{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:58:27Z","timestamp":1782280707939,"version":"3.54.5"},"posted":{"date-parts":[[2025,9,27]]},"group-title":"Biophysics","reference-count":63,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,9,27]],"date-time":"2025-09-27T00:00:00Z","timestamp":1758931200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,9,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Capsid assembly modulators (CAMs) represent a promising antiviral strategy against hepatitis B virus (HBV), but their effects on preformed capsids remain incompletely understood. Here, all-atom molecular dynamics (MD) simulations of intact HBV capsids complexed with prototypical CAM-As (HAP1, HAP18) and CAM-Es (AT130), reveal how structural changes induced by small molecule binding in the interdimer interfaces propagate through the shell lattice to yield global morphological consequences. Each quasi-equivalent interface exhibits a unique response: A sites, located within the pentameric capsomers, are unfilled in these systems and altered marginally by the presence of CAMs in neighboring interfaces. B sites are the most open and \u201cCAM-ready,\u201d suggesting uptake requires minimal conformational perturbation on the local or global level. C sites emerge as hubs of allosteric control and the key drug target, as their occupancy creates local distortion that is broadcast to adjacent sites, driving capsid faceting and \u2013 in the case of CAM-As \u2013 the destabilization that precedes dissociation in favor of aberrant assembly. D sites, unfilled in these systems, act as structural sinks, absorbing distortions from adjacent interfaces within the hexameric capsomers. The extent of C site adjustment and the nature of D site counterbalance varies with CAM chemotype, highlighting the divergent effects of CAM-As versus CAM-Es. The tensegrity relationship between the four quasi-equivalent interfaces couples them into a global network for strain redistribution that is functionally allosteric, with CAM binding sites displaying signs of both positive and negative cooperativity. These new insights into HBV capsid dynamics clarify how CAMs alter them on the microsecond timescale and suggest that targeting strain redistribution in mature core particles could be leveraged therapeutically.<\/jats:p>\n                <jats:sec>\n                  <jats:title>Author summary<\/jats:title>\n                  <jats:p>Hepatitis B is a major cause of chronic liver disease worldwide. The virus relies on a protein shell, called the capsid, to protect and deliver its genetic material to the host cell during infection. Some experimental drug molecules attack this shell, either forcing it to assemble incorrectly or breaking it apart after it has formed. To understand how these molecules work, we used powerful computer simulations to model the capsid at the level of individual atoms. We discovered that when molecules bind the capsid at certain sites, they create strain that spreads across the shell, sometimes leading to large distortions and instability. These insights explain how small molecules can disrupt the virus and point the way toward designing better antiviral therapies.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.09.24.678444","type":"posted-content","created":{"date-parts":[[2025,9,28]],"date-time":"2025-09-28T05:55:11Z","timestamp":1759038911000},"source":"Crossref","is-referenced-by-count":1,"title":["Mechanistic insights into CAM-induced disruption of HBV capsids revealed by all-atom MD simulations"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8766-789X","authenticated-orcid":false,"given":"Carolina","family":"P\u00e9rez-Segura","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0292-0922","authenticated-orcid":false,"given":"Boon Chong","family":"Goh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4685-8291","authenticated-orcid":false,"given":"Jodi A.","family":"Hadden-Perilla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"issue":"6","key":"2025093015201154000_2025.09.24.678444v1.1","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1016\/S2468-1253(24)00089-X","article-title":"WHO 2024 hepatitis B guidelines: an opportunity to transform care","volume":"9","year":"2024","journal-title":"The lancet Gastroenterology & hepatology"},{"issue":"1","key":"2025093015201154000_2025.09.24.678444v1.2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.7774\/cevr.2020.9.1.1","article-title":"Hepatitis B vaccination and immunotherapies: an update","volume":"9","year":"2020","journal-title":"Clinical and experimental vaccine research"},{"issue":"1","key":"2025093015201154000_2025.09.24.678444v1.3","doi-asserted-by":"crossref","first-page":"48","DOI":"10.3748\/wjg.v13.i1.48","article-title":"Hepatitis B virus replication","volume":"13","year":"2007","journal-title":"World journal of gastroenterology: WJG"},{"issue":"1","key":"2025093015201154000_2025.09.24.678444v1.4","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1146\/annurev-virology-110615-042238","article-title":"The structural biology of hepatitis B virus: form and function","volume":"3","year":"2016","journal-title":"Annual review of virology"},{"issue":"5","key":"2025093015201154000_2025.09.24.678444v1.5","doi-asserted-by":"crossref","first-page":"757","DOI":"10.3390\/v13050757","article-title":"Early steps of hepatitis B life cycle: from capsid nuclear import to cccDNA formation","volume":"13","year":"2021","journal-title":"Viruses"},{"key":"2025093015201154000_2025.09.24.678444v1.6","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a021394"},{"issue":"2","key":"2025093015201154000_2025.09.24.678444v1.7","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1021\/acs.jcim.7b00471","article-title":"Identification of factors promoting HBV capsid self-assembly by assembly-promoting antivirals","volume":"58","year":"2018","journal-title":"J Chem Inf Model"},{"key":"2025093015201154000_2025.09.24.678444v1.8","doi-asserted-by":"publisher","DOI":"10.1038\/386091a0"},{"key":"2025093015201154000_2025.09.24.678444v1.9","doi-asserted-by":"publisher","DOI":"10.1016\/S1097-2765(01)80009-5"},{"key":"2025093015201154000_2025.09.24.678444v1.10","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02033-09"},{"key":"2025093015201154000_2025.09.24.678444v1.11","doi-asserted-by":"publisher","DOI":"10.1021\/acschembio.0c00481"},{"key":"2025093015201154000_2025.09.24.678444v1.12","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.4c08871"},{"key":"2025093015201154000_2025.09.24.678444v1.13","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00933-06"},{"key":"2025093015201154000_2025.09.24.678444v1.14","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2013.06.013"},{"key":"2025093015201154000_2025.09.24.678444v1.15","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.03058-15"},{"issue":"8","key":"2025093015201154000_2025.09.24.678444v1.16","first-page":"10","article-title":"Capsid assembly modulators have a dual mechanism of action in primary human hepatocytes infected with hepatitis B virus","volume":"61","year":"2017","journal-title":"Antimicrobial agents and chemotherapy"},{"key":"2025093015201154000_2025.09.24.678444v1.17","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01360-08"},{"key":"2025093015201154000_2025.09.24.678444v1.18","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0409732102"},{"key":"2025093015201154000_2025.09.24.678444v1.19","doi-asserted-by":"publisher","DOI":"10.1021\/cb100275b"},{"key":"2025093015201154000_2025.09.24.678444v1.20","doi-asserted-by":"crossref","first-page":"105080","DOI":"10.1016\/j.antiviral.2021.105080","article-title":"Identification of hepatitis B virus core protein residues critical for capsid assembly, pgRNA encapsidation and resistance to capsid assembly modulators","volume":"191","year":"2021","journal-title":"Antiviral research"},{"issue":"5","key":"2025093015201154000_2025.09.24.678444v1.21","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.3390\/jcm11051349","article-title":"Capsid assembly modulators as antiviral agents against HBV: molecular mechanisms and clinical perspectives","volume":"11","year":"2022","journal-title":"Journal of Clinical Medicine"},{"issue":"6","key":"2025093015201154000_2025.09.24.678444v1.22","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1021\/acschembio.0c00320","article-title":"Local Stabilization of Subunit-Subunit Contacts Causes Global Destabilization of Hepatitis B Virus Capsids","volume":"15","year":"2020","journal-title":"ACS Chem Biol"},{"key":"2025093015201154000_2025.09.24.678444v1.23","doi-asserted-by":"crossref","first-page":"103082","DOI":"10.1016\/j.sbi.2025.103082","article-title":"Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff","volume":"93","year":"2025","journal-title":"Current Opinion in Structural Biology"},{"key":"2025093015201154000_2025.09.24.678444v1.24","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpclett.6b00517"},{"key":"2025093015201154000_2025.09.24.678444v1.25","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.32478"},{"issue":"4","key":"2025093015201154000_2025.09.24.678444v1.26","doi-asserted-by":"crossref","first-page":"564","DOI":"10.3390\/v13040564","article-title":"All-atom MD simulations of the HBV capsid complexed with AT130 reveal secondary and tertiary structural changes and mechanisms of allostery","volume":"13","year":"2021","journal-title":"Viruses"},{"key":"2025093015201154000_2025.09.24.678444v1.27","doi-asserted-by":"publisher","DOI":"10.7554\/Elife.31473"},{"key":"2025093015201154000_2025.09.24.678444v1.28","doi-asserted-by":"crossref","unstructured":"Kim C , Schlicksup CJ , P\u00e9rez-Segura C , Hadden-Perilla JA , Wang JCY , Zlotnick Structure of the hepatitis B virus capsid quasi-6-fold with a trapped Cterminal domain reveals capsid movements associated with domain exit. Journal of Biological Chemistry. 2023;299(9).","DOI":"10.1016\/j.jbc.2023.105104"},{"key":"2025093015201154000_2025.09.24.678444v1.29","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.18.9556"},{"key":"2025093015201154000_2025.09.24.678444v1.30","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.1c02040"},{"key":"2025093015201154000_2025.09.24.678444v1.31","doi-asserted-by":"publisher","DOI":"10.1167\/9.8.25"},{"issue":"12","key":"2025093015201154000_2025.09.24.678444v1.32","doi-asserted-by":"crossref","first-page":"5104","DOI":"10.1021\/acs.jcim.9b01010","article-title":"Heteroaryldihydropyrimidines alter capsid assembly by adjusting the binding affinity and pattern of the Hepatitis B virus core protein","volume":"59","year":"2019","journal-title":"J Chem Inf Model"},{"issue":"20","key":"2025093015201154000_2025.09.24.678444v1.33","first-page":"e01082","article-title":"Assembly properties of hepatitis B virus core protein mutants correlate with their resistance to assembly-directed antivirals","volume":"92","year":"2018","journal-title":"J Virol"},{"issue":"8","key":"2025093015201154000_2025.09.24.678444v1.34","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1021\/acschembio.8b00283","article-title":"An assembly-activating site in the hepatitis B virus capsid protein can also trigger disassembly","volume":"13","year":"2018","journal-title":"ACS Chemical Biology"},{"key":"2025093015201154000_2025.09.24.678444v1.35","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibs.2008.05.009"},{"key":"2025093015201154000_2025.09.24.678444v1.36","unstructured":"Fuller RB , Applewhite E. Synergetics: Explorations in the geometry of thinking. Macmillan Publishing Co. Inc.; 1998."},{"key":"2025093015201154000_2025.09.24.678444v1.37","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2013.02.021"},{"key":"2025093015201154000_2025.09.24.678444v1.38","doi-asserted-by":"publisher","DOI":"10.1021\/bi049571k"},{"key":"2025093015201154000_2025.09.24.678444v1.39","doi-asserted-by":"crossref","unstructured":"Zoulim F , Zlotnick A , Buchholz S , Donaldson E , Fry J , Gaggar A , et al. Nomen-clature of HBV core protein-targeting antivirals. Nat Rev Gastroenterol Hepatol. 2022:1\u20133.","DOI":"10.1038\/s41575-022-00700-z"},{"key":"2025093015201154000_2025.09.24.678444v1.40","doi-asserted-by":"crossref","unstructured":"Pang YT , Pavlova A , Tajkhorshid E , Gumbart JC . Parameterization of a drug molecule with a halogen \u03c3-hole particle using ffTK: Implementation, testing, and comparison. The Journal of Chemical Physics. 2020;153(16).","DOI":"10.1063\/5.0022802"},{"key":"2025093015201154000_2025.09.24.678444v1.41","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1513803112"},{"key":"2025093015201154000_2025.09.24.678444v1.42","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-36219-3"},{"issue":"2","key":"2025093015201154000_2025.09.24.678444v1.43","first-page":"e01395","article-title":"Core Protein-Directed Antivirals and Importin \u03b2 Can Synergistically Disrupt Hepatitis B Virus Capsids","volume":"96","year":"2022","journal-title":"Journal of virology"},{"issue":"47","key":"2025093015201154000_2025.09.24.678444v1.44","doi-asserted-by":"crossref","first-page":"11565","DOI":"10.1021\/acs.jpcb.4c05060","article-title":"Effect of Pregenomic RNA on the Mechanical Stability of HBV Capsid by Coarse-Grained Molecular Simulations","volume":"128","year":"2024","journal-title":"The Journal of Physical Chemistry B"},{"key":"2025093015201154000_2025.09.24.678444v1.45","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01912-13"},{"key":"2025093015201154000_2025.09.24.678444v1.46","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2012.04.012"},{"key":"2025093015201154000_2025.09.24.678444v1.47","doi-asserted-by":"publisher","DOI":"10.3390\/v9030056"},{"key":"2025093015201154000_2025.09.24.678444v1.48","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1006658"},{"key":"2025093015201154000_2025.09.24.678444v1.49","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2016.02.009"},{"key":"2025093015201154000_2025.09.24.678444v1.50","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2021.05.013"},{"issue":"12","key":"2025093015201154000_2025.09.24.678444v1.51","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.3390\/pathogens13121100","article-title":"Targeting HBV cccDNA levels: key to achieving complete cure of chronic hepatitis B","volume":"13","year":"2024","journal-title":"Pathogens"},{"issue":"1","key":"2025093015201154000_2025.09.24.678444v1.52","doi-asserted-by":"crossref","first-page":"62","DOI":"10.3390\/biom15010062","article-title":"HBV cccDNA: The Molecular Reservoir of Hepatitis B Persistence and Challenges to Achieve Viral Eradication","volume":"15","year":"2025","journal-title":"Biomolecules"},{"key":"2025093015201154000_2025.09.24.678444v1.53","doi-asserted-by":"publisher","DOI":"10.1021\/ct300400x"},{"key":"2025093015201154000_2025.09.24.678444v1.54","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21367"},{"key":"2025093015201154000_2025.09.24.678444v1.55","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23422"},{"key":"2025093015201154000_2025.09.24.678444v1.56","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"2025093015201154000_2025.09.24.678444v1.57","unstructured":"Frisch MJ . Gaussian 03 Rev. E. 01. http:\/\/wwwgaussiancom\/. 2004."},{"key":"2025093015201154000_2025.09.24.678444v1.58","doi-asserted-by":"publisher","DOI":"10.1016\/B978-0-12-381270-4.00019-6"},{"issue":"8","key":"2025093015201154000_2025.09.24.678444v1.59","doi-asserted-by":"crossref","first-page":"1414","DOI":"10.1016\/j.str.2015.05.017","article-title":"Atomic modeling of an immature retroviral lattice using molecular dynamics and mutagenesis","volume":"23","year":"2015","journal-title":"Structure"},{"key":"2025093015201154000_2025.09.24.678444v1.60","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm276"},{"key":"2025093015201154000_2025.09.24.678444v1.61","doi-asserted-by":"publisher","DOI":"10.1063\/1.445869"},{"key":"2025093015201154000_2025.09.24.678444v1.62","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20289"},{"key":"2025093015201154000_2025.09.24.678444v1.63","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.9b00324"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.09.24.678444","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:06:53Z","timestamp":1782277613000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.09.24.678444"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,27]]},"references-count":63,"URL":"https:\/\/doi.org\/10.1101\/2025.09.24.678444","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1371\/journal.ppat.1013566","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2025,9,27]]},"subtype":"preprint"}}