{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T01:06:52Z","timestamp":1785546412380,"version":"3.56.0"},"reference-count":38,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computational Biology and Chemistry"],"published-print":{"date-parts":[[2026,10]]},"DOI":"10.1016\/j.compbiolchem.2026.109182","type":"journal-article","created":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T23:15:35Z","timestamp":1781738135000},"page":"109182","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"P2","title":["Structure-based discovery of PARP15 inhibitors with enhanced binding energetics and stability via quantum refinement for targeted breast cancer therapy"],"prefix":"10.1016","volume":"124","author":[{"given":"Najah","family":"Albadari","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed","family":"Alafnan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-9067-4397","authenticated-orcid":false,"given":"Mohammed A.","family":"Almuhayfir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-9415-5683","authenticated-orcid":false,"given":"Abdulaziz F.","family":"Alsaud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0047-6238","authenticated-orcid":false,"given":"Ahmed A.","family":"Alhamzani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed A.","family":"Aljohani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amr S.","family":"Abouzied","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.compbiolchem.2026.109182_bib1","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1002\/jcb.30232","article-title":"Structure-based virtual screening and biological evaluation of novel inhibitors of mycobacterium Z-ring formation","volume":"123","author":"Alexey","year":"2022","journal-title":"J. Cell. Biochem."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib2","doi-asserted-by":"crossref","unstructured":"Almeleebia T.M., Ahamad S., Ahmad I., et al (n.d.). Frontiers | Identification of PARP12 Inhibitors By Virtual Screening and Molecular Dynamics Simulations. https:\/\/doi.org\/10.3389\/fphar.2022.847499.","DOI":"10.3389\/fphar.2022.847499"},{"key":"10.1016\/j.compbiolchem.2026.109182_bib3","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1038\/s41416-024-02827-z","article-title":"BRCA-mutated breast cancer: the unmet need, challenges and therapeutic benefits of genetic testing","volume":"131","author":"Arun","year":"2024","journal-title":"Br. J. Cancer"},{"key":"10.1016\/j.compbiolchem.2026.109182_bib4","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib5","doi-asserted-by":"crossref","unstructured":"Bowers K., Chow E., Xu H., et al (2006) Molecular Dynamics---Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters. p 84.","DOI":"10.1145\/1188455.1188544"},{"key":"10.1016\/j.compbiolchem.2026.109182_bib6","unstructured":"Breast cancer. \u3008https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/breast-cancer\u3009. Accessed 4 Feb 2026."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib7","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1002\/jcc.20290","article-title":"The Amber biomolecular simulation programs","volume":"26","author":"Case","year":"2005","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib8","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.1501240","article-title":"Regulation of protein-ligand binding affinity by hydrogen bond pairing","volume":"2","author":"Chen","year":"2016","journal-title":"Sci. Adv."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib9","series-title":"Protein Dynamics","first-page":"193","article-title":"Principal Component Analysis: A Method for Determining the Essential Dynamics of Proteins","author":"David","year":"2014"},{"key":"10.1016\/j.compbiolchem.2026.109182_bib10","unstructured":"E P, P M, P F, et al (n.d.)Free-energy Landscape, Principal Component Analysis, and Structural Clustering to Identify Representative Conformations from Molecular Dynamics Simulations: the Myoglobin Case. PubMed."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib11","unstructured":"E W, H L, J W, et al (2020) Development and Evaluation of MM\/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities. PubMed."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib12","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1140\/epjst\/e2011-01525-9","article-title":"SHAKE parallelization","volume":"200","author":"Elber","year":"2011","journal-title":"Eur. Phys. J. Spec. Top."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib13","first-page":"1","article-title":"Descriptive epidemiology of female breast cancer around the world: incidence, mortality, and sociodemographic risks and disparities","author":"Elhawary","year":"2025","journal-title":"Int. J. Environ. Health Res."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib14","doi-asserted-by":"crossref","DOI":"10.1016\/j.physa.2019.122210","article-title":"Langevin thermostat for robust configurational and kinetic sampling","volume":"534","author":"Farago","year":"2019","journal-title":"Phys. Stat. Mech. Appl."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib15","doi-asserted-by":"crossref","first-page":"2695","DOI":"10.1093\/bioinformatics\/btl461","article-title":"Bio3d: an R package for the comparative analysis of protein structures","volume":"22","author":"Grant","year":"2006","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2026.109182_bib16","unstructured":"H H, B C, D Z, G H (2020) Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods. PubMed."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib17","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1002\/minf.201100135","article-title":"Free energy calculations by the molecular mechanics Poisson\u2212 Boltzmann surface area method","volume":"31","author":"Homeyer","year":"2012","journal-title":"Mol. Inform."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib18","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1208\/s12248-014-9621-8","article-title":"Many approved drugs have bioactive analogs with different target annotations","volume":"16","author":"Hu","year":"2014","journal-title":"AAPS J."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib19","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib20","unstructured":"J E, D S-M, Af T, S F (2021) AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. PubMed."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib21","first-page":"24","article-title":"It is important to compute intramolecular hydrogen bonding in drug design?","volume":"5","author":"J. R","year":"2017","journal-title":"Am. J. Model. Optim."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib22","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiolchem.2020.107322","article-title":"Geo-measures: a PyMOL plugin for protein structure ensembles analysis","volume":"87","author":"Kagami","year":"2020","journal-title":"Comput. Biol. Chem."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib23","first-page":"1","article-title":"Global patterns and trends in breast cancer incidence and mortality across 185 countries","author":"Kim","year":"2025","journal-title":"Nat. Med."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib24","doi-asserted-by":"crossref","first-page":"W448","DOI":"10.1093\/nar\/gkv306","article-title":"MTiOpenScreen: a web server for structure-based virtual screening","volume":"43","author":"Labb\u00e9","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib25","doi-asserted-by":"crossref","first-page":"2043","DOI":"10.1021\/acs.jcim.8b00462","article-title":"GPU-accelerated molecular dynamics and free energy methods in Amber18: performance enhancements and new features","volume":"58","author":"Lee","year":"2018","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib26","doi-asserted-by":"crossref","first-page":"9954","DOI":"10.1021\/jp003020w","article-title":"Structure and dynamics of the TIP3P, SPC, and SPC\/E water models at 298 K","volume":"105","author":"Mark","year":"2001","journal-title":"J. Phys. Chem. A"},{"key":"10.1016\/j.compbiolchem.2026.109182_bib27","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1186\/1471-2105-7-339","article-title":"Tools for integrated sequence-structure analysis with UCSF Chimera","volume":"7","author":"Meng","year":"2006","journal-title":"BMC Bioinforma."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib28","doi-asserted-by":"crossref","first-page":"480","DOI":"10.2174\/1570180819666220922103109","article-title":"Molecular docking: principles, advances, and its applications in DrugDiscovery","volume":"21","author":"Muhammed","year":"2024","journal-title":"Lett. Drug. Des. Discov."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib29","doi-asserted-by":"crossref","first-page":"10093","DOI":"10.1021\/jo301612a","article-title":"Density Functional Theory (B3LYP) Study of Substituent Effects on O\u2013H Bond Dissociation Enthalpies of trans-Resveratrol Derivatives and the Role of Intramolecular Hydrogen Bonds","volume":"77","author":"Nazarparvar","year":"2012","journal-title":"J. Org. Chem."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib30","doi-asserted-by":"crossref","first-page":"22","DOI":"10.3390\/ph17010022","article-title":"Computer-Aided drug design and drug discovery: a prospective analysis","volume":"17","author":"Niazi","year":"2023","journal-title":"Pharmaceuticals"},{"key":"10.1016\/j.compbiolchem.2026.109182_bib31","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.physe.2016.01.024","article-title":"Density Functional Theory (DFT) modeling and Monte Carlo simulation assessment of inhibition performance of some carbohydrazide Schiff bases for steel corrosion","volume":"80","author":"Obot","year":"2016","journal-title":"Phys. E Low. -Dimens. Syst. Nanostruct."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib32","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera--a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib33","doi-asserted-by":"crossref","first-page":"3878","DOI":"10.1021\/ct400314y","article-title":"Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald","volume":"9","author":"Salomon-Ferrer","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib34","unstructured":"The Root Mean Square Deviations (RMSD) plots. RMSDs for (A) Apripitant;\u2026 | Download Scientific Diagram. \u3008https:\/\/www.researchgate.net\/figure\/The-Root-Mean-Square-Deviations-RMSD-plots-RMSDs-for-A-Apripitant-B-Barnidipine_fig1_344309089\u3009. Accessed 7 Apr 2025."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib35","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib36","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1002\/jcc.20035","article-title":"Development and testing of a general amber force field","volume":"25","author":"Wang","year":"2004","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib37","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.bbrc.2022.06.070","article-title":"Crystal structures of the catalytic domain of human PARP15 in complex with small molecule inhibitors","volume":"622","author":"Zhou","year":"2022","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"10.1016\/j.compbiolchem.2026.109182_bib38","article-title":"Immunotherapy resistance in triple-negative breast cancer: molecular mechanisms, tumor microenvironment, and therapeutic implications","volume":"15","author":"Zhou","year":"2025","journal-title":"Front. Oncol."}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927126003087?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927126003087?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T23:42:45Z","timestamp":1785541365000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927126003087"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10]]},"references-count":38,"alternative-id":["S1476927126003087"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2026.109182","relation":{},"ISSN":["1476-9271"],"issn-type":[{"value":"1476-9271","type":"print"}],"subject":[],"published":{"date-parts":[[2026,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Structure-based discovery of PARP15 inhibitors with enhanced binding energetics and stability via quantum refinement for targeted breast cancer therapy","name":"articletitle","label":"Article Title"},{"value":"Computational Biology and Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2026.109182","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"109182"}}