhui Medical University , ,","place":["Hefei, China, 230032"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3238-569X","authenticated-orcid":true,"given":"Jiabin","family":"Li","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital of Anhui Medical University , , ,","place":["Hefei, China, 230022"]},{"name":"Anhui Medical University , , ,","place":["Hefei, China, 230032"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2461-4325","authenticated-orcid":true,"given":"Jiqing","family":"Ye","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital of Anhui Medical University , , ,","place":["Hefei, China, 230022"]},{"name":"Anhui Medical University , , ,","place":["Hefei, China, 230032"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,13]]},"reference":[{"key":"2026083104330200400_cit1","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1021\/acs.jcim.5b00702","article-title":"Deciphering the complexity of ligand\u2013protein\nrecognition pathways using supervised molecular dynamics (SuMD) simulations","volume":"56","author":"Cuzzolin","year":"2016","journal-title":"J. Chem. Inf. Model."},{"key":"2026083104330200400_cit2","doi-asserted-by":"publisher","first-page":"5481","DOI":"10.1021\/bi8002023","article-title":"Residence time of receptor\u2013\nligand complexes\nand its effect on biological function","volume":"47","author":"Tummino","year":"2008","journal-title":"Biochemistry"},{"key":"2026083104330200400_cit3","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1016\/j.drudis.2013.02.007","article-title":"Molecular determinants\nof drug\u2013receptor binding kinetics","volume":"18","author":"Pan","year":"2013","journal-title":"Drug\nDiscovery Today"},{"key":"2026083104330200400_cit4","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1021\/acs.jcim.9b00497","article-title":"Residence\ntime prediction of type 1 and 2 kinase inhibitors from unbinding simulations","volume":"60","author":"Braka","year":"2020","journal-title":"J. Chem. Inf. Model."},{"key":"2026083104330200400_cit5","doi-asserted-by":"publisher","first-page":"2251","DOI":"10.1042\/BCJ20160170","article-title":"The intricate\nregulation and complex functions of the Class III phosphoinositide\n3-kinase Vps34","volume":"473","author":"Backer","year":"2016","journal-title":"Biochem. J."},{"key":"2026083104330200400_cit6","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1146\/annurev-biochem-061516-044820","article-title":"Mechanisms of autophagy\ninitiation","volume":"86","author":"Hurley","year":"2017","journal-title":"Annu. Rev. Biochem."},{"key":"2026083104330200400_cit7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1042\/BJ20071427","article-title":"The regulation\nand function of Class III PI3Ks: novel roles for Vps34","volume":"410","author":"Backer","year":"2008","journal-title":"Biochem. J."},{"issue":"18","key":"2026083104330200400_cit8","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aax7881","article-title":"Inhibition of Vps34\nreprograms cold into hot inflamed tumors and improves anti\u2013PD-1\/PD-L1\nimmunotherapy","volume":"6","author":"Noman","year":"2020","journal-title":"Sci. Adv."},{"issue":"5","key":"2026083104330200400_cit9","doi-asserted-by":"publisher","DOI":"10.1002\/cmdc.202400580","article-title":"Virtual Screening and\nBiological Evaluation of Natural Products as Novel VPS34 Inhibitors\nthat Modulate Autophagy","volume":"20","author":"Feng","year":"2025","journal-title":"ChemMedChem"},{"key":"2026083104330200400_cit10","doi-asserted-by":"publisher","first-page":"4656","DOI":"10.1021\/acs.jmedchem.7b01019","article-title":"Design of\nsmall molecule autophagy\nmodulators: a promising druggable strategy","volume":"61","author":"He","year":"2018","journal-title":"J. Med. Chem."},{"key":"2026083104330200400_cit11","doi-asserted-by":"publisher","first-page":"1638","DOI":"10.1126\/science.1184429","article-title":"Shaping development\nof autophagy\ninhibitors with the structure of the lipid kinase Vps34","volume":"327","author":"Miller","year":"2010","journal-title":"Science"},{"issue":"12","key":"2026083104330200400_cit12","doi-asserted-by":"publisher","first-page":"1013","DOI":"10.1038\/nchembio.1681","article-title":"A highly potent and\nselective Vps34 inhibitor alters vesicle trafficking and autophagy","volume":"10","author":"Ronan","year":"2014","journal-title":"Nat. Chem. Biol."},{"issue":"10","key":"2026083104330200400_cit13","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1038\/s41389-020-00278-8","article-title":"Antileukemic activity of the VPS34-IN1 inhibitor in\nacute myeloid leukemia","volume":"9","author":"Meunier","year":"2020","journal-title":"Oncogenesis"},{"issue":"17","key":"2026083104330200400_cit14","doi-asserted-by":"publisher","first-page":"11500","DOI":"10.1021\/acs.jmedchem.1c01180","article-title":"Structure-based design\nof potent, selective, and orally bioavailable VPS34 kinase inhibitors","volume":"65","author":"Hu","year":"2022","journal-title":"J. Med. Chem."},{"key":"2026083104330200400_cit15","doi-asserted-by":"publisher","first-page":"3703","DOI":"10.1007\/s11030-025-11330-3","article-title":"Understanding the structural stability and plasticity of VPS34 protein\ndetermined by selective\/nonselective inhibitors: insights from molecular\ndynamics simulations","volume":"30","author":"Yu","year":"2026","journal-title":"Mol. Diversity"},{"key":"2026083104330200400_cit16","doi-asserted-by":"publisher","first-page":"12788","DOI":"10.1021\/acs.chemrev.0c00534","article-title":"Thermodynamics and\nkinetics of drug-target binding\nby molecular simulation","volume":"120","author":"Decherchi","year":"2020","journal-title":"Chem. Rev."},{"key":"2026083104330200400_cit17","doi-asserted-by":"publisher","first-page":"7736","DOI":"10.1039\/D5NJ00498E","article-title":"A hinge motif unveils the cryptic\nstructural determinants of selective inhibitors towards PI3K\u03b1\nand VPS34","volume":"49","author":"Wang","year":"2025","journal-title":"New J. Chem."},{"key":"2026083104330200400_cit18","doi-asserted-by":"publisher","first-page":"1882","DOI":"10.1021\/acs.jctc.9b01153","article-title":"Transient\nstates and barriers from\nmolecular simulations and the milestoning theory: Kinetics in ligand\u2013protein\nrecognition and compound design","volume":"16","author":"Tang","year":"2020","journal-title":"J. Chem. Theory\nComput."},{"key":"2026083104330200400_cit19","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1016\/j.tibs.2022.11.003","article-title":"Advances in computational methods for ligand binding\nkinetics","volume":"48","author":"Sohraby","year":"2023","journal-title":"Trends Biochem. Sci."},{"key":"2026083104330200400_cit20","doi-asserted-by":"publisher","first-page":"13118","DOI":"10.1073\/pnas.1104614108","article-title":"Pathway and mechanism\nof drug binding to G-protein-coupled receptors","volume":"108","author":"Dror","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026083104330200400_cit21","doi-asserted-by":"publisher","first-page":"5649","DOI":"10.1021\/acs.jctc.3c00660","article-title":"Kinetics from\nmetadynamics: Principles, applications,\nand outlook","volume":"19","author":"Ray","year":"2023","journal-title":"J. Chem. Theory Comput."},{"key":"2026083104330200400_cit22","doi-asserted-by":"publisher","first-page":"1473","DOI":"10.1021\/acs.jcim.8b00261","article-title":"Steered molecular\ndynamics simulation\nin rational drug design","volume":"58","author":"Do","year":"2018","journal-title":"J. Chem. Inf. Model."},{"issue":"7","key":"2026083104330200400_cit23","doi-asserted-by":"publisher","first-page":"3859","DOI":"10.1021\/acs.jctc.8b00230","article-title":"Estimation of drug-target\nresidence times by \u03c4-random acceleration molecular dynamics\nsimulations","volume":"14","author":"Kokh","year":"2018","journal-title":"J. Chem. Theory Comput."},{"key":"2026083104330200400_cit24","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1021\/ci400766b","article-title":"Supervised molecular\ndynamics (SuMD) as a helpful tool to depict\nGPCR\u2013ligand recognition pathway in a nanosecond time scale","volume":"54","author":"Sabbadin","year":"2014","journal-title":"J. Chem. Inf. Model."},{"key":"2026083104330200400_cit25","doi-asserted-by":"publisher","first-page":"1804","DOI":"10.1021\/acs.jcim.9b01094","article-title":"A supervised molecular dynamics approach\nto unbiased ligand\u2013protein unbinding","volume":"60","author":"Deganutti","year":"2020","journal-title":"J. Chem. Inf. Model."},{"issue":"4","key":"2026083104330200400_cit26","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1016\/j.str.2017.02.009","article-title":"Exploring\nprotein-peptide\nrecognition pathways using a supervised molecular dynamics approach","volume":"25","author":"Salmaso","year":"2017","journal-title":"Structure"},{"issue":"3","key":"2026083104330200400_cit27","doi-asserted-by":"publisher","first-page":"985","DOI":"10.1021\/acs.jmedchem.5b01483","article-title":"The Rational Design\nof Selective Benzoxazepin Inhibitors of the \u03b1-Isoform\nof Phosphoinositide 3-Kinase Culminating in the Identification of\n(S)-2-((2-(1-Isopropyl-1 H-1, 2, 4-triazol-5-yl)-5, 6-dihydrobenzo\n[f] imidazo [1, 2-d][1, 4] oxazepin-9-yl) oxy) propanamide (GDC-0326)","volume":"59","author":"Heffron","year":"2016","journal-title":"J. Med. Chem."},{"key":"2026083104330200400_cit28","doi-asserted-by":"publisher","first-page":"43891","DOI":"10.1021\/acsomega.5c04628","article-title":"Structural Modeling of NTPDase-Substrate Complexes\nPreserving Catalytic Experimental Features","volume":"10","author":"de Moraes","year":"2025","journal-title":"ACS Omega"},{"issue":"25","key":"2026083104330200400_cit29","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2500a visualization\nsystem for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"issue":"1","key":"2026083104330200400_cit30","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1021\/acs.jctc.9b00591","article-title":"ff19SB: amino-acid-specific\nprotein backbone parameters trained against quantum mechanics energy\nsurfaces in solution","volume":"16","author":"Tian","year":"2020","journal-title":"J. Chem. Theory Comput."},{"key":"2026083104330200400_cit31","doi-asserted-by":"publisher","first-page":"114502","DOI":"10.1063\/5.0019056","article-title":"A fast and\nhigh-quality charge model for the next generation general AMBER force\nfield","volume":"153","author":"He","year":"2020","journal-title":"J. Chem. Phys."},{"key":"2026083104330200400_cit32","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison\nof simple potential functions for simulating liquid water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J. Chem. Phys."},{"issue":"5","key":"2026083104330200400_cit33","doi-asserted-by":"publisher","first-page":"5045","DOI":"10.1103\/PhysRevE.59.5045","article-title":"Mechanical\nand Langevin thermostats: Gulton staircase problem","volume":"59","author":"Munakata","year":"1999","journal-title":"Phys. Rev. E"},{"issue":"1","key":"2026083104330200400_cit34","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1063\/1.1420460","article-title":"Constant pressure hybrid Molecular\nDynamics\u2013Monte\nCarlo simulations","volume":"116","author":"Faller","year":"2002","journal-title":"J. Chem. Phys."},{"key":"2026083104330200400_cit35","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1002\/1096-987X(20010415)22:5&lt;501::AID-JCC1021&gt;3.0.CO;2-V","article-title":"A fast SHAKE algorithm\nto solve distance constraint equations for small molecules in molecular\ndynamics simulations","volume":"22","author":"Kra\u0308utler","year":"2001","journal-title":"J. Comput. Chem."},{"key":"2026083104330200400_cit36","doi-asserted-by":"publisher","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A smooth particle\nmesh Ewald method","volume":"103","author":"Essmann","year":"1995","journal-title":"J. Chem. Phys."},{"key":"2026083104330200400_cit37","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1023\/A:1008763014207","article-title":"Combined molecular\nmechanical and continuum solvent\napproach (MM-PBSA\/GBSA) to predict ligand binding","volume":"18","author":"Massova","year":"2000","journal-title":"Perspect. Drug Discovery Des."},{"issue":"20","key":"2026083104330200400_cit38","doi-asserted-by":"publisher","first-page":"6183","DOI":"10.1021\/acs.jcim.3c01153","article-title":"AmberTools","volume":"63","author":"Case","year":"2023","journal-title":"J. Chem. Inf. Model."},{"key":"2026083104330200400_cit39","doi-asserted-by":"publisher","first-page":"1528","DOI":"10.1016\/j.bpj.2015.08.015","article-title":"MDTraj: a modern\nopen library for the analysis of molecular\ndynamics trajectories","volume":"109","author":"McGibbon","year":"2015","journal-title":"Biophys. J."},{"key":"2026083104330200400_cit40","doi-asserted-by":"publisher","first-page":"2319","DOI":"10.1002\/jcc.21787","article-title":"MDAnalysis:\na toolkit for the analysis of molecular dynamics simulations","volume":"32","author":"Michaud-Agrawal","year":"2011","journal-title":"J. Comput. Chem."},{"key":"2026083104330200400_cit41","doi-asserted-by":"publisher","first-page":"4584","DOI":"10.1021\/acs.jctc.7b00500","article-title":"POVME 3.0: Software for mapping binding\npocket flexibility","volume":"13","author":"Wagner","year":"2017","journal-title":"J. Chem. Theory Comput."},{"key":"2026083104330200400_cit42","unstructured":"Alan, G.\n          ,  WHAM: the weighted histogram\nanalysis method, version 2.1.0; http:\/\/membrane.urmc.rochester.edu\/wordpress\/?page_id=126."},{"key":"2026083104330200400_cit43","doi-asserted-by":"publisher","first-page":"1895","DOI":"10.1021\/acs.jcim.7b00075","article-title":"Characterizing\ndrug\u2013target residence time with metadynamics: How to achieve\ndissociation rate efficiently without losing accuracy against time-consuming\napproaches","volume":"57","author":"Sun","year":"2017","journal-title":"J. Chem. Inf. Model."},{"key":"2026083104330200400_cit44","doi-asserted-by":"publisher","first-page":"968","DOI":"10.1021\/acs.jcim.7b00640","article-title":"Role of molecular\ninteractions and protein rearrangement\nin the dissociation kinetics of p38\u03b1 MAP kinase type-I\/II\/III\ninhibitors","volume":"58","author":"You","year":"2018","journal-title":"J. Chem. Inf. Model."},{"key":"2026083104330200400_cit45","doi-asserted-by":"publisher","first-page":"5622","DOI":"10.1039\/C5CP06257H","article-title":"Computational study\non the unbinding pathways of B-RAF inhibitors and its implication\nfor the difference of residence time: insight from random acceleration\nand steered molecular dynamics simulations","volume":"18","author":"Niu","year":"2016","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2026083104330200400_cit46","doi-asserted-by":"publisher","first-page":"1632","DOI":"10.1021\/ct9000685","article-title":"ACEMD: accelerating biomolecular\ndynamics in the microsecond time scale","volume":"5","author":"Harvey","year":"2009","journal-title":"J. Chem.\nTheory Comput."}],"container-title":["Journal of Chemical Information\nand Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.6c01571","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/66\/16\/10242\/66521798\/acs.jcim.6c01571.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/66\/16\/10242\/66521798\/acs.jcim.6c01571.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T08:33:45Z","timestamp":1788165225000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article\/66\/16\/10242\/5254081\/A-Kinetic-Origin-of-Vps34-IN-3-Selectivity-for"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,13]]},"references-count":46,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2026,8,13]]},"published-print":{"date-parts":[[2026,8,24]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.6c01571","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,13]]}}}