{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T17:03:41Z","timestamp":1790096621185,"version":"4.0.1"},"reference-count":27,"publisher":"American Chemical Society (ACS)","issue":"37","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006502","name":"Defense Sciences Office, DARPA","doi-asserted-by":"publisher","award":["HR001123S0038-ABC-FP-010"],"award-info":[{"award-number":["HR001123S0038-ABC-FP-010"]}],"id":[{"id":"10.13039\/100006502","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>General anesthetics such as propofol and etomidate exert their clinical effects primarily through positive allosteric modulation of \u03b3-aminobutyric acid type A receptors (GABAAR). Despite decades of research, the quantitative structure\u2013activity relationships governing anesthetic binding remain incompletely characterized at the atomic level. Here, we employ rigorous alchemical free energy perturbation (FEP) calculations using a CHARMm GPU-accelerated protocol to compute relative binding free energies for a series of 13 propofol analogs at the wild-type GABAAR, as well as for the stereoisomeric pair of etomidate (R-etomidate vs S-etomidate). For propofol analogs at the wild-type receptor, computed relative binding free energies (\u0394\u0394G) correlate with experimentally measured GABA EC50 potentiation values, with propofol (2,6-diisopropylphenol) and disec-butylphenol predicted as the most potent analogs, consistent with experimental data (Pearson r = 0.85, 95% CI 0.50\u20130.96, p = 0.001; mean of three independent runs). For etomidate, FEP calculations correctly predict that R-etomidate binds approximately 1.8 kcal\/mol more favorably than S-etomidate, corresponding to a \u223c10-fold difference in potency consistent with the known stereoselective pharmacology of this agent. These results demonstrate that alchemical FEP calculations, implemented through a standardized computational protocol, can quantitatively rank-order anesthetic binding affinities and discriminate stereoisomeric preferences at Cys-loop receptor binding sites, providing a framework for rational design of next-generation anesthetic agents that is more quantitatively robust than simple molecular docking methodologies.<\/jats:p>","DOI":"10.1021\/acsomega.6c08745","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T20:02:36Z","timestamp":1788984156000},"page":"56651-56663","source":"Crossref","is-referenced-by-count":0,"title":["Alchemical Free\nEnergy Perturbation Predicts Relative\nBinding Affinities of Propofol Analogs and Etomidate Stereoisomers\nat the GABAAR"],"prefix":"10.1021","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4879-2302","authenticated-orcid":true,"given":"Pritam Kumar","family":"Panda","sequence":"first","affiliation":[{"name":"Stanford University School of Medicine , , , ,","place":["Stanford, California, United States, 94305"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9062-0566","authenticated-orcid":true,"given":"Edward J.","family":"Bertaccini","sequence":"additional","affiliation":[{"name":"Stanford University School of Medicine , , , ,","place":["Stanford, California, United States, 94305"]},{"name":"Palo Alto VA Health Care System , , , ,","place":["Palo Alto, California, United States, 94304"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"issue":"7","key":"2026092211023489400_cit1","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1016\/j.tips.2019.05.001","article-title":"Towards\na Comprehensive Understanding of Anesthetic Mechanisms of Action:\nA Decade of Discovery","volume":"40","author":"Hemmings","year":"2019","journal-title":"Trends Pharmacol. Sci."},{"issue":"1","key":"2026092211023489400_cit2","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/j.neuropharm.2008.07.045","article-title":"GABA A receptors: subtypes provide diversity of function\nand pharmacology","volume":"56","author":"Olsen","year":"2009","journal-title":"Neuropharmacology"},{"key":"2026092211023489400_cit3","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1007\/3-540-28082-0_9","article-title":"Pathophysiology\nand pharmacology of GABA(A) receptors","volume-title":"Handbook of Experimental Pharmacology","author":"Mo\u0308hler","year":"2005"},{"issue":"2","key":"2026092211023489400_cit4","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1007\/s00441-006-0284-3","article-title":"GABA(A) receptor\ndiversity and pharmacology","volume":"326","author":"Mo\u0308hler","year":"2006","journal-title":"Cell Tissue Res."},{"issue":"7330","key":"2026092211023489400_cit5","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1038\/nature09647","article-title":"X-ray structures\nof general anaesthetics bound to a\npentameric ligand-gated ion channel","volume":"469","author":"Nury","year":"2011","journal-title":"Nature"},{"issue":"7740","key":"2026092211023489400_cit6","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1038\/s41586-018-0832-5","article-title":"GABAA receptor signalling mechanisms revealed\nby structural pharmacology","volume":"565","author":"Masiulis","year":"2019","journal-title":"Nature"},{"issue":"31","key":"2026092211023489400_cit7","doi-asserted-by":"publisher","first-page":"15706","DOI":"10.1073\/pnas.1822076116","article-title":"A newly developed anesthetic based\non a unique chemical core","volume":"116","author":"Cayla","year":"2019","journal-title":"Proc. Natl. Acad.\nSci. U.S.A."},{"issue":"7","key":"2026092211023489400_cit8","doi-asserted-by":"publisher","first-page":"10779","DOI":"10.18632\/oncotarget.14616","article-title":"Functional sites for anesthetics in GABAA receptors","volume":"8","author":"Maldifassi","year":"2017","journal-title":"Oncotarget"},{"issue":"7824","key":"2026092211023489400_cit9","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1038\/s41586-020-2654-5","article-title":"Shared\nstructural mechanisms of general anaesthetics and benzodiazepines","volume":"585","author":"Kim","year":"2020","journal-title":"Nature"},{"issue":"1","key":"2026092211023489400_cit10","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1016\/S0022-3565(24)29544-6","article-title":"General anesthetic\npotencies of a series of propofol\nanalogs correlate with potency for potentiation of gamma-aminobutyric\nacid (GABA) current at the GABA(A) receptor but not with lipid solubility","volume":"297","author":"Krasowski","year":"2001","journal-title":"J. Pharmacol. Exp. Ther."},{"issue":"12","key":"2026092211023489400_cit11","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.1021\/jm00186a013","article-title":"Synthesis, biological\nevaluation, and preliminary structure-activity\nconsiderations of a series of alkylphenols as intravenous anesthetic\nagents","volume":"23","author":"James","year":"1980","journal-title":"J. Med. Chem."},{"issue":"20","key":"2026092211023489400_cit12","doi-asserted-by":"publisher","first-page":"11031","DOI":"10.1073\/pnas.94.20.11031","article-title":"The interaction\nof the general anesthetic etomidate with the gamma-aminobutyric acid\ntype A receptor is influenced by a single amino acid","volume":"94","author":"Belelli","year":"1997","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"issue":"6","key":"2026092211023489400_cit13","doi-asserted-by":"publisher","first-page":"1235","DOI":"10.1097\/ALN.0b013e3182567df3","article-title":"Two etomidate\nsites in \u03b11\u03b22\u03b32\n\u03b3-aminobutyric acid type A receptors contribute equally and\nnoncooperatively to modulation of channel gating","volume":"116","author":"Guitchounts","year":"2012","journal-title":"Anesthesiology"},{"issue":"2","key":"2026092211023489400_cit14","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1096\/fj.02-0611fje","article-title":"General anesthetic actions in vivo strongly\nattenuated by a point mutation in the GABA(A) receptor beta3 subunit","volume":"17","author":"Jurd","year":"2003","journal-title":"FASEB J."},{"issue":"8","key":"2026092211023489400_cit15","doi-asserted-by":"publisher","first-page":"1420","DOI":"10.1063\/1.1740409","article-title":"High-Temperature\nEquation of State by a Perturbation Method. I. Nonpolar Gases","volume":"22","author":"Zwanzig","year":"1954","journal-title":"J. Chem. Phys."},{"issue":"3","key":"2026092211023489400_cit16","doi-asserted-by":"publisher","first-page":"638","DOI":"10.1021\/acs.jmedchem.7b00681","article-title":"Free Energy\nMethods in Drug Design:\nProspects of \u2033Alchemical Perturbation\u2033 in Medicinal\nChemistry","volume":"61","author":"Williams-Noonan","year":"2018","journal-title":"J. Med. Chem."},{"issue":"7","key":"2026092211023489400_cit17","doi-asserted-by":"publisher","first-page":"2695","DOI":"10.1021\/ja512751q","article-title":"Accurate and reliable\nprediction of relative ligand binding potency\nin prospective drug discovery by way of a modern free-energy calculation\nprotocol and force field","volume":"137","author":"Wang","year":"2015","journal-title":"J. Am. Chem. Soc."},{"issue":"12","key":"2026092211023489400_cit18","doi-asserted-by":"publisher","first-page":"2911","DOI":"10.1021\/acs.jcim.7b00564","article-title":"Relative Binding\nFree Energy Calculations\nin Drug Discovery: Recent Advances and Practical Considerations","volume":"57","author":"Cournia","year":"2017","journal-title":"J. Chem. Inf. Model."},{"issue":"13","key":"2026092211023489400_cit20","doi-asserted-by":"publisher","first-page":"1549","DOI":"10.1002\/jcc.10306","article-title":"Detailed analysis of\ngrid-based molecular docking: A case study of CDOCKER-A CHARMm-based\nMD docking algorithm","volume":"24","author":"Wu","year":"2003","journal-title":"J. Comput. Chem."},{"issue":"2","key":"2026092211023489400_cit21","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1213\/01.ane.0000253029.67331.8d","article-title":"The common chemical motifs within\nanesthetic binding sites","volume":"104","author":"Bertaccini","year":"2007","journal-title":"Anesth. Analg."},{"issue":"5","key":"2026092211023489400_cit22","doi-asserted-by":"publisher","first-page":"924","DOI":"10.1038\/sj.bjp.0702164","article-title":"Binding, gating,\naffinity and efficacy: the interpretation of structure-activity relationships\nfor agonists and of the effects of mutating receptors","volume":"125","author":"Colquhoun","year":"1998","journal-title":"Br. J. Pharmacol."},{"issue":"4","key":"2026092211023489400_cit23","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1002\/jcc.21367","article-title":"CHARMM general\nforce field: A force field for drug-like molecules compatible with\nthe CHARMM all-atom additive biological force fields","volume":"31","author":"Vanommeslaeghe","year":"2010","journal-title":"J. Comput. Chem."},{"issue":"10","key":"2026092211023489400_cit24","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1021\/ct300180w","article-title":"Treatment of Halogen\nBonding in the OPLS-AA Force Field;\nApplication to Potent Anti-HIV Agents","volume":"8","author":"Jorgensen","year":"2012","journal-title":"J. Chem.\nTheory Comput"},{"issue":"40","key":"2026092211023489400_cit25","doi-asserted-by":"publisher","first-page":"12771","DOI":"10.1021\/acs.jpcb.5b05897","article-title":"Insights into the Nature of Anesthetic-Protein\nInteractions: An ONIOM Study","volume":"119","author":"Qiu","year":"2015","journal-title":"J. Phys. Chem.\nB"},{"issue":"1","key":"2026092211023489400_cit26","doi-asserted-by":"publisher","DOI":"10.33011\/livecoms.2.1.18378","article-title":"Best Practices\nfor Alchemical Free Energy Calculations\n[Article v1.0]","volume":"2","author":"Mey","year":"2020","journal-title":"Living J. Comput. Mol. Sci."},{"key":"2026092211023489400_cit27","unstructured":"Bertaccini, E. J.\n          \n          The Application of Alchemical Free\nEnergy Perturbation Calculations\nto More Robust Correlations of Anesthetic-Protein Binding Energies\nwith Potency [Poster presentation]\n          International\nSociety for Anesthetic Pharmacology (ISAP) Annual Meeting\n          2022."},{"issue":"3","key":"2026092211023489400_cit28","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1097\/ALN.0b013e3181ff72b5","article-title":"Clinical\nand molecular pharmacology of etomidate","volume":"114","author":"Forman","year":"2011","journal-title":"Anesthesiology"}],"container-title":["ACS Omega"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acsomega.6c08745","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/11\/37\/56651\/68465040\/acsomega.6c08745.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/11\/37\/56651\/68465040\/acsomega.6c08745.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T16:04:18Z","timestamp":1790093058000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/acsodf\/article\/11\/37\/56651\/5427300\/Alchemical-Free-Energy-Perturbation-Predicts"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,9]]},"references-count":27,"journal-issue":{"issue":"37","published-online":{"date-parts":[[2026,9,9]]},"published-print":{"date-parts":[[2026,9,22]]}},"URL":"https:\/\/doi.org\/10.1021\/acsomega.6c08745","relation":{},"ISSN":["2470-1343"],"issn-type":[{"value":"2470-1343","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,9]]}}}