{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T03:39:08Z","timestamp":1764733148614,"version":"3.46.0"},"reference-count":84,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T00:00:00Z","timestamp":1764720000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T00:00:00Z","timestamp":1764720000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100001411","name":"Indian Council of Medical Research","doi-asserted-by":"publisher","award":["DDR\/IIRPIG-2024\/02509"],"award-info":[{"award-number":["DDR\/IIRPIG-2024\/02509"]}],"id":[{"id":"10.13039\/501100001411","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2026,12]]},"DOI":"10.1007\/s10822-025-00724-y","type":"journal-article","created":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T03:33:39Z","timestamp":1764732819000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Targeting the deSUMOylase Ulp2 in Candida glabrata for antifungal therapies: in silico identification of silymarin and honokiol as potential inhibitors"],"prefix":"10.1007","volume":"40","author":[{"given":"Dipika","family":"Gupta","sequence":"first","affiliation":[]},{"given":"Sowmya","family":"Andole","sequence":"additional","affiliation":[]},{"given":"Krishnaveni","family":"Mishra","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,12,3]]},"reference":[{"key":"724_CR1","doi-asserted-by":"publisher","first-page":"e428","DOI":"10.1016\/S1473-3099(23)00692-8","volume":"24","author":"DW Denning","year":"2024","unstructured":"Denning DW (2024) Global incidence and mortality of severe fungal disease. Lancet Infect Dis 24:e428\u2013e438. https:\/\/doi.org\/10.1016\/S1473-3099(23)00692-8","journal-title":"Lancet Infect Dis"},{"key":"724_CR2","doi-asserted-by":"publisher","first-page":"S445","DOI":"10.1093\/infdis\/jix131","volume":"216","author":"MC Arendrup","year":"2017","unstructured":"Arendrup MC, Patterson TF (2017) Multidrug-resistant Candida: epidemiology, molecular mechanisms, and treatment. J Infect Dis 216:S445\u2013S451. https:\/\/doi.org\/10.1093\/infdis\/jix131","journal-title":"J Infect Dis"},{"key":"724_CR3","doi-asserted-by":"publisher","first-page":"1287","DOI":"10.2147\/IDR.S249864","volume":"13","author":"M Ademe","year":"2020","unstructured":"Ademe M, Girma F (2020) Candida auris: from multidrug resistance to pan-resistant strains. Infect Drug Resist 13:1287\u20131294. https:\/\/doi.org\/10.2147\/IDR.S249864","journal-title":"Infect Drug Resist"},{"key":"724_CR4","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2217948119","author":"A McDermott","year":"2022","unstructured":"McDermott A (2022) Drug-resistant fungi on the rise. Proc Natl Acad Sci U S A. https:\/\/doi.org\/10.1073\/pnas.2217948119","journal-title":"Proc Natl Acad Sci U S A"},{"key":"724_CR5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1009005","volume":"16","author":"L Simonicova","year":"2020","unstructured":"Simonicova L, Moye-Rowley WS (2020) Functional information from clinically-derived drug resistant forms of the Candida glabrata Pdr1 transcription factor. PLoS Genet 16:e1009005. https:\/\/doi.org\/10.1371\/journal.pgen.1009005","journal-title":"PLoS Genet"},{"key":"724_CR6","doi-asserted-by":"publisher","first-page":"4690","DOI":"10.1128\/AAC.03255-14","volume":"58","author":"CD Pham","year":"2014","unstructured":"Pham CD, Iqbal N, Bolden CB, Kuykendall RJ, Harrison LH, Farley MM et al (2014) Role of FKS mutations in Candida glabrata: MIC values, echinocandin resistance, and multidrug resistance. Antimicrob Agents Chemother 58:4690\u20134696. https:\/\/doi.org\/10.1128\/AAC.03255-14","journal-title":"Antimicrob Agents Chemother"},{"issue":"Suppl 6","key":"724_CR7","doi-asserted-by":"publisher","first-page":"S612","DOI":"10.1093\/cid\/civ791","volume":"61","author":"DS Perlin","year":"2015","unstructured":"Perlin DS (2015) Echinocandin resistance in Candida. Clin Infect Dis 61(Suppl 6):S612-617. https:\/\/doi.org\/10.1093\/cid\/civ791","journal-title":"Clin Infect Dis"},{"key":"724_CR8","doi-asserted-by":"publisher","first-page":"3690","DOI":"10.1128\/AAC.00443-09","volume":"53","author":"G Garcia-Effron","year":"2009","unstructured":"Garcia-Effron G, Lee S, Park S, Cleary JD, Perlin DS (2009) Effect of Candida glabrata FKS1 and FKS2 mutations on echinocandin sensitivity and kinetics of 1,3-beta-D-glucan synthase: implication for the existing susceptibility breakpoint. Antimicrob Agents Chemother 53:3690\u20133699. https:\/\/doi.org\/10.1128\/AAC.00443-09","journal-title":"Antimicrob Agents Chemother"},{"key":"724_CR9","doi-asserted-by":"publisher","DOI":"10.7759\/cureus.16445","volume":"13","author":"V Gursoy","year":"2021","unstructured":"Gursoy V, Ozkalemkas F, Ozkocaman V, Serenli Yegen Z, Ethem Pinar I, Ener B et al (2021) Conventional amphotericin B associated nephrotoxicity in patients with hematologic malignancies. Cureus 13:e16445. https:\/\/doi.org\/10.7759\/cureus.16445","journal-title":"Cureus"},{"key":"724_CR10","doi-asserted-by":"publisher","first-page":"9","DOI":"10.4103\/0253-7613.62396","volume":"42","author":"ND Grover","year":"2010","unstructured":"Grover ND (2010) Echinocandins: a ray of hope in antifungal drug therapy. Indian J Pharmacol 42:9\u201311. https:\/\/doi.org\/10.4103\/0253-7613.62396","journal-title":"Indian J Pharmacol"},{"key":"724_CR11","doi-asserted-by":"publisher","first-page":"3110","DOI":"10.1111\/febs.15319","volume":"287","author":"AB Celen","year":"2020","unstructured":"Celen AB, Sahin U (2020) Sumoylation on its 25th anniversary: mechanisms, pathology, and emerging concepts. FEBS J 287:3110\u20133140. https:\/\/doi.org\/10.1111\/febs.15319","journal-title":"FEBS J"},{"key":"724_CR12","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s12929-024-01003-y","volume":"31","author":"C-H Huang","year":"2024","unstructured":"Huang C-H, Yang T-T, Lin K-I (2024) Mechanisms and functions of SUMOylation in health and disease: a review focusing on immune cells. J Biomed Sci 31:16. https:\/\/doi.org\/10.1186\/s12929-024-01003-y","journal-title":"J Biomed Sci"},{"key":"724_CR13","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1038\/nrm2293","volume":"8","author":"R Geiss-Friedlander","year":"2007","unstructured":"Geiss-Friedlander R, Melchior F (2007) Concepts in sumoylation: a decade on. Nat Rev Mol Cell Biol 8:947\u2013956. https:\/\/doi.org\/10.1038\/nrm2293","journal-title":"Nat Rev Mol Cell Biol"},{"key":"724_CR14","doi-asserted-by":"publisher","first-page":"26799","DOI":"10.1074\/jbc.272.43.26799","volume":"272","author":"ES Johnson","year":"1997","unstructured":"Johnson ES, Blobel G (1997) Ubc9p is the conjugating enzyme for the ubiquitin-like protein Smt3p. J Biol Chem 272:26799\u201326802. https:\/\/doi.org\/10.1074\/jbc.272.43.26799","journal-title":"J Biol Chem"},{"key":"724_CR15","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1016\/s0092-8674(01)00519-0","volume":"107","author":"M Hochstrasser","year":"2001","unstructured":"Hochstrasser M (2001) SP-RING for SUMO: new functions bloom for a ubiquitin-like protein. Cell 107:5\u20138. https:\/\/doi.org\/10.1016\/s0092-8674(01)00519-0","journal-title":"Cell"},{"key":"724_CR16","doi-asserted-by":"publisher","first-page":"2367","DOI":"10.1128\/MCB.20.7.2367-2377.2000","volume":"20","author":"SJ Li","year":"2000","unstructured":"Li SJ, Hochstrasser M (2000) The yeast ULP2 (SMT4) gene encodes a novel protease specific for the ubiquitin-like Smt3 protein. Mol Cell Biol 20:2367\u20132377. https:\/\/doi.org\/10.1128\/MCB.20.7.2367-2377.2000","journal-title":"Mol Cell Biol"},{"key":"724_CR17","doi-asserted-by":"publisher","first-page":"44113","DOI":"10.1074\/jbc.M308357200","volume":"278","author":"GR Bylebyl","year":"2003","unstructured":"Bylebyl GR, Belichenko I, Johnson ES (2003) The SUMO isopeptidase Ulp2 prevents accumulation of SUMO chains in yeast. J Biol Chem 278:44113\u201344120. https:\/\/doi.org\/10.1074\/jbc.M308357200","journal-title":"J Biol Chem"},{"key":"724_CR18","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/j.bbadis.2008.12.008","volume":"1792","author":"JH Kim","year":"2009","unstructured":"Kim JH, Baek SH (2009) Emerging roles of desumoylating enzymes. Biochim Biophys Acta 1792:155\u2013162. https:\/\/doi.org\/10.1016\/j.bbadis.2008.12.008","journal-title":"Biochim Biophys Acta"},{"key":"724_CR19","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1007\/978-1-4419-6676-6_16","volume":"54","author":"M Miteva","year":"2010","unstructured":"Miteva M, Keusekotten K, Hofmann K, Praefcke GJK, Dohmen RJ (2010) Sumoylation as a signal for polyubiquitylation and proteasomal degradation. Subcell Biochem 54:195\u2013214. https:\/\/doi.org\/10.1007\/978-1-4419-6676-6_16","journal-title":"Subcell Biochem"},{"key":"724_CR20","doi-asserted-by":"publisher","DOI":"10.3390\/jof6010032","volume":"6","author":"MS Sahu","year":"2020","unstructured":"Sahu MS, Patra S, Kumar K, Kaur R (2020) SUMOylation in human pathogenic fungi: role in physiology and virulence. J Fungi 6:32. https:\/\/doi.org\/10.3390\/jof6010032","journal-title":"J Fungi"},{"key":"724_CR21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1012742","volume":"20","author":"D Gupta","year":"2024","unstructured":"Gupta D, Shukla R, Mishra K (2024) SUMO-targeted Ubiquitin Ligases as crucial mediators of protein homeostasis in Candida glabrata. PLoS Pathog 20:e1012742. https:\/\/doi.org\/10.1371\/journal.ppat.1012742","journal-title":"PLoS Pathog"},{"key":"724_CR22","doi-asserted-by":"publisher","first-page":"12105","DOI":"10.1074\/jbc.RA118.003022","volume":"293","author":"CP de Albuquerque","year":"2018","unstructured":"de Albuquerque CP, Suhandynata RT, Carlson CR, Yuan W-T, Zhou H (2018) Binding to small ubiquitin-like modifier and the nucleolar protein Csm1 regulates substrate specificity of the Ulp2 protease. J Biol Chem 293:12105\u201312119. https:\/\/doi.org\/10.1074\/jbc.RA118.003022","journal-title":"J Biol Chem"},{"key":"724_CR23","doi-asserted-by":"publisher","first-page":"2825","DOI":"10.3390\/cells10112825","volume":"10","author":"T-Y Yau","year":"2021","unstructured":"Yau T-Y, Sander W, Eidson C, Courey AJ (2021) SUMO interacting motifs: structure and function. Cells 10:2825. https:\/\/doi.org\/10.3390\/cells10112825","journal-title":"Cells"},{"key":"724_CR24","doi-asserted-by":"publisher","first-page":"3484","DOI":"10.1016\/j.csbj.2020.10.037","volume":"18","author":"D Gupta","year":"2020","unstructured":"Gupta D, Garapati HS, Kakumanu AVS, Shukla R, Mishra K (2020) SUMOylation in fungi: a potential target for intervention. Comput Struct Biotechnol J 18:3484\u20133493. https:\/\/doi.org\/10.1016\/j.csbj.2020.10.037","journal-title":"Comput Struct Biotechnol J"},{"key":"724_CR25","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1091\/mbc.E10-07-0632","volume":"22","author":"MD Leach","year":"2011","unstructured":"Leach MD, Stead DA, Argo E, Brown AJP (2011) Identification of sumoylation targets, combined with inactivation of SMT3, reveals the impact of sumoylation upon growth, morphology, and stress resistance in the pathogen Candida albicans. Mol Biol Cell 22:687\u2013702. https:\/\/doi.org\/10.1091\/mbc.E10-07-0632","journal-title":"Mol Biol Cell"},{"key":"724_CR26","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1534\/genetics.118.301769","volume":"211","author":"A Islam","year":"2019","unstructured":"Islam A, Tebbji F, Mallick J, Regan H, Dumeaux V, Omran RP et al (2019) Mms21: a putative SUMO E3 ligase in Candida albicans that negatively regulates invasiveness and filamentation, and is required for the genotoxic and cellular stress response. Genetics 211:579\u2013595. https:\/\/doi.org\/10.1534\/genetics.118.301769","journal-title":"Genetics"},{"key":"724_CR27","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1111\/mmi.13108","volume":"98","author":"M Yan","year":"2015","unstructured":"Yan M, Nie X, Wang H, Gao N, Liu H, Chen J (2015) SUMOylation of Wor1 by a novel SUMO E3 ligase controls cell fate in Candida albicans. Mol Microbiol 98:69\u201389. https:\/\/doi.org\/10.1111\/mmi.13108","journal-title":"Mol Microbiol"},{"key":"724_CR28","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.1111\/mmi.12421","volume":"90","author":"R Harting","year":"2013","unstructured":"Harting R, Bayram O, Laubinger K, Valerius O, Braus GH (2013) Interplay of the fungal sumoylation network for control of multicellular development. Mol Microbiol 90:1125\u20131145. https:\/\/doi.org\/10.1111\/mmi.12421","journal-title":"Mol Microbiol"},{"key":"724_CR29","doi-asserted-by":"publisher","first-page":"728","DOI":"10.1016\/j.fgb.2007.12.009","volume":"45","author":"KH Wong","year":"2008","unstructured":"Wong KH, Todd RB, Oakley BR, Oakley CE, Hynes MJ, Davis MA (2008) Sumoylation in Aspergillus nidulans: sumO inactivation, overexpression and live-cell imaging. Fungal Genet Biol 45:728\u2013737. https:\/\/doi.org\/10.1016\/j.fgb.2007.12.009","journal-title":"Fungal Genet Biol"},{"key":"724_CR30","doi-asserted-by":"publisher","first-page":"7607","DOI":"10.1128\/AEM.01743-08","volume":"74","author":"E Szewczyk","year":"2008","unstructured":"Szewczyk E, Chiang Y-M, Oakley CE, Davidson AD, Wang CCC, Oakley BR (2008) Identification and characterization of the asperthecin gene cluster of Aspergillus nidulans. Appl Environ Microbiol 74:7607\u20137612. https:\/\/doi.org\/10.1128\/AEM.01743-08","journal-title":"Appl Environ Microbiol"},{"key":"724_CR31","doi-asserted-by":"publisher","DOI":"10.3390\/jof3010010","volume":"3","author":"L Aslanyan","year":"2017","unstructured":"Aslanyan L, Sanchez DA, Valdebenito S, Eugenin EA, Ramos RL, Martinez LR (2017) The crucial role of biofilms in Cryptococcus neoformans survival within macrophages and colonization of the central nervous system. J Fungi 3:10. https:\/\/doi.org\/10.3390\/jof3010010","journal-title":"J Fungi"},{"key":"724_CR32","doi-asserted-by":"publisher","first-page":"495","DOI":"10.15698\/mic2018.11.656","volume":"5","author":"FL Mayer","year":"2018","unstructured":"Mayer FL, S\u00e1nchez-Le\u00f3n E, Kronstad JW (2018) A chemical genetic screen reveals a role for proteostasis in capsule and biofilm formation by Cryptococcus neoformans. Microb Cell 5:495\u2013510. https:\/\/doi.org\/10.15698\/mic2018.11.656","journal-title":"Microb Cell"},{"key":"724_CR33","doi-asserted-by":"publisher","first-page":"22213","DOI":"10.1038\/s41598-024-73039-x","volume":"14","author":"J Song","year":"2024","unstructured":"Song J, Chen H, Xie D, Li J, Huang B, Wang Z (2024) The SUMO gene MrSmt3 is involved in SUMOylation, conidiation and stress response in Metarhizium robertsii. Sci Rep 14:22213. https:\/\/doi.org\/10.1038\/s41598-024-73039-x","journal-title":"Sci Rep"},{"key":"724_CR34","doi-asserted-by":"publisher","unstructured":"Azizullah null, Noman M, Gao Y, Wang H, Xiong X, Wang J, et al. The SUMOylation pathway regulates the pathogenicity of Fusarium oxysporum f. sp. niveum in watermelon through stabilizing the pH regulator FonPalC via SUMOylation. Microbiol Res 2024;281:127632. https:\/\/doi.org\/10.1016\/j.micres.2024.127632.","DOI":"10.1016\/j.micres.2024.127632"},{"key":"724_CR35","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.chembiol.2009.01.009","volume":"16","author":"I Fukuda","year":"2009","unstructured":"Fukuda I, Ito A, Hirai G, Nishimura S, Kawasaki H, Saitoh H et al (2009) Ginkgolic acid inhibits protein SUMOylation by blocking formation of the E1-SUMO intermediate. Chem Biol 16:133\u2013140. https:\/\/doi.org\/10.1016\/j.chembiol.2009.01.009","journal-title":"Chem Biol"},{"key":"724_CR36","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/s44319-023-00010-8","volume":"25","author":"JB McNeil","year":"2024","unstructured":"McNeil JB, Lee S-K, Oliinyk A, Raina S, Garg J, Moallem M et al (2024) 1,10-phenanthroline inhibits sumoylation and reveals that yeast SUMO modifications are highly transient. EMBO Rep 25:68\u201381. https:\/\/doi.org\/10.1038\/s44319-023-00010-8","journal-title":"EMBO Rep"},{"key":"724_CR37","doi-asserted-by":"publisher","first-page":"17","DOI":"10.21775\/cimb.035.017","volume":"35","author":"S Chen","year":"2020","unstructured":"Chen S, Dong D, Xin W, Zhou H (2020) Progress in the discovery of small molecule modulators of DeSUMOylation. Curr Issues Mol Biol 35:17\u201334. https:\/\/doi.org\/10.21775\/cimb.035.017","journal-title":"Curr Issues Mol Biol"},{"key":"724_CR38","doi-asserted-by":"publisher","first-page":"3892","DOI":"10.2174\/0929867327666200810135039","volume":"28","author":"CM Brackett","year":"2021","unstructured":"Brackett CM, Blagg BSJ (2021) Current status of SUMOylation inhibitors. CMC 28:3892\u20133912. https:\/\/doi.org\/10.2174\/0929867327666200810135039","journal-title":"CMC"},{"key":"724_CR39","doi-asserted-by":"publisher","first-page":"19573","DOI":"10.1074\/jbc.M115.706044","volume":"291","author":"R Gujjula","year":"2016","unstructured":"Gujjula R, Veeraiah S, Kumar K, Thakur SS, Mishra K, Kaur R (2016) Identification of components of the SUMOylation machinery in Candida glabrata: ROLE OF THE DESUMOYLATION PEPTIDASE CgUlp2 IN VIRULENCE. J Biol Chem 291:19573\u201319589. https:\/\/doi.org\/10.1074\/jbc.M115.706044","journal-title":"J Biol Chem"},{"key":"724_CR40","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H et al (2000) The Protein Data Bank. Nucleic Acids Res 28:235\u2013242. https:\/\/doi.org\/10.1093\/nar\/28.1.235","journal-title":"Nucleic Acids Res"},{"key":"724_CR41","doi-asserted-by":"publisher","first-page":"W296","DOI":"10.1093\/nar\/gky427","volume":"46","author":"A Waterhouse","year":"2018","unstructured":"Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R et al (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46:W296-303. https:\/\/doi.org\/10.1093\/nar\/gky427","journal-title":"Nucleic Acids Res"},{"key":"724_CR42","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC et al (2004) UCSF chimera\u2014a visualization system for exploratory research and analysis. J Comput Chem 25:1605\u20131612. https:\/\/doi.org\/10.1002\/jcc.20084","journal-title":"J Comput Chem"},{"key":"724_CR43","doi-asserted-by":"publisher","first-page":"W384","DOI":"10.1093\/nar\/gkt458","volume":"41","author":"L Heo","year":"2013","unstructured":"Heo L, Park H, Seok C (2013) Galaxyrefine: protein structure refinement driven by side-chain repacking. Nucleic Acids Res 41:W384-388. https:\/\/doi.org\/10.1093\/nar\/gkt458","journal-title":"Nucleic Acids Res"},{"key":"724_CR44","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1107\/S0021889892009944","volume":"26","author":"RA Laskowski","year":"1993","unstructured":"Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283\u2013291. https:\/\/doi.org\/10.1107\/S0021889892009944","journal-title":"J Appl Crystallogr"},{"key":"724_CR45","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1002\/pro.3289","volume":"27","author":"RA Laskowski","year":"2018","unstructured":"Laskowski RA, Jab\u0142o\u0144ska J, Pravda L, Va\u0159ekov\u00e1 RS, Thornton JM (2018) Pdbsum: structural summaries of PDB entries. Protein Sci 27:129\u2013134. https:\/\/doi.org\/10.1002\/pro.3289","journal-title":"Protein Sci"},{"key":"724_CR46","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","volume":"596","author":"J Jumper","year":"2021","unstructured":"Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O et al (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596:583\u2013589. https:\/\/doi.org\/10.1038\/s41586-021-03819-2","journal-title":"Nature"},{"key":"724_CR47","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/s41592-022-01488-1","volume":"19","author":"M Mirdita","year":"2022","unstructured":"Mirdita M, Sch\u00fctze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M (2022) ColabFold: making protein folding accessible to all. Nat Methods 19:679\u2013682. https:\/\/doi.org\/10.1038\/s41592-022-01488-1","journal-title":"Nat Methods"},{"key":"724_CR48","doi-asserted-by":"publisher","first-page":"2074","DOI":"10.1093\/bioinformatics\/bts310","volume":"28","author":"A Volkamer","year":"2012","unstructured":"Volkamer A, Kuhn D, Rippmann F, Rarey M (2012) DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. Bioinformatics 28:2074\u20132075. https:\/\/doi.org\/10.1093\/bioinformatics\/bts310","journal-title":"Bioinformatics"},{"key":"724_CR49","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1111\/j.1747-0285.2006.00384.x","volume":"67","author":"SL Dixon","year":"2006","unstructured":"Dixon SL, Smondyrev AM, Rao SN (2006) PHASE: a novel approach to pharmacophore modeling and 3D database searching. Chem Biol Drug Des 67:370\u2013372. https:\/\/doi.org\/10.1111\/j.1747-0285.2006.00384.x","journal-title":"Chem Biol Drug Des"},{"key":"724_CR50","doi-asserted-by":"publisher","first-page":"W442","DOI":"10.1093\/nar\/gkw287","volume":"44","author":"J Sunseri","year":"2016","unstructured":"Sunseri J, Koes DR (2016) Pharmit: interactive exploration of chemical space. Nucleic Acids Res 44:W442-448. https:\/\/doi.org\/10.1093\/nar\/gkw287","journal-title":"Nucleic Acids Res"},{"key":"724_CR51","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1038\/nprot.2016.169","volume":"12","author":"D Kozakov","year":"2017","unstructured":"Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C et al (2017) The ClusPro web server for protein\u2013protein docking. Nat Protoc 12:255\u2013278. https:\/\/doi.org\/10.1038\/nprot.2016.169","journal-title":"Nat Protoc"},{"key":"724_CR52","doi-asserted-by":"publisher","first-page":"1071","DOI":"10.1016\/j.str.2020.06.006","volume":"28","author":"IT Desta","year":"2020","unstructured":"Desta IT, Porter KA, Xia B, Kozakov D, Vajda S (2020) Performance and its limits in rigid body protein-protein docking. Structure 28:1071-1081.e3. https:\/\/doi.org\/10.1016\/j.str.2020.06.006","journal-title":"Structure"},{"key":"724_CR53","doi-asserted-by":"publisher","first-page":"W96","DOI":"10.1093\/nar\/gkh354","volume":"32","author":"SR Comeau","year":"2004","unstructured":"Comeau SR, Gatchell DW, Vajda S, Camacho CJ (2004) Cluspro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res 32:W96-99. https:\/\/doi.org\/10.1093\/nar\/gkh354","journal-title":"Nucleic Acids Res"},{"key":"724_CR54","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1093\/protein\/8.2.127","volume":"8","author":"AC Wallace","year":"1995","unstructured":"Wallace AC, Laskowski RA, Thornton JM (1995) Ligplot: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng Des Sel 8:127\u2013134. https:\/\/doi.org\/10.1093\/protein\/8.2.127","journal-title":"Protein Eng Des Sel"},{"key":"724_CR55","doi-asserted-by":"publisher","first-page":"2371","DOI":"10.1021\/ci800166p","volume":"48","author":"OV Stroganov","year":"2008","unstructured":"Stroganov OV, Novikov FN, Stroylov VS, Kulkov V, Chilov GG (2008) Lead finder: an approach to improve accuracy of protein\u2212ligand docking, binding energy estimation, and virtual screening. J Chem Inf Model 48:2371\u20132385. https:\/\/doi.org\/10.1021\/ci800166p","journal-title":"J Chem Inf Model"},{"key":"724_CR56","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","volume":"1\u20132","author":"MJ Abraham","year":"2015","unstructured":"Abraham MJ, Murtola T, Schulz R, P\u00e1ll S, Smith JC, Hess B et al (2015) GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1\u20132:19\u201325. https:\/\/doi.org\/10.1016\/j.softx.2015.06.001","journal-title":"SoftwareX"},{"key":"724_CR57","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1093\/bioinformatics\/btt055","volume":"29","author":"S Pronk","year":"2013","unstructured":"Pronk S, P\u00e1ll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R et al (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29:845\u2013854. https:\/\/doi.org\/10.1093\/bioinformatics\/btt055","journal-title":"Bioinformatics"},{"key":"724_CR58","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1002\/jcc.540040211","volume":"4","author":"BR Brooks","year":"1983","unstructured":"Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) charmm\u202f: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187\u2013217. https:\/\/doi.org\/10.1002\/jcc.540040211","journal-title":"J Comput Chem"},{"key":"724_CR59","doi-asserted-by":"publisher","DOI":"10.1063\/5.0040966","volume":"154","author":"AC Simmonett","year":"2021","unstructured":"Simmonett AC, Brooks BR (2021) A compression strategy for particle mesh Ewald theory. J Chem Phys 154:054112. https:\/\/doi.org\/10.1063\/5.0040966","journal-title":"J Chem Phys"},{"key":"724_CR60","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0119264","volume":"10","author":"L Mart\u00ednez","year":"2015","unstructured":"Mart\u00ednez L (2015) Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PLoS ONE 10:e0119264. https:\/\/doi.org\/10.1371\/journal.pone.0119264","journal-title":"PLoS ONE"},{"key":"724_CR61","doi-asserted-by":"publisher","DOI":"10.1155\/2012\/173521","volume":"2012","author":"W Schreiner","year":"2012","unstructured":"Schreiner W, Karch R, Knapp B, Ilieva N (2012) Relaxation estimation of RMSD in molecular dynamics immunosimulations. Comput Math Methods Med 2012:173521. https:\/\/doi.org\/10.1155\/2012\/173521","journal-title":"Comput Math Methods Med"},{"key":"724_CR62","doi-asserted-by":"publisher","first-page":"2793","DOI":"10.1007\/s11030-022-10395-8","volume":"26","author":"S Manandhar","year":"2022","unstructured":"Manandhar S, Sankhe R, Priya K, Hari G, Kumar BH, Mehta CH et al (2022) Molecular dynamics and structure-based virtual screening and identification of natural compounds as Wnt signaling modulators: possible therapeutics for Alzheimer\u2019s disease. Mol Divers 26:2793\u20132811. https:\/\/doi.org\/10.1007\/s11030-022-10395-8","journal-title":"Mol Divers"},{"key":"724_CR63","doi-asserted-by":"publisher","first-page":"12085","DOI":"10.3390\/ijms232012085","volume":"23","author":"M Brand","year":"2022","unstructured":"Brand M, Bommeli EB, R\u00fctimann M, Lindenmann U, Riedl R (2022) Discovery of a dual SENP1 and SENP2 inhibitor. Int J Mol Sci 23:12085. https:\/\/doi.org\/10.3390\/ijms232012085","journal-title":"Int J Mol Sci"},{"key":"724_CR64","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1134\/S0026893308040195","volume":"42","author":"MY Lobanov","year":"2008","unstructured":"Lobanov MY, Bogatyreva NS, Galzitskaya OV (2008) Radius of gyration as an indicator of protein structure compactness. Mol Biol 42:623\u2013628. https:\/\/doi.org\/10.1134\/S0026893308040195","journal-title":"Mol Biol"},{"key":"724_CR65","doi-asserted-by":"publisher","first-page":"5797","DOI":"10.1021\/acs.jctc.8b00413","volume":"14","author":"H Huang","year":"2018","unstructured":"Huang H, Simmerling C (2018) Fast pairwise approximation of solvent accessible surface area for implicit solvent simulations of proteins on CPUs and GPUs. J Chem Theory Comput 14:5797\u20135814. https:\/\/doi.org\/10.1021\/acs.jctc.8b00413","journal-title":"J Chem Theory Comput"},{"key":"724_CR66","first-page":"308","volume":"14","author":"G Karimi","year":"2011","unstructured":"Karimi G, Vahabzadeh M, Lari P, Rashedinia M, Moshiri M (2011) Silymarin\u201d, a promising pharmacological agent for treatment of diseases. Iran J Basic Med Sci 14:308\u2013317","journal-title":"Iran J Basic Med Sci"},{"key":"724_CR67","doi-asserted-by":"publisher","DOI":"10.3390\/cancers12010048","volume":"12","author":"CP Ong","year":"2019","unstructured":"Ong CP, Lee WL, Tang YQ, Yap WH (2019) Honokiol: a review of its anticancer potential and mechanisms. Cancers (Basel) 12:48. https:\/\/doi.org\/10.3390\/cancers12010048","journal-title":"Cancers (Basel)"},{"key":"724_CR68","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.22038\/IJBMS.2022.63200.13961","volume":"25","author":"SA Emadi","year":"2022","unstructured":"Emadi SA, Ghasemzadeh Rahbardar M, Mehri S, Hosseinzadeh H (2022) A review of therapeutic potentials of milk thistle (Silybum marianum L.) and its main constituent, silymarin, on cancer, and their related patents. Iran J Basic Med Sci 25:1166\u20131176. https:\/\/doi.org\/10.22038\/IJBMS.2022.63200.13961","journal-title":"Iran J Basic Med Sci"},{"key":"724_CR69","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0117695","volume":"10","author":"L Sun","year":"2015","unstructured":"Sun L, Liao K, Wang D (2015) Effects of magnolol and honokiol on adhesion, yeast-hyphal transition, and formation of biofilm by Candida albicans. PLoS ONE 10:e0117695. https:\/\/doi.org\/10.1371\/journal.pone.0117695","journal-title":"PLoS ONE"},{"key":"724_CR70","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1167\/iovs.61.4.48","volume":"61","author":"L Zhan","year":"2020","unstructured":"Zhan L, Peng X, Lin J, Zhang Y, Gao H, Zhu Y et al (2020) Honokiol reduces fungal load, Toll-Like Receptor-2, and inflammatory cytokines in Aspergillus fumigatus keratitis. Invest Ophthalmol Vis Sci 61:48. https:\/\/doi.org\/10.1167\/iovs.61.4.48","journal-title":"Invest Ophthalmol Vis Sci"},{"key":"724_CR71","doi-asserted-by":"publisher","first-page":"293","DOI":"10.3390\/pathogens12020293","volume":"12","author":"L Martins-Santana","year":"2023","unstructured":"Martins-Santana L, Rezende CP, Rossi A, Martinez-Rossi NM, Almeida F (2023) Addressing microbial resistance worldwide: challenges over controlling life-threatening fungal infections. Pathogens 12:293. https:\/\/doi.org\/10.3390\/pathogens12020293","journal-title":"Pathogens"},{"key":"724_CR72","doi-asserted-by":"publisher","DOI":"10.1093\/g3journal\/jkac224","volume":"12","author":"NT Case","year":"2022","unstructured":"Case NT, Berman J, Blehert DS, Cramer RA, Cuomo C, Currie CR et al (2022) The future of fungi: threats and opportunities. G3 Genes|Genomes|Genetics 12:jkac224. https:\/\/doi.org\/10.1093\/g3journal\/jkac224","journal-title":"G3 Genes|Genomes|Genetics"},{"key":"724_CR73","doi-asserted-by":"publisher","first-page":"1837","DOI":"10.1534\/g3.120.401271","volume":"10","author":"NT Case","year":"2020","unstructured":"Case NT, Heitman J, Cowen LE (2020) The rise of fungi: a report on the CIFAR program fungal kingdom: threats & opportunities inaugural meeting. G3 Genes|Genomes|Genetics 10:1837\u20131842. https:\/\/doi.org\/10.1534\/g3.120.401271","journal-title":"G3 Genes|Genomes|Genetics"},{"key":"724_CR74","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.mib.2018.02.005","volume":"45","author":"NM Revie","year":"2018","unstructured":"Revie NM, Iyer KR, Robbins N, Cowen LE (2018) Antifungal drug resistance: evolution, mechanisms and impact. Curr Opin Microbiol 45:70\u201376. https:\/\/doi.org\/10.1016\/j.mib.2018.02.005","journal-title":"Curr Opin Microbiol"},{"key":"724_CR75","doi-asserted-by":"publisher","first-page":"e393","DOI":"10.1016\/S1473-3099(17)30442-5","volume":"17","author":"D Armstrong-James","year":"2017","unstructured":"Armstrong-James D, Brown GD, Netea MG, Zelante T, Gresnigt MS, van de Veerdonk FL et al (2017) Immunotherapeutic approaches to treatment of fungal diseases. Lancet Infect Dis 17:e393-402. https:\/\/doi.org\/10.1016\/S1473-3099(17)30442-5","journal-title":"Lancet Infect Dis"},{"key":"724_CR76","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2217948119","volume":"119","author":"A McDermott","year":"2022","unstructured":"McDermott A (2022) Drug-resistant fungi on the rise. Proc Natl Acad Sci USA 119:e2217948119. https:\/\/doi.org\/10.1073\/pnas.2217948119","journal-title":"Proc Natl Acad Sci USA"},{"key":"724_CR77","doi-asserted-by":"publisher","first-page":"1984","DOI":"10.1021\/acs.jcim.3c01439","volume":"64","author":"AJ Ruiz-Moreno","year":"2024","unstructured":"Ruiz-Moreno AJ, Cedillo-Gonz\u00e1lez R, Cordova-Bahena L, An Z, Medina-Franco JL, Velasco-Vel\u00e1zquez MA (2024) Consensus pharmacophore strategy for identifying novel SARS-Cov-2 Mpro inhibitors from large chemical libraries. J Chem Inf Model 64:1984\u20131995. https:\/\/doi.org\/10.1021\/acs.jcim.3c01439","journal-title":"J Chem Inf Model"},{"key":"724_CR78","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1089\/ars.2009.2440","volume":"11","author":"LE Fried","year":"2009","unstructured":"Fried LE, Arbiser JL (2009) Honokiol, a multifunctional antiangiogenic and antitumor agent. Antioxid Redox Signal 11:1139\u20131148. https:\/\/doi.org\/10.1089\/ars.2009.2440","journal-title":"Antioxid Redox Signal"},{"key":"724_CR79","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1016\/j.ejmech.2016.06.018","volume":"122","author":"Y Zhao","year":"2016","unstructured":"Zhao Y, Wang Z, Zhang J, Zhou H (2016) Identification of SENP1 inhibitors through in silico screening and rational drug design. Eur J Med Chem 122:178\u2013184. https:\/\/doi.org\/10.1016\/j.ejmech.2016.06.018","journal-title":"Eur J Med Chem"},{"key":"724_CR80","doi-asserted-by":"publisher","first-page":"2389","DOI":"10.1021\/acschembio.9b00402","volume":"14","author":"Y Jia","year":"2019","unstructured":"Jia Y, Claessens LA, Vertegaal ACO, Ovaa H (2019) Chemical tools and biochemical assays for SUMO specific proteases (SENPs). ACS Chem Biol 14:2389\u20132395. https:\/\/doi.org\/10.1021\/acschembio.9b00402","journal-title":"ACS Chem Biol"},{"key":"724_CR81","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1016\/j.csbj.2015.03.001","volume":"13","author":"A Kumar","year":"2015","unstructured":"Kumar A, Zhang KYJ (2015) Advances in the development of SUMO specific protease (SENP) inhibitors. Comput Struct Biotechnol J 13:204\u2013211. https:\/\/doi.org\/10.1016\/j.csbj.2015.03.001","journal-title":"Comput Struct Biotechnol J"},{"key":"724_CR82","doi-asserted-by":"publisher","first-page":"1435","DOI":"10.1021\/cb400177q","volume":"8","author":"IG Madu","year":"2013","unstructured":"Madu IG, Namanja AT, Su Y, Wong S, Li Y-J, Chen Y (2013) Identification and characterization of a new chemotype of noncovalent SENP inhibitors. ACS Chem Biol 8:1435\u20131441. https:\/\/doi.org\/10.1021\/cb400177q","journal-title":"ACS Chem Biol"},{"key":"724_CR83","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1042\/BJ20052030","volume":"397","author":"LN Shen","year":"2006","unstructured":"Shen LN, Dong C, Liu H, Naismith JH, Hay RT (2006) The structure of SENP1-SUMO-2 complex suggests a structural basis for discrimination between SUMO paralogues during processing. Biochem J 397:279\u2013288. https:\/\/doi.org\/10.1042\/BJ20052030","journal-title":"Biochem J"},{"key":"724_CR84","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2022.167875","volume":"434","author":"Y Li","year":"2022","unstructured":"Li Y, De Bol\u00f2s A, Amador V, Reverter D (2022) Structural basis for the SUMO2 isoform specificity of SENP7. J Mol Biol 434:167875. https:\/\/doi.org\/10.1016\/j.jmb.2022.167875","journal-title":"J Mol Biol"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-025-00724-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10822-025-00724-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-025-00724-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T03:33:40Z","timestamp":1764732820000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10822-025-00724-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,3]]},"references-count":84,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["724"],"URL":"https:\/\/doi.org\/10.1007\/s10822-025-00724-y","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,3]]},"assertion":[{"value":"7 July 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 November 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 December 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"13"}}