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An emerging treatment for LSDs is the use of pharmacological chaperones, small molecules that enhance total cellular activity of the target lysosomal protein. We have systematically studied thirteen inhibitors, which provide good lead compounds for the development of GAA chaperones. We have verified binding on GAA at low and neutral pH, mapping the range of pH during transport to lysosomes. These ligands inhibit GAA competitively and reversibly, and a few of the compounds show higher molecular stabilisation capacity than would be expected from their binding affinity. These molecules also increase lysosomal localisation of GAA variants in cells. In order to understand the specific molecular mechanism of the interactions, we docked the compounds to a homology model of the human GAA. Three factors contribute to the tightness of binding. Firstly, well\u2010positioned hydroxy groups are essential to orient the ligand and make the binding specific. Secondly, the open nature of the GAA active site allows both large and small ligands to bind. The third and most important binding determinant is the positive charge on the ligand, which is neutralised by Asp\u2009518 or Asp\u2009616 on GAA. Our study creates a firm basis for the design of drugs to treat Pompe disease, as it provides a comparable study of the ligand properties. Our analysis suggests a useful drug design framework for specific pharmacological chaperones for human GAA.<\/jats:p>","DOI":"10.1002\/cmdc.201200309","type":"journal-article","created":{"date-parts":[[2012,9,11]],"date-time":"2012-09-11T21:43:39Z","timestamp":1347399819000},"page":"1943-1953","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Systematic Structure\u2013Activity Study on Potential Chaperone Lead Compounds for Acid \u03b1\u2010Glucosidase"],"prefix":"10.1002","volume":"7","author":[{"given":"Chiara","family":"Bruckmann","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heidi","family":"Repo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elina","family":"Kuokkanen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henri","family":"Xhaard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pirkko","family":"Heikinheimo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2012,9,11]]},"reference":[{"key":"e_1_2_7_1_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M404008200"},{"key":"e_1_2_7_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-440X(97)80072-3"},{"key":"e_1_2_7_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2007.10.069"},{"key":"e_1_2_7_4_2","unstructured":"McKusick\u2032s Online Mendelian Inheritance in Man (OMIM) McKusick\u2013 Nathans Institute of Genetic Medicine Johns Hopkins University (Baltimore MD USA) National Center for Biotechnology Information National Library of Medicine (Bethesda MD USA) 2009;http:\/\/www.ncbi.nlm.nih.gov\/omim."},{"key":"e_1_2_7_5_2","doi-asserted-by":"publisher","DOI":"10.1002\/humu.20745"},{"key":"e_1_2_7_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg963"},{"key":"e_1_2_7_7_2","doi-asserted-by":"publisher","DOI":"10.1212\/01.wnl.0000251268.41188.04"},{"key":"e_1_2_7_8_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1010383421286"},{"key":"e_1_2_7_9_2","doi-asserted-by":"publisher","DOI":"10.1177\/0883073807302598"},{"key":"e_1_2_7_10_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00415-009-5275-3"},{"key":"e_1_2_7_11_2","doi-asserted-by":"publisher","DOI":"10.1517\/14656566.8.4.427"},{"key":"e_1_2_7_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/mt.2009.53"},{"key":"e_1_2_7_13_2","doi-asserted-by":"publisher","DOI":"10.1515\/BC.2008.009"},{"key":"e_1_2_7_14_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi9002265"},{"key":"e_1_2_7_15_2","doi-asserted-by":"publisher","DOI":"10.1152\/ajpcell.00426.2005"},{"key":"e_1_2_7_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cca.2008.02.014"},{"key":"e_1_2_7_17_2","doi-asserted-by":"publisher","DOI":"10.1097\/01.gim.0000217785.19262.9e"},{"key":"e_1_2_7_18_2","doi-asserted-by":"publisher","DOI":"10.2174\/092986706789803035"},{"key":"e_1_2_7_19_2","doi-asserted-by":"publisher","DOI":"10.1345\/aph.19269"},{"key":"e_1_2_7_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.nurt.2008.08.009"},{"key":"e_1_2_7_21_2","doi-asserted-by":"publisher","DOI":"10.3109\/00365517409082492"},{"key":"e_1_2_7_22_2","doi-asserted-by":"crossref","first-page":"8263","DOI":"10.1016\/S0021-9258(19)83905-4","volume":"261","author":"Grabowski G. 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