{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:28:24Z","timestamp":1772166504034,"version":"3.50.1"},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,11,4]],"date-time":"2020-11-04T00:00:00Z","timestamp":1604448000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,11,4]],"date-time":"2020-11-04T00:00:00Z","timestamp":1604448000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Projekt DEAL"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Sugar units in natural products are pharmacokinetically important but often redundant and therefore obstructing the study of the structure and function of the aglycon. Therefore, it is recommended to remove the sugars before a theoretical or experimental study of a molecule. Deglycogenases, enzymes that specialized in sugar removal from small molecules, are often used in laboratories to perform this task. However, there is no standardized computational procedure to perform this task in silico. In this work, we present a systematic approach for in silico removal of ring and linear sugars from molecular structures. Particular attention is given to molecules of biological origin and to their structural specificities. This approach is made available in two forms, through a free and open web application and as standalone open-source software.<\/jats:p>","DOI":"10.1186\/s13321-020-00467-y","type":"journal-article","created":{"date-parts":[[2020,11,4]],"date-time":"2020-11-04T04:08:39Z","timestamp":1604462919000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Too sweet: cheminformatics for deglycosylation in natural products"],"prefix":"10.1186","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1554-6666","authenticated-orcid":false,"given":"Jonas","family":"Schaub","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0722-4229","authenticated-orcid":false,"given":"Achim","family":"Zielesny","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6966-0814","authenticated-orcid":false,"given":"Christoph","family":"Steinbeck","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9359-7149","authenticated-orcid":false,"given":"Maria","family":"Sorokina","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,11,4]]},"reference":[{"key":"467_CR1","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.2174\/138955706778993003","volume":"6","author":"B Becker","year":"2006","unstructured":"Becker B, Condie G, Le Thanh G, Meutermans W (2006) Carbohydrate-based scaffolds in drug discovery. Mini Rev Med Chem 6:1299\u20131309. https:\/\/doi.org\/10.2174\/138955706778993003 [cito:citeAsAuthority]","journal-title":"Mini Rev Med Chem"},{"key":"467_CR2","doi-asserted-by":"publisher","first-page":"1164","DOI":"10.1002\/cmdc.200600150","volume":"1","author":"W Meutermans","year":"2006","unstructured":"Meutermans W, Le GT, Becker B (2006) Carbohydrates as scaffolds in drug discovery. ChemMedChem 1:1164\u20131194. https:\/\/doi.org\/10.1002\/cmdc.200600150 [cito:citeAsAuthority]","journal-title":"ChemMedChem"},{"key":"467_CR3","doi-asserted-by":"crossref","unstructured":"Thorson JS, Vogt T, Wong CH. Glycosylated natural products. Wiley Online Library; 2003 [cito:citeAsAuthority]","DOI":"10.1002\/3527602437.ch25"},{"key":"467_CR4","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1039\/np9971400099","volume":"14","author":"AC Weymouth-Wilson","year":"1997","unstructured":"Weymouth-Wilson AC (1997) The role of carbohydrates in biologically active natural products. Nat Prod Rep 14:99. https:\/\/doi.org\/10.1039\/np9971400099 [cito:citeAsAuthority]","journal-title":"Nat Prod Rep"},{"key":"467_CR5","doi-asserted-by":"publisher","first-page":"9814","DOI":"10.1002\/anie.200801204","volume":"47","author":"CJ Thibodeaux","year":"2008","unstructured":"Thibodeaux CJ, Melan\u00e7on CE, Liu H (2008) Natural product sugar biosynthesis and enzymatic glycodiversification. Angew Chem Int Ed Engl 47:9814\u20139859. https:\/\/doi.org\/10.1002\/anie.200801204 [cito:citeAsAuthority]","journal-title":"Angew Chem Int Ed Engl"},{"key":"467_CR6","doi-asserted-by":"publisher","first-page":"7591","DOI":"10.1039\/C4CS00426D","volume":"44","author":"SI Elshahawi","year":"2015","unstructured":"Elshahawi SI, Shaaban KA, Kharel MK, Thorson JS (2015) A comprehensive review of glycosylated bacterial natural products. Chem Soc Rev 44:7591\u20137697. https:\/\/doi.org\/10.1039\/C4CS00426D [cito:usesDataFrom]","journal-title":"Chem Soc Rev"},{"key":"467_CR7","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1021\/acs.jnatprod.5b01055","volume":"79","author":"DJ Newman","year":"2016","unstructured":"Newman DJ, Cragg GM (2016) Natural products as sources of new drugs from 1981 to 2014. J Nat Prod 79:629\u2013661. https:\/\/doi.org\/10.1021\/acs.jnatprod.5b01055 [cito:citeAsAuthority]","journal-title":"J Nat Prod"},{"key":"467_CR8","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1039\/B503215F","volume":"1","author":"A Luzhetskyy","year":"2005","unstructured":"Luzhetskyy A, Vente A, Bechthold A (2005) Glycosyltransferases involved in the biosynthesis of biologically active natural products that contain oligosaccharides. Mol Biosyst 1:117\u2013126. https:\/\/doi.org\/10.1039\/B503215F [cito:citeAsAuthority]","journal-title":"Mol Biosyst"},{"key":"467_CR9","doi-asserted-by":"publisher","first-page":"701","DOI":"10.1016\/S1359-6446(03)02751-X","volume":"8","author":"G Le Thanh","year":"2003","unstructured":"Le Thanh G, Abbenante G, Becker B, Grathwohl M, Halliday J, Tometzki G et al (2003) Molecular diversity through sugar scaffolds. Drug Discov Today 8:701\u2013709. https:\/\/doi.org\/10.1016\/S1359-6446(03)02751-X [cito:citeAsAuthority]","journal-title":"Drug Discov Today"},{"key":"467_CR10","doi-asserted-by":"publisher","DOI":"10.2174\/0929867013372193","author":"V Kren","year":"2001","unstructured":"Kren V, Martinkova L (2001) Glycosides in medicine: \u201cthe role of glycosidic residue in biological activity.\u201d Curr Med Chem. https:\/\/doi.org\/10.2174\/0929867013372193 [cito:citeAsAuthority]","journal-title":"Curr Med Chem"},{"key":"467_CR11","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1002\/jsfa.6900","volume":"95","author":"M Kim","year":"2015","unstructured":"Kim M, Lee J, Han J (2015) Deglycosylation of isoflavone C-glycosides by newly isolated human intestinal bacteria. J Sci Food Agric 95:1925\u20131931. https:\/\/doi.org\/10.1002\/jsfa.6900","journal-title":"J Sci Food Agric"},{"key":"467_CR12","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/S1381-1177(01)00041-8","volume":"16","author":"A Shafiee","year":"2001","unstructured":"Shafiee A, Tsipouras A, Bouffard A, Onishi JC, Guan Z, Motamedi H (2001) Enzymatic deglycosylation of enfumafungin, a triterpene glycoside natural product, and its chemically synthesized analogues. J Mol Catal B Enzym 16:27\u201332. https:\/\/doi.org\/10.1016\/S1381-1177(01)00041-8","journal-title":"J Mol Catal B Enzym"},{"key":"467_CR13","doi-asserted-by":"publisher","first-page":"17272","DOI":"10.1073\/pnas.0503647102","volume":"102","author":"MA Koch","year":"2005","unstructured":"Koch MA, Schuffenhauer A, Scheck M, Wetzel S, Casaulta M, Odermatt A et al (2005) Charting biologically relevant chemical space: a structural classification of natural products (SCONP). Proc Natl Acad Sci 102:17272\u201317277. https:\/\/doi.org\/10.1073\/pnas.0503647102 [cito:citeAsAuthority]","journal-title":"Proc Natl Acad Sci"},{"key":"467_CR14","doi-asserted-by":"publisher","first-page":"892","DOI":"10.1039\/B715668P","volume":"25","author":"K Grabowski","year":"2008","unstructured":"Grabowski K, Baringhaus K-H, Schneider G (2008) Scaffold diversity of natural products: inspiration for combinatorial library design. Nat Prod Rep 25:892\u2013904. https:\/\/doi.org\/10.1039\/B715668P [cito:citesForInformation]","journal-title":"Nat Prod Rep"},{"key":"467_CR15","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1021\/ci700286x","volume":"48","author":"P Ertl","year":"2008","unstructured":"Ertl P, Roggo S, Schuffenhauer A (2008) Natural product-likeness score and its application for prioritization of compound libraries. J Chem Inf Model 48:68\u201374. https:\/\/doi.org\/10.1021\/ci700286x [cito:citesForInformation]","journal-title":"J Chem Inf Model"},{"key":"467_CR16","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1038\/s41597-020-0547-y","volume":"7","author":"H Dashti","year":"2020","unstructured":"Dashti H, Westler WM, Wedell JR, Demler OV, Eghbalnia HR, Markley JL et al (2020) Probabilistic identification of saccharide moieties in biomolecules and their protein complexes. Sci Data 7:210. https:\/\/doi.org\/10.1038\/s41597-020-0547-y [cito:citesForInformation]","journal-title":"Sci Data"},{"key":"467_CR17","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1186\/s13321-017-0213-3","volume":"9","author":"T Sch\u00e4fer","year":"2017","unstructured":"Sch\u00e4fer T, Kriege N, Humbeck L, Klein K, Koch O, Mutzel P (2017) Scaffold Hunter: a comprehensive visual analytics framework for drug discovery. J Cheminform 9:28. https:\/\/doi.org\/10.1186\/s13321-017-0213-3 [cito:citesForInformation]","journal-title":"J Cheminform"},{"key":"467_CR18","unstructured":"Scaffold Hunter. SourceForge. https:\/\/sourceforge.net\/projects\/scaffoldhunter\/ . Accessed 4 May 2020"},{"key":"467_CR19","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s13321-017-0220-4","volume":"9","author":"EL Willighagen","year":"2017","unstructured":"Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N et al (2017) The Chemistry Development Kit (CDK) v.20: atom typing, depiction, molecular formulas, and substructure searching. J Cheminform 9:33. https:\/\/doi.org\/10.1186\/s13321-017-0220-4 [cito:usesMethodIn]","journal-title":"J Cheminform"},{"key":"467_CR20","unstructured":"RingSearch (cdk 1.5.15 API). https:\/\/cdk.github.io\/cdk\/1.5\/docs\/api\/org\/openscience\/cdk\/ringsearch\/RingSearch.html . Accessed 20 May 2020 [cito:usesMethodIn]"},{"key":"467_CR21","doi-asserted-by":"publisher","unstructured":"Sorokina M, Steinbeck C (2020) COCONUT: the COlleCtion of Open NatUral producTs. https:\/\/doi.org\/10.5281\/zenodo.3778405 [cito:usesDataFrom]","DOI":"10.5281\/zenodo.3778405"},{"key":"467_CR22","doi-asserted-by":"publisher","first-page":"2324","DOI":"10.1021\/acs.jcim.5b00559","volume":"55","author":"T Sterling","year":"2015","unstructured":"Sterling T, Irwin JJ (2015) ZINC 15\u2014ligand discovery for everyone. J Chem Inf Model 55:2324\u20132337. https:\/\/doi.org\/10.1021\/acs.jcim.5b00559 [cito:usesDataFrom]","journal-title":"J Chem Inf Model"},{"key":"467_CR23","unstructured":"Daylight theory: SMARTS\u2014a language for describing molecular patterns. https:\/\/www.daylight.com\/dayhtml\/doc\/theory\/theory.smarts.html . Accessed 18 May 2020 [cito:citesForInformation]"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-020-00467-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s13321-020-00467-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-020-00467-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,11]],"date-time":"2023-10-11T06:43:11Z","timestamp":1697006591000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-020-00467-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,11,4]]},"references-count":23,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["467"],"URL":"https:\/\/doi.org\/10.1186\/s13321-020-00467-y","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-50194\/v3","asserted-by":"object"},{"id-type":"doi","id":"10.21203\/rs.3.rs-50194\/v2","asserted-by":"object"},{"id-type":"doi","id":"10.21203\/rs.3.rs-50194\/v1","asserted-by":"object"}]},"ISSN":["1758-2946"],"issn-type":[{"value":"1758-2946","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,11,4]]},"assertion":[{"value":"27 July 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 October 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 November 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"67"}}