JankovicV1, Pmc, Checkpoint, bibRecord, 000197

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: Application to DJ-1 and Glucocerebrosidase

Identifieur interne : 000197 ( Pmc/Checkpoint ); précédent : 000196; suivant : 000198

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: Application to DJ-1 and Glucocerebrosidase

Auteurs : Melissa Landon ; Raquel Lieberman ; Quyen Hoang ; Shulin Ju ; Jose Caaveiro ; Susan Orwig ; Dima Kozakov ; Ryan Brenke ; Gwo Chuang ; Dmitry Beglov ; Sandor Vajda ; Gregory Petsko ; Dagmar Ringe

Source :

Journal of computer-aided molecular design [ 0920-654X ] ; 2009.

RBID : PMC:2889209

Abstract

The identification of hot spots, i.e. binding regions that contribute substantially to the free energy of ligand binding, is a critical step for structure-based drug design. Here we present the application of two fragment-based methods to the detection of hot spots for DJ-1 and glucocerebrosidase (GCase), targets for the development of therapeutics for Parkinson’s and Gaucher’s diseases respectively. While the structures of these two proteins are known, binding information is lacking. In this study we employ both the multiple solvent crystal structures (MSCS) method and the FTMap algorithm to identify regions suitable for the development of pharmacological chaperones for DJ-1 and GCase. Comparison of data derived via MSCS and FTMap also shows that FTMap, a computational method for the identification of fragment binding hot spots, is an accurate and robust alternative to the performance of expensive and difficult MSCS experiments.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889209

DOI: 10.1007/s10822-009-9283-2
PubMed: 19521672
PubMed Central: 2889209

Affiliations:

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Le document en format XML

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<author><name sortKey="Landon, Melissa R" sort="Landon, Melissa R" uniqKey="Landon M" first="Melissa" last="Landon">Melissa Landon</name>
<affiliation><nlm:aff id="A1"> Department of Biochemistry, Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham MA USA</nlm:aff>
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<author><name sortKey="Lieberman, Raquel L" sort="Lieberman, Raquel L" uniqKey="Lieberman R" first="Raquel" last="Lieberman">Raquel Lieberman</name>
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<author><name sortKey="Hoang, Quyen Q" sort="Hoang, Quyen Q" uniqKey="Hoang Q" first="Quyen" last="Hoang">Quyen Hoang</name>
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<author><name sortKey="Caaveiro, Jose M M" sort="Caaveiro, Jose M M" uniqKey="Caaveiro J" first="Jose" last="Caaveiro">Jose Caaveiro</name>
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<author><name sortKey="Orwig, Susan D" sort="Orwig, Susan D" uniqKey="Orwig S" first="Susan" last="Orwig">Susan Orwig</name>
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<author><name sortKey="Kozakov, Dima" sort="Kozakov, Dima" uniqKey="Kozakov D" first="Dima" last="Kozakov">Dima Kozakov</name>
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<author><name sortKey="Brenke, Ryan" sort="Brenke, Ryan" uniqKey="Brenke R" first="Ryan" last="Brenke">Ryan Brenke</name>
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</affiliation>
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<author><name sortKey="Chuang, Gwo Yu" sort="Chuang, Gwo Yu" uniqKey="Chuang G" first="Gwo" last="Chuang">Gwo Chuang</name>
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<author><name sortKey="Beglov, Dmitry" sort="Beglov, Dmitry" uniqKey="Beglov D" first="Dmitry" last="Beglov">Dmitry Beglov</name>
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<author><name sortKey="Vajda, Sandor" sort="Vajda, Sandor" uniqKey="Vajda S" first="Sandor" last="Vajda">Sandor Vajda</name>
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<author><name sortKey="Petsko, Gregory A" sort="Petsko, Gregory A" uniqKey="Petsko G" first="Gregory" last="Petsko">Gregory Petsko</name>
<affiliation><nlm:aff id="A1"> Department of Biochemistry, Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham MA USA</nlm:aff>
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</author>
<author><name sortKey="Ringe, Dagmar" sort="Ringe, Dagmar" uniqKey="Ringe D" first="Dagmar" last="Ringe">Dagmar Ringe</name>
<affiliation><nlm:aff id="A1"> Department of Biochemistry, Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham MA USA</nlm:aff>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Detection of ligand binding hot spots on protein surfaces via fragment-based methods: Application to DJ-1 and Glucocerebrosidase</title>
<author><name sortKey="Landon, Melissa R" sort="Landon, Melissa R" uniqKey="Landon M" first="Melissa" last="Landon">Melissa Landon</name>
<affiliation><nlm:aff id="A1"> Department of Biochemistry, Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham MA USA</nlm:aff>
<wicri:noCountry code="subfield">Waltham MA USA</wicri:noCountry>
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<author><name sortKey="Lieberman, Raquel L" sort="Lieberman, Raquel L" uniqKey="Lieberman R" first="Raquel" last="Lieberman">Raquel Lieberman</name>
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<wicri:noCountry code="subfield">Atlanta GA USA</wicri:noCountry>
</affiliation>
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<author><name sortKey="Hoang, Quyen Q" sort="Hoang, Quyen Q" uniqKey="Hoang Q" first="Quyen" last="Hoang">Quyen Hoang</name>
<affiliation><nlm:aff id="A1"> Department of Biochemistry, Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham MA USA</nlm:aff>
<wicri:noCountry code="subfield">Waltham MA USA</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Ju, Shulin" sort="Ju, Shulin" uniqKey="Ju S" first="Shulin" last="Ju">Shulin Ju</name>
<affiliation><nlm:aff id="A1"> Department of Biochemistry, Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham MA USA</nlm:aff>
<wicri:noCountry code="subfield">Waltham MA USA</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Caaveiro, Jose M M" sort="Caaveiro, Jose M M" uniqKey="Caaveiro J" first="Jose" last="Caaveiro">Jose Caaveiro</name>
<affiliation><nlm:aff id="A1"> Department of Biochemistry, Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham MA USA</nlm:aff>
<wicri:noCountry code="subfield">Waltham MA USA</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Orwig, Susan D" sort="Orwig, Susan D" uniqKey="Orwig S" first="Susan" last="Orwig">Susan Orwig</name>
<affiliation><nlm:aff id="A2"> School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA USA</nlm:aff>
<wicri:noCountry code="subfield">Atlanta GA USA</wicri:noCountry>
</affiliation>
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<author><name sortKey="Kozakov, Dima" sort="Kozakov, Dima" uniqKey="Kozakov D" first="Dima" last="Kozakov">Dima Kozakov</name>
<affiliation><nlm:aff id="A3"> Department of Biomedical Engineering, Boston University, Boston MA USA</nlm:aff>
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</affiliation>
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<author><name sortKey="Brenke, Ryan" sort="Brenke, Ryan" uniqKey="Brenke R" first="Ryan" last="Brenke">Ryan Brenke</name>
<affiliation><nlm:aff id="A4"> Department of Bioinformatics Graduate Program, Boston University, Boston MA USA</nlm:aff>
<wicri:noCountry code="subfield">Boston MA USA</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Chuang, Gwo Yu" sort="Chuang, Gwo Yu" uniqKey="Chuang G" first="Gwo" last="Chuang">Gwo Chuang</name>
<affiliation><nlm:aff id="A3"> Department of Biomedical Engineering, Boston University, Boston MA USA</nlm:aff>
<wicri:noCountry code="subfield">Boston MA USA</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Beglov, Dmitry" sort="Beglov, Dmitry" uniqKey="Beglov D" first="Dmitry" last="Beglov">Dmitry Beglov</name>
<affiliation><nlm:aff id="A3"> Department of Biomedical Engineering, Boston University, Boston MA USA</nlm:aff>
<wicri:noCountry code="subfield">Boston MA USA</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Vajda, Sandor" sort="Vajda, Sandor" uniqKey="Vajda S" first="Sandor" last="Vajda">Sandor Vajda</name>
<affiliation><nlm:aff id="A3"> Department of Biomedical Engineering, Boston University, Boston MA USA</nlm:aff>
<wicri:noCountry code="subfield">Boston MA USA</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Petsko, Gregory A" sort="Petsko, Gregory A" uniqKey="Petsko G" first="Gregory" last="Petsko">Gregory Petsko</name>
<affiliation><nlm:aff id="A1"> Department of Biochemistry, Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham MA USA</nlm:aff>
<wicri:noCountry code="subfield">Waltham MA USA</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Ringe, Dagmar" sort="Ringe, Dagmar" uniqKey="Ringe D" first="Dagmar" last="Ringe">Dagmar Ringe</name>
<affiliation><nlm:aff id="A1"> Department of Biochemistry, Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham MA USA</nlm:aff>
<wicri:noCountry code="subfield">Waltham MA USA</wicri:noCountry>
</affiliation>
</author>
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<series><title level="j">Journal of computer-aided molecular design</title>
<idno type="ISSN">0920-654X</idno>
<idno type="e-ISSN">1573-4951</idno>
<imprint><date when="2009">2009</date>
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<front><div type="abstract" xml:lang="en"><p id="P1">The identification of hot spots, i.e. binding regions that contribute substantially to the free energy of ligand binding, is a critical step for structure-based drug design. Here we present the application of two fragment-based methods to the detection of hot spots for DJ-1 and glucocerebrosidase (GCase), targets for the development of therapeutics for Parkinson’s and Gaucher’s diseases respectively. While the structures of these two proteins are known, binding information is lacking. In this study we employ both the multiple solvent crystal structures (MSCS) method and the FTMap algorithm to identify regions suitable for the development of pharmacological chaperones for DJ-1 and GCase. Comparison of data derived via MSCS and FTMap also shows that FTMap, a computational method for the identification of fragment binding hot spots, is an accurate and robust alternative to the performance of expensive and difficult MSCS experiments.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article" xml:lang="EN"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
  <pmc-dir>properties manuscript</pmc-dir>
  <front><journal-meta><journal-id journal-id-type="nlm-journal-id">8710425</journal-id>
<journal-id journal-id-type="pubmed-jr-id">5015</journal-id>
<journal-id journal-id-type="nlm-ta">J Comput Aided Mol Des</journal-id>
<journal-title>Journal of computer-aided molecular design</journal-title>
<issn pub-type="ppub">0920-654X</issn>
<issn pub-type="epub">1573-4951</issn>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">19521672</article-id>
<article-id pub-id-type="pmc">2889209</article-id>
<article-id pub-id-type="doi">10.1007/s10822-009-9283-2</article-id>
<article-id pub-id-type="manuscript">NIHMS146734</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Detection of ligand binding hot spots on protein surfaces via fragment-based methods: Application to DJ-1 and Glucocerebrosidase</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Landon</surname>
<given-names>Melissa R.</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lieberman</surname>
<given-names>Raquel L.</given-names>
</name>
<xref rid="A2" ref-type="aff">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hoang</surname>
<given-names>Quyen Q.</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ju</surname>
<given-names>Shulin</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Caaveiro</surname>
<given-names>Jose M. M.</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
<xref rid="FN2" ref-type="author-notes">a</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Orwig</surname>
<given-names>Susan D.</given-names>
</name>
<xref rid="A2" ref-type="aff">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kozakov</surname>
<given-names>Dima</given-names>
</name>
<xref rid="A3" ref-type="aff">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Brenke</surname>
<given-names>Ryan</given-names>
</name>
<xref rid="A4" ref-type="aff">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chuang</surname>
<given-names>Gwo-Yu</given-names>
</name>
<xref rid="A3" ref-type="aff">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Beglov</surname>
<given-names>Dmitry</given-names>
</name>
<xref rid="A3" ref-type="aff">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Vajda</surname>
<given-names>Sandor</given-names>
</name>
<xref rid="A3" ref-type="aff">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Petsko</surname>
<given-names>Gregory A.</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ringe</surname>
<given-names>Dagmar</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
<xref rid="FN1" ref-type="author-notes">b</xref>
</contrib>
</contrib-group>
<aff id="A1"><label>1</label>
 Department of Biochemistry, Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham MA USA</aff>
<aff id="A2"><label>2</label>
 School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA USA</aff>
<aff id="A3"><label>3</label>
 Department of Biomedical Engineering, Boston University, Boston MA USA</aff>
<aff id="A4"><label>4</label>
 Department of Bioinformatics Graduate Program, Boston University, Boston MA USA</aff>
<author-notes><corresp id="FN1"><label>b</label>
To whom correspondence should be addressed: 415 South Street MS 029, Waltham, MA 02454. <email>ringe@brandeis.edu</email>
, Telephone: 781.736.4902, Fax: 781.736.2405</corresp>
<fn id="FN2" fn-type="present-address"><label>a</label>
<p>Current Address: Physical Biochemistry Laboratory, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo Japan</p>
</fn>
</author-notes>
<pub-date pub-type="nihms-submitted"><day>21</day>
<month>9</month>
<year>2009</year>
</pub-date>
<pub-date pub-type="epub"><day>12</day>
<month>6</month>
<year>2009</year>
</pub-date>
<pub-date pub-type="ppub"><day>12</day>
<month>6</month>
<year>2009</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>1</day>
<month>12</month>
<year>2010</year>
</pub-date>
<elocation-id>10.1007/s10822-009-9283-2</elocation-id>
<abstract><p id="P1">The identification of hot spots, i.e. binding regions that contribute substantially to the free energy of ligand binding, is a critical step for structure-based drug design. Here we present the application of two fragment-based methods to the detection of hot spots for DJ-1 and glucocerebrosidase (GCase), targets for the development of therapeutics for Parkinson’s and Gaucher’s diseases respectively. While the structures of these two proteins are known, binding information is lacking. In this study we employ both the multiple solvent crystal structures (MSCS) method and the FTMap algorithm to identify regions suitable for the development of pharmacological chaperones for DJ-1 and GCase. Comparison of data derived via MSCS and FTMap also shows that FTMap, a computational method for the identification of fragment binding hot spots, is an accurate and robust alternative to the performance of expensive and difficult MSCS experiments.</p>
</abstract>
<kwd-group><kwd>fragment-based drug design</kwd>
<kwd>structure-based drug design</kwd>
<kwd>hot spot identification</kwd>
<kwd>DJ-1</kwd>
<kwd>glucocerebrosidase</kwd>
<kwd>Parkinson’s disease</kwd>
<kwd>Gaucher’s disease</kwd>
<kwd>pharmacological chaperones</kwd>
</kwd-group>
<contract-num rid="GM1">R01 GM064700-08
||GM</contract-num>
<contract-num rid="GM1">R01 GM064700-07
||GM</contract-num>
<contract-sponsor id="GM1">National Institute of General Medical Sciences : NIGMS</contract-sponsor>
</article-meta>
</front>
</pmc>
<affiliations><list></list>
<tree><noCountry><name sortKey="Beglov, Dmitry" sort="Beglov, Dmitry" uniqKey="Beglov D" first="Dmitry" last="Beglov">Dmitry Beglov</name>
<name sortKey="Brenke, Ryan" sort="Brenke, Ryan" uniqKey="Brenke R" first="Ryan" last="Brenke">Ryan Brenke</name>
<name sortKey="Caaveiro, Jose M M" sort="Caaveiro, Jose M M" uniqKey="Caaveiro J" first="Jose" last="Caaveiro">Jose Caaveiro</name>
<name sortKey="Chuang, Gwo Yu" sort="Chuang, Gwo Yu" uniqKey="Chuang G" first="Gwo" last="Chuang">Gwo Chuang</name>
<name sortKey="Hoang, Quyen Q" sort="Hoang, Quyen Q" uniqKey="Hoang Q" first="Quyen" last="Hoang">Quyen Hoang</name>
<name sortKey="Ju, Shulin" sort="Ju, Shulin" uniqKey="Ju S" first="Shulin" last="Ju">Shulin Ju</name>
<name sortKey="Kozakov, Dima" sort="Kozakov, Dima" uniqKey="Kozakov D" first="Dima" last="Kozakov">Dima Kozakov</name>
<name sortKey="Landon, Melissa R" sort="Landon, Melissa R" uniqKey="Landon M" first="Melissa" last="Landon">Melissa Landon</name>
<name sortKey="Lieberman, Raquel L" sort="Lieberman, Raquel L" uniqKey="Lieberman R" first="Raquel" last="Lieberman">Raquel Lieberman</name>
<name sortKey="Orwig, Susan D" sort="Orwig, Susan D" uniqKey="Orwig S" first="Susan" last="Orwig">Susan Orwig</name>
<name sortKey="Petsko, Gregory A" sort="Petsko, Gregory A" uniqKey="Petsko G" first="Gregory" last="Petsko">Gregory Petsko</name>
<name sortKey="Ringe, Dagmar" sort="Ringe, Dagmar" uniqKey="Ringe D" first="Dagmar" last="Ringe">Dagmar Ringe</name>
<name sortKey="Vajda, Sandor" sort="Vajda, Sandor" uniqKey="Vajda S" first="Sandor" last="Vajda">Sandor Vajda</name>
</noCountry>
</tree>
</affiliations>
</record>

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Detection of ligand binding hot spots on protein surfaces via fragment-based methods: Application to DJ-1 and Glucocerebrosidase

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: Application to DJ-1 and Glucocerebrosidase

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