Investigating the dynamic aspects of drug-protein recognition through a combination of MD and NMR analyses: implications for the development of protein-protein interaction inhibitors
In this paper, we investigate the dynamic aspects of the molecular recognition between a small molecule ligand and a flat, exposed protein surface, representing a typical target in the development of protein-protein interaction inhibitors. Specifically, we analyze the complex between the protein Fib...
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| Veröffentlicht in: | PloS one 2014-05, Vol.9 (5), p.e97153-e97153 |
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| creator | Meli, Massimiliano Pagano, Katiuscia Ragona, Laura Colombo, Giorgio |
| description | In this paper, we investigate the dynamic aspects of the molecular recognition between a small molecule ligand and a flat, exposed protein surface, representing a typical target in the development of protein-protein interaction inhibitors. Specifically, we analyze the complex between the protein Fibroblast Growth Factor 2 (FGF2) and a recently discovered small molecule inhibitor, labeled sm27 for which the binding site and the residues mainly involved in small molecule recognition have been previously characterized. We have approached this problem using microsecond MD simulations and NMR-based characterizations of the dynamics of the apo and holo states of the system. Using direct combination and cross-validation of the results of the two techniques, we select the set of conformational states that best recapitulate the principal dynamic and structural properties of the complex. We then use this information to generate a multi-structure representation of the sm27-FGF2 interaction. We propose this kind of representation and approach as a useful tool in particular for the characterization of systems where the mutual dynamic influence between the interacting partners is expected to play an important role. The results presented can also be used to generate new rules for the rational expansion of the chemical diversity space of FGF2 inhibitors. |
| doi_str_mv | 10.1371/journal.pone.0097153 |
| format | Article |
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Specifically, we analyze the complex between the protein Fibroblast Growth Factor 2 (FGF2) and a recently discovered small molecule inhibitor, labeled sm27 for which the binding site and the residues mainly involved in small molecule recognition have been previously characterized. We have approached this problem using microsecond MD simulations and NMR-based characterizations of the dynamics of the apo and holo states of the system. Using direct combination and cross-validation of the results of the two techniques, we select the set of conformational states that best recapitulate the principal dynamic and structural properties of the complex. We then use this information to generate a multi-structure representation of the sm27-FGF2 interaction. We propose this kind of representation and approach as a useful tool in particular for the characterization of systems where the mutual dynamic influence between the interacting partners is expected to play an important role. The results presented can also be used to generate new rules for the rational expansion of the chemical diversity space of FGF2 inhibitors.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0097153</identifier><identifier>PMID: 24865844</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Binding Sites ; Biochemistry ; Biology and Life Sciences ; Enzymes ; Fibroblast growth factor ; Fibroblast growth factor 2 ; Fibroblast Growth Factor 2 - chemistry ; Fibroblast Growth Factor 2 - metabolism ; Fibroblast growth factors ; Fibroblasts ; Growth factors ; Humans ; Inhibitors ; Ligands ; Models, Molecular ; Molecular Dynamics Simulation ; NMR ; Nuclear magnetic resonance ; Nuclear Magnetic Resonance, Biomolecular ; Physical Sciences ; Protein Binding ; Protein Conformation ; Protein interaction ; Protein Interaction Domains and Motifs - drug effects ; Protein-protein interactions ; Proteins ; Recognition ; Representations ; Simulation ; Small Molecule Libraries - chemistry ; Small Molecule Libraries - metabolism ; Spectrum analysis</subject><ispartof>PloS one, 2014-05, Vol.9 (5), p.e97153-e97153</ispartof><rights>COPYRIGHT 2014 Public Library of Science</rights><rights>2014 Meli et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2014 Meli et al 2014 Meli et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-74ca2ac343cc20da255cf8447d56c88f8830558cdd0758e6353dd17d780682d03</citedby><cites>FETCH-LOGICAL-c692t-74ca2ac343cc20da255cf8447d56c88f8830558cdd0758e6353dd17d780682d03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035249/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035249/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2095,2914,23846,27903,27904,53770,53772,79347,79348</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24865844$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Roccatano, Danilo</contributor><creatorcontrib>Meli, Massimiliano</creatorcontrib><creatorcontrib>Pagano, Katiuscia</creatorcontrib><creatorcontrib>Ragona, Laura</creatorcontrib><creatorcontrib>Colombo, Giorgio</creatorcontrib><title>Investigating the dynamic aspects of drug-protein recognition through a combination of MD and NMR analyses: implications for the development of protein-protein interaction inhibitors</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>In this paper, we investigate the dynamic aspects of the molecular recognition between a small molecule ligand and a flat, exposed protein surface, representing a typical target in the development of protein-protein interaction inhibitors. Specifically, we analyze the complex between the protein Fibroblast Growth Factor 2 (FGF2) and a recently discovered small molecule inhibitor, labeled sm27 for which the binding site and the residues mainly involved in small molecule recognition have been previously characterized. We have approached this problem using microsecond MD simulations and NMR-based characterizations of the dynamics of the apo and holo states of the system. Using direct combination and cross-validation of the results of the two techniques, we select the set of conformational states that best recapitulate the principal dynamic and structural properties of the complex. We then use this information to generate a multi-structure representation of the sm27-FGF2 interaction. We propose this kind of representation and approach as a useful tool in particular for the characterization of systems where the mutual dynamic influence between the interacting partners is expected to play an important role. The results presented can also be used to generate new rules for the rational expansion of the chemical diversity space of FGF2 inhibitors.</description><subject>Binding Sites</subject><subject>Biochemistry</subject><subject>Biology and Life Sciences</subject><subject>Enzymes</subject><subject>Fibroblast growth factor</subject><subject>Fibroblast growth factor 2</subject><subject>Fibroblast Growth Factor 2 - chemistry</subject><subject>Fibroblast Growth Factor 2 - metabolism</subject><subject>Fibroblast growth factors</subject><subject>Fibroblasts</subject><subject>Growth factors</subject><subject>Humans</subject><subject>Inhibitors</subject><subject>Ligands</subject><subject>Models, Molecular</subject><subject>Molecular Dynamics Simulation</subject><subject>NMR</subject><subject>Nuclear magnetic resonance</subject><subject>Nuclear Magnetic Resonance, Biomolecular</subject><subject>Physical Sciences</subject><subject>Protein Binding</subject><subject>Protein Conformation</subject><subject>Protein interaction</subject><subject>Protein Interaction Domains and Motifs - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Meli, Massimiliano</au><au>Pagano, Katiuscia</au><au>Ragona, Laura</au><au>Colombo, Giorgio</au><au>Roccatano, Danilo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Investigating the dynamic aspects of drug-protein recognition through a combination of MD and NMR analyses: implications for the development of protein-protein interaction inhibitors</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2014-05-27</date><risdate>2014</risdate><volume>9</volume><issue>5</issue><spage>e97153</spage><epage>e97153</epage><pages>e97153-e97153</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>In this paper, we investigate the dynamic aspects of the molecular recognition between a small molecule ligand and a flat, exposed protein surface, representing a typical target in the development of protein-protein interaction inhibitors. Specifically, we analyze the complex between the protein Fibroblast Growth Factor 2 (FGF2) and a recently discovered small molecule inhibitor, labeled sm27 for which the binding site and the residues mainly involved in small molecule recognition have been previously characterized. We have approached this problem using microsecond MD simulations and NMR-based characterizations of the dynamics of the apo and holo states of the system. Using direct combination and cross-validation of the results of the two techniques, we select the set of conformational states that best recapitulate the principal dynamic and structural properties of the complex. We then use this information to generate a multi-structure representation of the sm27-FGF2 interaction. We propose this kind of representation and approach as a useful tool in particular for the characterization of systems where the mutual dynamic influence between the interacting partners is expected to play an important role. The results presented can also be used to generate new rules for the rational expansion of the chemical diversity space of FGF2 inhibitors.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24865844</pmid><doi>10.1371/journal.pone.0097153</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Binding Sites Biochemistry Biology and Life Sciences Enzymes Fibroblast growth factor Fibroblast growth factor 2 Fibroblast Growth Factor 2 - chemistry Fibroblast Growth Factor 2 - metabolism Fibroblast growth factors Fibroblasts Growth factors Humans Inhibitors Ligands Models, Molecular Molecular Dynamics Simulation NMR Nuclear magnetic resonance Nuclear Magnetic Resonance, Biomolecular Physical Sciences Protein Binding Protein Conformation Protein interaction Protein Interaction Domains and Motifs - drug effects Protein-protein interactions Proteins Recognition Representations Simulation Small Molecule Libraries - chemistry Small Molecule Libraries - metabolism Spectrum analysis |
| title | Investigating the dynamic aspects of drug-protein recognition through a combination of MD and NMR analyses: implications for the development of protein-protein interaction inhibitors |
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