Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis
Identifieur interne : 000271 ( Main/Exploration ); précédent : 000270; suivant : 000272Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis
Auteurs : Emna Harigua-Souiai [France, Tunisie] ; Isidro Cortes-Ciriano [France] ; Nathan Desdouits [France] ; Thérèse E. Malliavin [France] ; Ikram Guizani [Tunisie] ; Michael Nilges [France] ; Arnaud Blondel [France] ; Guillaume Bouvier [France]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2015.
Descripteurs français
- KwdFr :
- Algorithmes (MeSH), Conception de médicament (MeSH), Ligands (MeSH), Protéines proto-oncogènes c-abl (composition chimique), Protéines proto-oncogènes c-abl (métabolisme), Simulation de docking moléculaire (méthodes), Sites de fixation (MeSH), Transcriptase inverse du VIH (composition chimique), Transcriptase inverse du VIH (métabolisme).
- MESH :
- composition chimique : Protéines proto-oncogènes c-abl, Transcriptase inverse du VIH.
- métabolisme : Protéines proto-oncogènes c-abl, Transcriptase inverse du VIH.
- méthodes : Simulation de docking moléculaire.
- Algorithmes, Conception de médicament, Ligands, Sites de fixation.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : HIV Reverse Transcriptase, Proto-Oncogene Proteins c-abl.
- chemical , metabolism : HIV Reverse Transcriptase, Proto-Oncogene Proteins c-abl.
- methods : Molecular Docking Simulation.
- Algorithms, Binding Sites, Drug Design, Ligands.
Abstract
Identifying druggable cavities on a protein surface is a crucial step in structure based drug design. The cavities have to present suitable size and shape, as well as appropriate chemical complementarity with ligands.
We present a novel cavity prediction method that analyzes results of virtual screening of specific ligands or fragment libraries by means of Self-Organizing Maps. We demonstrate the method with two thoroughly studied proteins where it successfully identified their active sites (AS) and relevant secondary binding sites (BS). Moreover, known active ligands mapped the AS better than inactive ones. Interestingly, docking a naive fragment library brought even more insight. We then systematically applied the method to the 102 targets from the DUD-E database, where it showed a 90% identification rate of the AS among the first three consensual clusters of the SOM, and in 82% of the cases as the first one. Further analysis by chemical decomposition of the fragments improved BS prediction. Chemical substructures that are representative of the active ligands preferentially mapped in the AS.
The new approach provides valuable information both on relevant BSs and on chemical features promoting bioactivity.
The online version of this article (doi:10.1186/s12859-015-0518-z) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12859-015-0518-z
PubMed: 25888251
PubMed Central: 4381396
Affiliations:
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Structurale et Chimie, 25, rue du Dr Roux, Paris, 75015 France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2298 7385</institution-id><institution-id institution-id-type="GRID">grid.418517.e</institution-id><institution>Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04,</institution><institution>Institut Pasteur de Tunis, Université Tunis el Manar – Tunisia,</institution></institution-wrap>13, Place Pasteur, Tunis, 1002 Tunisia</nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>13, Place Pasteur, Tunis</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff3">University of Carthage, Faculty of sciences of Bizerte – Tunisia, Jarzouna, 7021 Tunisia</nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>University of Carthage, Faculty of sciences of Bizerte – Tunisia, Jarzouna</wicri:regionArea></affiliation></author><author><name sortKey="Cortes Ciriano, Isidro" sort="Cortes Ciriano, Isidro" uniqKey="Cortes Ciriano I" first="Isidro" last="Cortes-Ciriano">Isidro Cortes-Ciriano</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris, 75015 France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris</wicri:regionArea></affiliation></author><author><name sortKey="Desdouits, Nathan" sort="Desdouits, Nathan" uniqKey="Desdouits N" first="Nathan" last="Desdouits">Nathan Desdouits</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris, 75015 France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris</wicri:regionArea></affiliation></author><author><name sortKey="Malliavin, Therese E" sort="Malliavin, Therese E" uniqKey="Malliavin T" first="Thérèse E" last="Malliavin">Thérèse E. Malliavin</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris, 75015 France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris</wicri:regionArea></affiliation></author><author><name sortKey="Guizani, Ikram" sort="Guizani, Ikram" uniqKey="Guizani I" first="Ikram" last="Guizani">Ikram Guizani</name><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2298 7385</institution-id><institution-id institution-id-type="GRID">grid.418517.e</institution-id><institution>Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04,</institution><institution>Institut Pasteur de Tunis, Université Tunis el Manar – Tunisia,</institution></institution-wrap>13, Place Pasteur, Tunis, 1002 Tunisia</nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>13, Place Pasteur, Tunis</wicri:regionArea></affiliation></author><author><name sortKey="Nilges, Michael" sort="Nilges, Michael" uniqKey="Nilges M" first="Michael" last="Nilges">Michael Nilges</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris, 75015 France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris</wicri:regionArea></affiliation></author><author><name sortKey="Blondel, Arnaud" sort="Blondel, Arnaud" uniqKey="Blondel A" first="Arnaud" last="Blondel">Arnaud Blondel</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris, 75015 France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris</wicri:regionArea></affiliation></author><author><name sortKey="Bouvier, Guillaume" sort="Bouvier, Guillaume" uniqKey="Bouvier G" first="Guillaume" last="Bouvier">Guillaume Bouvier</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris, 75015 France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris</wicri:regionArea></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms (MeSH)</term><term>Binding Sites (MeSH)</term><term>Drug Design (MeSH)</term><term>HIV Reverse Transcriptase (chemistry)</term><term>HIV Reverse Transcriptase (metabolism)</term><term>Ligands (MeSH)</term><term>Molecular Docking Simulation (methods)</term><term>Proto-Oncogene Proteins c-abl (chemistry)</term><term>Proto-Oncogene Proteins c-abl (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes (MeSH)</term><term>Conception de médicament (MeSH)</term><term>Ligands (MeSH)</term><term>Protéines proto-oncogènes c-abl (composition chimique)</term><term>Protéines proto-oncogènes c-abl (métabolisme)</term><term>Simulation de docking moléculaire (méthodes)</term><term>Sites de fixation (MeSH)</term><term>Transcriptase inverse du VIH (composition chimique)</term><term>Transcriptase inverse du VIH (métabolisme)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>HIV Reverse Transcriptase</term><term>Proto-Oncogene Proteins c-abl</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>HIV Reverse Transcriptase</term><term>Proto-Oncogene Proteins c-abl</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Protéines proto-oncogènes c-abl</term><term>Transcriptase inverse du VIH</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Molecular Docking Simulation</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines proto-oncogènes c-abl</term><term>Transcriptase inverse du VIH</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Simulation de docking moléculaire</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Binding Sites</term><term>Drug Design</term><term>Ligands</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Conception de médicament</term><term>Ligands</term><term>Sites de fixation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Identifying druggable cavities on a protein surface is a crucial step in structure based drug design. The cavities have to present suitable size and shape, as well as appropriate chemical complementarity with ligands.</p></sec><sec><title>Results</title><p>We present a novel cavity prediction method that analyzes results of virtual screening of specific ligands or fragment libraries by means of Self-Organizing Maps. We demonstrate the method with two thoroughly studied proteins where it successfully identified their active sites (AS) and relevant secondary binding sites (BS). Moreover, known active ligands mapped the AS better than inactive ones. Interestingly, docking a naive fragment library brought even more insight. We then systematically applied the method to the 102 targets from the DUD-E database, where it showed a 90% identification rate of the AS among the first three consensual clusters of the SOM, and in 82% of the cases as the first one. Further analysis by chemical decomposition of the fragments improved BS prediction. Chemical substructures that are representative of the active ligands preferentially mapped in the AS.</p></sec><sec><title>Conclusion</title><p>The new approach provides valuable information both on relevant BSs and on chemical features promoting bioactivity.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12859-015-0518-z) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Liang, J" uniqKey="Liang J">J Liang</name></author><author><name sortKey="Woodward, C" uniqKey="Woodward C">C Woodward</name></author><author><name sortKey="Edelsbrunner, H" uniqKey="Edelsbrunner H">H Edelsbrunner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="An, J" uniqKey="An J">J An</name></author><author><name sortKey="Totrov, M" uniqKey="Totrov M">M 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sortKey="Owen, Dj" uniqKey="Owen D">DJ Owen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Morris, Gm" uniqKey="Morris G">GM Morris</name></author><author><name sortKey="Goodsell, Ds" uniqKey="Goodsell D">DS Goodsell</name></author><author><name sortKey="Halliday, Rs" uniqKey="Halliday R">RS Halliday</name></author><author><name sortKey="Huey, R" uniqKey="Huey R">R Huey</name></author><author><name sortKey="Hart, We" uniqKey="Hart W">WE Hart</name></author><author><name sortKey="Belew, Rk" uniqKey="Belew R">RK Belew</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kuntz, Id" uniqKey="Kuntz I">ID Kuntz</name></author><author><name sortKey="Blaney, Jm" uniqKey="Blaney J">JM Blaney</name></author><author><name sortKey="Oatley, Sj" uniqKey="Oatley S">SJ Oatley</name></author><author><name sortKey="Langridge, R" uniqKey="Langridge R">R Langridge</name></author><author><name sortKey="Ferrin, Te" uniqKey="Ferrin T">TE Ferrin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Laskowski, Ra" uniqKey="Laskowski R">RA Laskowski</name></author><author><name sortKey="Luscombe, Nm" uniqKey="Luscombe N">NM Luscombe</name></author><author><name sortKey="Swindells, Mb" uniqKey="Swindells M">MB Swindells</name></author><author><name sortKey="Thornton, Jm" uniqKey="Thornton J">JM Thornton</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>France</li><li>Tunisie</li></country></list><tree><country name="France"><noRegion><name sortKey="Harigua Souiai, Emna" sort="Harigua Souiai, Emna" uniqKey="Harigua Souiai E" first="Emna" last="Harigua-Souiai">Emna Harigua-Souiai</name></noRegion><name sortKey="Blondel, Arnaud" sort="Blondel, Arnaud" uniqKey="Blondel A" first="Arnaud" last="Blondel">Arnaud Blondel</name><name sortKey="Bouvier, Guillaume" sort="Bouvier, Guillaume" uniqKey="Bouvier G" first="Guillaume" last="Bouvier">Guillaume Bouvier</name><name sortKey="Cortes Ciriano, Isidro" sort="Cortes Ciriano, Isidro" uniqKey="Cortes Ciriano I" first="Isidro" last="Cortes-Ciriano">Isidro Cortes-Ciriano</name><name sortKey="Desdouits, Nathan" sort="Desdouits, Nathan" uniqKey="Desdouits N" first="Nathan" last="Desdouits">Nathan Desdouits</name><name sortKey="Malliavin, Therese E" sort="Malliavin, Therese E" uniqKey="Malliavin T" first="Thérèse E" last="Malliavin">Thérèse E. Malliavin</name><name sortKey="Nilges, Michael" sort="Nilges, Michael" uniqKey="Nilges M" first="Michael" last="Nilges">Michael Nilges</name></country><country name="Tunisie"><noRegion><name sortKey="Harigua Souiai, Emna" sort="Harigua Souiai, Emna" uniqKey="Harigua Souiai E" first="Emna" last="Harigua-Souiai">Emna Harigua-Souiai</name></noRegion><name sortKey="Guizani, Ikram" sort="Guizani, Ikram" uniqKey="Guizani I" first="Ikram" last="Guizani">Ikram Guizani</name><name sortKey="Harigua Souiai, Emna" sort="Harigua Souiai, Emna" uniqKey="Harigua Souiai E" first="Emna" last="Harigua-Souiai">Emna Harigua-Souiai</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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