Using Fragment Cocktail Crystallography To Assist Inhibitor Design of Trypanosoma brucei Nucleoside 2-Deoxyribosyltransferase
The 1.8 Å resolution de novo structure of nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6) from Trypanosoma brucei (TbNDRT) has been determined by SAD a phasing in an unliganded state and several ligand-bound states. This enzyme is important in the salvage pathway of nucleoside recycling. To identi...
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| Veröffentlicht in: | Journal of medicinal chemistry 2006-10, Vol.49 (20), p.5939-5946 |
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| creator | Bosch, Jürgen Robien, Mark A Mehlin, Christopher Boni, Erica Riechers, Aaron Buckner, Frederick S Van Voorhis, Wesley C Myler, Peter J Worthey, Elizabeth A DeTitta, George Luft, Joseph R Lauricella, Angela Gulde, Stacey Anderson, Lori A Kalyuzhniy, Oleksandr Neely, Helen M Ross, Jenni Earnest, Thomas N Soltis, Michael Schoenfeld, Lori Zucker, Frank Merritt, Ethan A Fan, Erkang Verlinde, Christophe L. M. J Hol, Wim G. J |
| description | The 1.8 Å resolution de novo structure of nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6) from Trypanosoma brucei (TbNDRT) has been determined by SAD a phasing in an unliganded state and several ligand-bound states. This enzyme is important in the salvage pathway of nucleoside recycling. To identify novel lead compounds, we exploited “fragment cocktail soaks”. Out of 304 compounds tried in 31 cocktails, four compounds could be identified crystallographically in the active site. In addition, we demonstrated that very short soaks of ∼10 s are sufficient even for rather hydrophobic ligands to bind in the active site groove, which is promising for the application of similar soaking experiments to less robust crystals of other proteins. |
| doi_str_mv | 10.1021/jm060429m |
| format | Article |
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Out of 304 compounds tried in 31 cocktails, four compounds could be identified crystallographically in the active site. In addition, we demonstrated that very short soaks of ∼10 s are sufficient even for rather hydrophobic ligands to bind in the active site groove, which is promising for the application of similar soaking experiments to less robust crystals of other proteins.</description><identifier>ISSN: 0022-2623</identifier><identifier>EISSN: 1520-4804</identifier><identifier>DOI: 10.1021/jm060429m</identifier><identifier>PMID: 17004709</identifier><identifier>CODEN: JMCMAR</identifier><language>eng</language><publisher>Washington, DC: American Chemical Society</publisher><subject>Amino Acid Sequence ; Animals ; Benzyl Alcohols - chemistry ; Benzyl Alcohols - pharmacology ; Binding Sites ; Biological and medical sciences ; Crystallography, X-Ray ; Indoles - chemistry ; Indoles - pharmacology ; Isoquinolines - chemistry ; Isoquinolines - pharmacology ; Ligands ; Medical sciences ; Miscellaneous ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Pentosyltransferases - antagonists & inhibitors ; Pentosyltransferases - chemistry ; Pharmacology. Drug treatments ; Quinolines - chemistry ; Quinolines - pharmacology ; Structure-Activity Relationship ; Trypanocidal Agents - chemistry ; Trypanocidal Agents - pharmacology ; Trypanosoma brucei brucei - drug effects ; Trypanosoma brucei brucei - enzymology</subject><ispartof>Journal of medicinal chemistry, 2006-10, Vol.49 (20), p.5939-5946</ispartof><rights>Copyright © 2006 American Chemical Society</rights><rights>2007 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a447t-416d6ee084e861f94bb1102704f15fac14f5d6c026dec60344d96c6e4d7916193</citedby><cites>FETCH-LOGICAL-a447t-416d6ee084e861f94bb1102704f15fac14f5d6c026dec60344d96c6e4d7916193</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/jm060429m$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/jm060429m$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>314,780,784,2765,27076,27924,27925,56738,56788</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18154117$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17004709$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bosch, Jürgen</creatorcontrib><creatorcontrib>Robien, Mark A</creatorcontrib><creatorcontrib>Mehlin, Christopher</creatorcontrib><creatorcontrib>Boni, Erica</creatorcontrib><creatorcontrib>Riechers, Aaron</creatorcontrib><creatorcontrib>Buckner, Frederick S</creatorcontrib><creatorcontrib>Van Voorhis, Wesley C</creatorcontrib><creatorcontrib>Myler, Peter J</creatorcontrib><creatorcontrib>Worthey, Elizabeth A</creatorcontrib><creatorcontrib>DeTitta, George</creatorcontrib><creatorcontrib>Luft, Joseph R</creatorcontrib><creatorcontrib>Lauricella, Angela</creatorcontrib><creatorcontrib>Gulde, Stacey</creatorcontrib><creatorcontrib>Anderson, Lori A</creatorcontrib><creatorcontrib>Kalyuzhniy, Oleksandr</creatorcontrib><creatorcontrib>Neely, Helen M</creatorcontrib><creatorcontrib>Ross, Jenni</creatorcontrib><creatorcontrib>Earnest, Thomas N</creatorcontrib><creatorcontrib>Soltis, Michael</creatorcontrib><creatorcontrib>Schoenfeld, Lori</creatorcontrib><creatorcontrib>Zucker, Frank</creatorcontrib><creatorcontrib>Merritt, Ethan A</creatorcontrib><creatorcontrib>Fan, Erkang</creatorcontrib><creatorcontrib>Verlinde, Christophe L. M. J</creatorcontrib><creatorcontrib>Hol, Wim G. J</creatorcontrib><title>Using Fragment Cocktail Crystallography To Assist Inhibitor Design of Trypanosoma brucei Nucleoside 2-Deoxyribosyltransferase</title><title>Journal of medicinal chemistry</title><addtitle>J. Med. Chem</addtitle><description>The 1.8 Å resolution de novo structure of nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6) from Trypanosoma brucei (TbNDRT) has been determined by SAD a phasing in an unliganded state and several ligand-bound states. This enzyme is important in the salvage pathway of nucleoside recycling. To identify novel lead compounds, we exploited “fragment cocktail soaks”. Out of 304 compounds tried in 31 cocktails, four compounds could be identified crystallographically in the active site. In addition, we demonstrated that very short soaks of ∼10 s are sufficient even for rather hydrophobic ligands to bind in the active site groove, which is promising for the application of similar soaking experiments to less robust crystals of other proteins.</description><subject>Amino Acid Sequence</subject><subject>Animals</subject><subject>Benzyl Alcohols - chemistry</subject><subject>Benzyl Alcohols - pharmacology</subject><subject>Binding Sites</subject><subject>Biological and medical sciences</subject><subject>Crystallography, X-Ray</subject><subject>Indoles - chemistry</subject><subject>Indoles - pharmacology</subject><subject>Isoquinolines - chemistry</subject><subject>Isoquinolines - pharmacology</subject><subject>Ligands</subject><subject>Medical sciences</subject><subject>Miscellaneous</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>Molecular Structure</subject><subject>Pentosyltransferases - antagonists & inhibitors</subject><subject>Pentosyltransferases - chemistry</subject><subject>Pharmacology. Drug treatments</subject><subject>Quinolines - chemistry</subject><subject>Quinolines - pharmacology</subject><subject>Structure-Activity Relationship</subject><subject>Trypanocidal Agents - chemistry</subject><subject>Trypanocidal Agents - pharmacology</subject><subject>Trypanosoma brucei brucei - drug effects</subject><subject>Trypanosoma brucei brucei - enzymology</subject><issn>0022-2623</issn><issn>1520-4804</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpt0MFu1DAQBmALgehSOPACyBeQOATGjuMkx7JlobACJLZny3EmW2-TePEkUnPouzfVrroXTnOYT79mfsbeCvgkQIrPuw40KFl2z9hCZBISVYB6zhYAUiZSy_SMvSLaAUAqZPqSnYkcQOVQLtj9Nfl-y1fRbjvsB74M7nawvuXLONFg2zZso93fTHwT-AWRp4Ff9Te-8kOI_BLJb3seGr6J0972gUJneRVHh57_Gl2LgXyNXCaXGO6m6KtAUztE21OD0RK-Zi8a2xK-Oc5zdr36ull-T9a_v10tL9aJVSofEiV0rRGhUFho0ZSqqsT8eA6qEVljnVBNVmsHUtfoNKRK1aV2GlWdl0KLMj1nHw65-xj-jUiD6Tw5bFvbYxjJ6KIEofJH-PEAXQxEERuzj76zcTICzGPX5qnr2b47ho5Vh_VJHsudwfsjsORs28x_O08nV4hMCZHPLjm4uV28e9rbeGt0nuaZ2fz5a8Qa0p9fVj_M-pRrHZldGGM_d_efAx8AKYWjLw</recordid><startdate>20061005</startdate><enddate>20061005</enddate><creator>Bosch, Jürgen</creator><creator>Robien, Mark A</creator><creator>Mehlin, Christopher</creator><creator>Boni, Erica</creator><creator>Riechers, Aaron</creator><creator>Buckner, Frederick S</creator><creator>Van Voorhis, Wesley C</creator><creator>Myler, Peter J</creator><creator>Worthey, Elizabeth A</creator><creator>DeTitta, George</creator><creator>Luft, Joseph R</creator><creator>Lauricella, Angela</creator><creator>Gulde, Stacey</creator><creator>Anderson, Lori A</creator><creator>Kalyuzhniy, Oleksandr</creator><creator>Neely, Helen M</creator><creator>Ross, Jenni</creator><creator>Earnest, Thomas N</creator><creator>Soltis, Michael</creator><creator>Schoenfeld, Lori</creator><creator>Zucker, Frank</creator><creator>Merritt, Ethan A</creator><creator>Fan, Erkang</creator><creator>Verlinde, Christophe L. 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Out of 304 compounds tried in 31 cocktails, four compounds could be identified crystallographically in the active site. In addition, we demonstrated that very short soaks of ∼10 s are sufficient even for rather hydrophobic ligands to bind in the active site groove, which is promising for the application of similar soaking experiments to less robust crystals of other proteins.</abstract><cop>Washington, DC</cop><pub>American Chemical Society</pub><pmid>17004709</pmid><doi>10.1021/jm060429m</doi><tpages>8</tpages></addata></record> |
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| subjects | Amino Acid Sequence Animals Benzyl Alcohols - chemistry Benzyl Alcohols - pharmacology Binding Sites Biological and medical sciences Crystallography, X-Ray Indoles - chemistry Indoles - pharmacology Isoquinolines - chemistry Isoquinolines - pharmacology Ligands Medical sciences Miscellaneous Models, Molecular Molecular Sequence Data Molecular Structure Pentosyltransferases - antagonists & inhibitors Pentosyltransferases - chemistry Pharmacology. Drug treatments Quinolines - chemistry Quinolines - pharmacology Structure-Activity Relationship Trypanocidal Agents - chemistry Trypanocidal Agents - pharmacology Trypanosoma brucei brucei - drug effects Trypanosoma brucei brucei - enzymology |
| title | Using Fragment Cocktail Crystallography To Assist Inhibitor Design of Trypanosoma brucei Nucleoside 2-Deoxyribosyltransferase |
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