{"id":30,"date":"2024-04-23T10:10:36","date_gmt":"2024-04-23T08:10:36","guid":{"rendered":"https:\/\/urbinocamdlab.wordpress.com\/?page_id=30"},"modified":"2026-09-01T09:58:38","modified_gmt":"2026-09-01T09:58:38","slug":"group_publications","status":"publish","type":"page","link":"https:\/\/camd.uniurb.it\/?page_id=30","title":{"rendered":"Publications"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>2026<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Sotillo N\u00fa\u00f1ez D, et al. Cholesterol Hot spot Automated Mapping Protocol (CHAMP): Identifying Cholesterol-Binding Hot Spots in Membrane Proteins. J Chem Inf Model. (2026). Accepted manuscript.<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Elisi GM, et al. <a href=\"https:\/\/pubs.acs.org\/aidcbc\/article\/doi\/10.1021\/acsinfecdis.6c00079\/5322741\">Second Generation of 2,2\u2032-Di(indol-3-yl)ethanamines as Antileishmanial Agents: Phenotypic Hit Identification and Pharmacophore Studies<\/a>. ACS Infect. Dis. (2026). Accepted manuscript.<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Peter S, et al. <a href=\"https:\/\/pubs.acs.org\/jcisd8\/article\/doi\/10.1021\/acs.jcim.6c00526\/5277363\/Residue-Interaction-Network-Reveals-Allosteric\">Residue Interaction Network Reveals Allosteric Pathways Linking Orthosteric and Intracellular Sites in Class A GPCRs<\/a>. J Chem Inf Model. (2026). Accepted manuscript.<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Coricello A, et al. <a href=\"https:\/\/www.eurekaselect.com\/article\/157389\">Bioisosteric Replacement of Carboxylic Acids in PPAR Agonists: A Mini Review.<\/a> Curr Top Med Chem. (2026). Accepted manuscript.<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Evangelista D, et al. <a href=\"https:\/\/pubs.acs.org\/jmcmar\/article\/69\/13\/14992\/5166709\/Machine-Learning-Based-Models-to-Predict-Drug\">Machine Learning-Based Models to Predict Drug-Induced Liver Injury (DILI) to Assist Medicinal Chemistry<\/a>. J. Med. Chem. 69(13):14992\u201315008&nbsp;(2026).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Wolf S, Bottegoni G, Nunes-Alves A, Wade R. Where do we go from here? <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1359644626001091\">Current state of drug\u2013target binding kinetics and a roadmap to their establishment in drug discovery campaigns<\/a>. Drug Discov. Today. 31(4):104704 (2026).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Yeon Kwon S, et al. <a href=\"https:\/\/academic.oup.com\/nar\/article\/54\/10\/gkag494\/8688746\">Combinatorial histone modifications direct ATP-dependent chromatin remodeling by NURF to promoter-proximal nucleosomes<\/a>. Nucleic Acids Res. 54, 10 (2026).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Aguti R et al. <a href=\"https:\/\/pubs.acs.org\/jcisd8\/article\/66\/7\/4187\/5138337\/Critical-Assessment-of-a-Structure-Based-Pipeline\">Critical Assessment of a Structure-Based Pipeline for Targeting the Long Noncoding RNA MALAT1<\/a>. J. Chem. Inf. Model. 66(7):4187\u20134201 (2026).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Brookes K, et al. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2352396426000460?via%3Dihub\">Disulfiram metabolite Cu(DDC)<sub>2<\/sub>&nbsp;enhances radionuclide uptake in vivo revealing insights into tumoural ablation resistance<\/a>. eBioMedicine. 125, 106165 (2026).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Bedini et al. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0223523425012103\">N-Acylaminoethyltetrahydroquinolines: A new class of melatonin receptor ligands with in vivo activity on glioblastoma<\/a>. Eur. J. Med. Chem. 303:118445 (2026).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>2025<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Retini M, et al. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1043661825004621\">Pyrazolone-based ERO1 inhibitors in ERO1-driven triple-negative breast cancer and SEPN1-related myopathy: Structure\u2013activity relationship and therapeutic potential<\/a>. Pharmacol. Res. 222, 108037 (2025).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Bresciani V, et al. <a href=\"https:\/\/pubs.acs.org\/jcisd8\/article\/65\/21\/11965\/3688161\/Dissecting-the-RAD51-BRC4-Interaction-Landscape\">Dissecting the RAD51\u2013BRC4 Interaction Landscape through Integrative Molecular Simulations and Experimental Biophysics<\/a>. J. Chem. Inf. Model. 65(21):11965\u201311978 (2025).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Elisi GM &amp; Bottegoni G. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0163725825001172\">Impact of G protein-coupled receptor conformation on signaling bias: Integrating simulations and biophysical experiments<\/a>. Pharmacology and Therapeutics 274, 108905 (2025).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Di Martino RMC, et al. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0223523425006646\" data-type=\"link\" data-id=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0223523425006646\">Rational optimization of D3R\/GSK-3\u03b2 dual target-directed ligands as potential treatment for bipolar disorder: Design, synthesis, X-ray crystallography, molecular dynamics simulations, in vitro ADME, and in vivo pharmacokinetic studies<\/a>. Eur J Med Chem. 297, 117899 (2025).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Coricello A, et al. <a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.5c00601\">Adiabatic-Bias Molecular Dynamics Simulations Reveal the Impact of Mutations on Muscarinic Antagonist Unbinding Kinetics<\/a>. J Chem Inf Model. 65(13):7129\u20137142 (2025).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Serra E, et al. <a href=\"https:\/\/pubs.acs.org\/doi\/full\/10.1021\/acs.jcim.5c00452\">Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein\u2013Ligand to RNA-Ligand Binding<\/a>. J Chem Inf Model. 65(12):6057\u20136072 (2025).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Varone E, et al. <a href=\"https:\/\/www.nature.com\/articles\/s41419-025-07426-1\" data-type=\"link\" data-id=\"https:\/\/www.nature.com\/articles\/s41419-025-07426-1\">Small molecule-mediated inhibition of the oxidoreductase ERO1A restrains aggressive breast cancer by impairing VEGF and PD-L1 in the tumor microenvironment<\/a>. Cell Death and Disease. 16(1):105 (2025).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Evangelista D, et al. <a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.4c02293\">Application of Deep Learning to Predict the Persistence, Bioaccumulation, and Toxicity of Pharmaceuticals<\/a>. J Chem Inf Model. 65(7):3248\u20133261 (2025).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>2024<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Peter S, Siragusa L, Thomas M, Palomba T, Cross S, O&#8217;Boyle NM, Bajusz D, Ferenczy GG, Keser\u0171 GM, Bottegoni G, Bender B, Chen I, De Graaf C. <a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.4c00819\">Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential<\/a>. J Chem Inf Model. 64(21):8176-8192. (2024)<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Zia S. R., Coricello A. &amp; Bottegoni G. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0959440X24000988\">Increased throughput in methods for simulating protein ligand binding and unbinding<\/a>. Curr. Opin. Struct. Biol. 87, 102871 (2024)<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Lembo V. &amp; Bottegoni G. <a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jmedchem.4c00838\">Systematic Investigation of Dual-Target-Directed Ligands<\/a>. J. Med. Chem. 67, 10374-10385 (2024).<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=%22J+Med+Chem%22%5Bjour%5D&amp;sort=date&amp;sort_order=desc\"><\/a><\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>2023<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Basagni F. et al. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0223523423007705?via%3Dihub\">Galantamine-memantine hybrids for Alzheimer\u2019s disease: The influence of linker rigidity in biological activity and pharmacokinetic properties<\/a>. Eur. J. Med. Chem. 261, 115803 (2023).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Buigues P. J. et al. <a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jctc.3c00023\">Investigating the Unbinding of Muscarinic Antagonists from the Muscarinic 3 Receptor<\/a>. J. Chem. Theory Comput. 19, 5260\u20135272 (2023).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>2022<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Lunerti V. et al. <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0014299922003491\">The multitarget FAAH inhibitor\/D3 partial agonist ARN15381 decreases nicotine self-administration in male rats. Eur. J. Pharmacol. 928, 175088<\/a> (2022).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Di Martino R. M. C., Cavalli A. &amp; Bottegoni G. <a href=\"https:\/\/www.tandfonline.com\/doi\/full\/10.1080\/13543776.2022.2049240\">Dopamine D3 receptor ligands: a patent review (2014\u20132020)<\/a>. Expert Opin. Ther. Pat. 32, 605\u2013627 (2022).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>2021<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Clayton S. A. et al. <a href=\"https:\/\/www.science.org\/doi\/10.1126\/sciadv.abl5182?url_ver=Z39.88-2003&amp;rfr_id=ori:rid:crossref.org&amp;rfr_dat=cr_pub%20%200pubmed\">Inflammation causes remodeling of mitochondrial cytochrome c oxidase mediated by the bifunctional gene C15orf48<\/a>. Sci. Adv. 7, 22\u201324 (2021).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><p style=\"text-align:justify\">Di Fruscia P. et al. <a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jmedchem.1c00575\">Discovery and SAR Evolution of Pyrazole Azabicyclo[3.2.1]octane Sulfonamides as a Novel Class of Non-Covalent N-Acylethanolamine-Hydrolyzing Acid Amidase (NAAA) Inhibitors for Oral Administration<\/a>. J. Med. Chem. 64, 13327\u201313355 (2021).<\/p><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>2026 Sotillo N\u00fa\u00f1ez D, et al. Cholesterol Hot spot Automated Mapping Protocol (CHAMP): Identifying Cholesterol-Binding Hot Spots in Membrane Proteins. J Chem Inf Model. (2026). Accepted manuscript. Elisi GM, et al. Second Generation of 2,2\u2032-Di(indol-3-yl)ethanamines as Antileishmanial Agents: Phenotypic Hit Identification and Pharmacophore Studies. ACS Infect. Dis. (2026). Accepted manuscript. Peter S, et al. Residue [&hellip;]<\/p>\n","protected":false},"author":6,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_editorskit_title_hidden":false,"_editorskit_reading_time":0,"_editorskit_is_block_options_detached":false,"_editorskit_block_options_position":"{}","footnotes":""},"class_list":["post-30","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/camd.uniurb.it\/index.php?rest_route=\/wp\/v2\/pages\/30","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/camd.uniurb.it\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/camd.uniurb.it\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/camd.uniurb.it\/index.php?rest_route=\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/camd.uniurb.it\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=30"}],"version-history":[{"count":14,"href":"https:\/\/camd.uniurb.it\/index.php?rest_route=\/wp\/v2\/pages\/30\/revisions"}],"predecessor-version":[{"id":392,"href":"https:\/\/camd.uniurb.it\/index.php?rest_route=\/wp\/v2\/pages\/30\/revisions\/392"}],"wp:attachment":[{"href":"https:\/\/camd.uniurb.it\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=30"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}