1301
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Agamennone M, Cesari L, Lalli D, Turlizzi E, Del Conte R, Turano P, Mangani S, Padova A. Fragmenting the S100B-p53 interaction: combined virtual/biophysical screening approaches to identify ligands. ChemMedChem 2010; 5:428-35. [PMID: 20077460 DOI: 10.1002/cmdc.200900393] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
S100B contributes to cell proliferation by binding the C terminus of p53 and inhibiting its tumor suppressor function. The use of multiple computational approaches to screen fragment libraries targeting the human S100B-p53 interaction site is reported. This in silico screening led to the identification of 280 novel prospective ligands. NMR spectroscopic experiments revealed specific binding at the p53 interaction site for a set of these compounds and confirmed their potential for further rational optimization. The X-ray crystal structure determined for one of the binders revealed key intermolecular interactions, thus paving the way for structure-based ligand optimization.
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Affiliation(s)
- Mariangela Agamennone
- Dipartimento di Scienze del Farmaco, Università "G. d'Annunzio", Via dei Vestini, 66013 Chieti, Italy
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1302
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Mousseau G, Raffy Q, Thomas OP, Agez M, Thai R, Renault JP, Pin S, Ochsenbein F, Cintrat JC, Rousseau B. Footprinting of protein interactions by tritium labeling. Biochemistry 2010; 49:4297-9. [PMID: 20415454 DOI: 10.1021/bi100031a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new footprinting method for mapping protein interactions has been developed, using tritium as a radioactive label. As residues involved in an interaction are less labeled when the complex is formed, they can be identified via comparison of the tritium incorporation of each residue of the bound protein with that of the unbound one. Application of this footprinting method to the complex formed by the histone H3 fragment H3(122-135) and the protein hAsf1A(1-156) afforded data in good agreement with NMR results.
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1303
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Hoelbl A, Schuster C, Kovacic B, Zhu B, Wickre M, Hoelzl MA, Fajmann S, Grebien F, Warsch W, Stengl G, Hennighausen L, Poli V, Beug H, Moriggl R, Sexl V. Stat5 is indispensable for the maintenance of bcr/abl-positive leukaemia. EMBO Mol Med 2010; 2:98-110. [PMID: 20201032 PMCID: PMC2906698 DOI: 10.1002/emmm.201000062] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Tumourigenesis caused by the Bcr/Abl oncoprotein is a multi-step process proceeding from initial to tumour-maintaining events and finally results in a complex tumour-supporting network. A key to successful cancer therapy is the identification of critical functional nodes in an oncogenic network required for disease maintenance. So far, the transcription factors Stat3 and Stat5a/b have been implicated in bcr/abl-induced initial transformation. However, to qualify as a potential drug target, a signalling pathway must be required for the maintenance of the leukaemic state. Data on the roles of Stat3 or Stat5a/b in leukaemia maintenance are elusive. Here, we show that both, Stat3 and Stat5 are necessary for initial transformation. However, Stat5- but not Stat3-deletion induces G0/G1 cell cycle arrest and apoptosis of imatinib-sensitive and imatinib-resistant stable leukaemic cells in vitro. Accordingly, Stat5-abrogation led to effective elimination of myeloid and lymphoid leukaemia maintenance in vivo. Hence, we identified Stat5 as a vulnerable point in the oncogenic network downstream of Bcr/Abl representing a case of non-oncogene addiction (NOA).
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Affiliation(s)
- Andrea Hoelbl
- Institute of Pharmacology, Centre of Biomolecular Medicine and Pharmacology, Medical University of Vienna, Austria
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1304
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Stein A, Aloy P. Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures. PLoS Comput Biol 2010; 6:e1000789. [PMID: 20502673 PMCID: PMC2873903 DOI: 10.1371/journal.pcbi.1000789] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 04/15/2010] [Indexed: 11/18/2022] Open
Abstract
Many biological responses to intra- and extracellular stimuli are regulated through complex networks of transient protein interactions where a globular domain in one protein recognizes a linear peptide from another, creating a relatively small contact interface. These peptide stretches are often found in unstructured regions of proteins, and contain a consensus motif complementary to the interaction surface displayed by their binding partners. While most current methods for the de novo discovery of such motifs exploit their tendency to occur in disordered regions, our work here focuses on another observation: upon binding to their partner domain, motifs adopt a well-defined structure. Indeed, through the analysis of all peptide-mediated interactions of known high-resolution three-dimensional (3D) structure, we found that the structure of the peptide may be as characteristic as the consensus motif, and help identify target peptides even though they do not match the established patterns. Our analyses of the structural features of known motifs reveal that they tend to have a particular stretched and elongated structure, unlike most other peptides of the same length. Accordingly, we have implemented a strategy based on a Support Vector Machine that uses this features, along with other structure-encoded information about binding interfaces, to search the set of protein interactions of known 3D structure and to identify unnoticed peptide-mediated interactions among them. We have also derived consensus patterns for these interactions, whenever enough information was available, and compared our results with established linear motif patterns and their binding domains. Finally, to cross-validate our identification strategy, we scanned interactome networks from four model organisms with our newly derived patterns to see if any of them occurred more often than expected. Indeed, we found significant over-representations for 64 domain-motif interactions, 46 of which had not been described before, involving over 6,000 interactions in total for which we could suggest the molecular details determining the binding. Protein-protein interactions are paramount in any aspect of the cellular life. Some proteins form large macromolecular complexes that execute core functionalities of the cell, while others transmit information in signalling networks to co-ordinate these processes. The latter type, of more transient nature, often occurs through the recognition of a small linear sequence motif in one protein by a specialized globular domain in the other. These peptide stretches often contain a consensus pattern complementary to the interaction surface displayed by their binding partners, and adopt a well-defined structure upon binding. Information that is currently available only from high-resolution three-dimensional (3D) structures, and that can be as characteristic as the consensus motif itself. In this manuscript, we present a strategy to identify novel domain-motif interactions (DMIs) among the set of protein complexes of known 3D structures, which provides information on the consensus motif and binding domain and also allows ready identification of the key interacting residues. A detailed knowledge of the interface is critical to plan further functional studies and for the development of interfering elements, be it drug-like compounds or novel engineered binding proteins or peptides. The small interfaces typical for DMIs make them interesting candidates for all these applications.
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Affiliation(s)
- Amelie Stein
- Institute for Research in Biomedicine, Joint IRB-BSC Program in Computational Biology, Barcelona, Spain
| | - Patrick Aloy
- Institute for Research in Biomedicine, Joint IRB-BSC Program in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- * E-mail:
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1305
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High-throughput sequencing for the identification of binding molecules from DNA-encoded chemical libraries. Bioorg Med Chem Lett 2010; 20:4188-92. [PMID: 20538458 DOI: 10.1016/j.bmcl.2010.05.053] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 05/12/2010] [Accepted: 05/13/2010] [Indexed: 11/21/2022]
Abstract
DNA-encoded chemical libraries are large collections of small organic molecules, individually coupled to DNA fragments that serve as amplifiable identification bar codes. The isolation of specific binders requires a quantitative analysis of the distribution of DNA fragments in the library before and after capture on an immobilized target protein of interest. Here, we show how Illumina sequencing can be applied to the analysis of DNA-encoded chemical libraries, yielding over 10 million DNA sequence tags per flow-lane. The technology can be used in a multiplex format, allowing the encoding and subsequent sequencing of multiple selections in the same experiment. The sequence distributions in DNA-encoded chemical library selections were found to be similar to the ones obtained using 454 technology, thus reinforcing the concept that DNA sequencing is an appropriate avenue for the decoding of library selections. The large number of sequences obtained with the Illumina method now enables the study of very large DNA-encoded chemical libraries (>500,000 compounds) and reduces decoding costs.
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1306
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Rao PPN, Kabir SN, Mohamed T. Nonsteroidal Anti-Inflammatory Drugs (NSAIDs): Progress in Small Molecule Drug Development. Pharmaceuticals (Basel) 2010; 3:1530-1549. [PMID: 27713316 PMCID: PMC4033995 DOI: 10.3390/ph3051530] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 04/22/2010] [Accepted: 05/12/2010] [Indexed: 02/06/2023] Open
Abstract
Ever since the discovery of aspirin, small molecule therapeutics have been widely prescribed to treat inflammation and pain. Aspirin and several small molecule NSAIDs are known to inhibit the enzymes cyclooxygenase-1 (COX-1) and -2 (COX-2). Despite the success of NSAIDs to treat inflammatory disorders, the development of a clinically useful small molecule NSAIDs with decreased side effect profiles is an ongoing effort. The recent discovery and development of selective COX-2 inhibitors was a step toward this direction. Emerging trends are represented by the progress in the development of hybrid agents such as nitric oxide donor-NSAIDs (NO-NSAIDs) and dual COX/lipoxygenase (LOX) inhibitors. This review focuses on the recent advances in the rational design of small molecule NSAIDs in therapy.
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Affiliation(s)
- Praveen P N Rao
- School of Pharmacy, Health Sciences Campus, University of Waterloo, 200 University Avenue W. Waterloo, ON, N2L 3G1 Canada.
| | - Saad N Kabir
- School of Pharmacy, Health Sciences Campus, University of Waterloo, 200 University Avenue W. Waterloo, ON, N2L 3G1 Canada
| | - Tarek Mohamed
- School of Pharmacy, Health Sciences Campus, University of Waterloo, 200 University Avenue W. Waterloo, ON, N2L 3G1 Canada
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1307
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Lavecchia A, Di Giovanni C, Novellino E. Inhibitors of Cdc25 phosphatases as anticancer agents: a patent review. Expert Opin Ther Pat 2010; 20:405-25. [PMID: 20166845 DOI: 10.1517/13543771003623232] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD The cell division cycle 25 (Cdc25) family of proteins are highly conserved dual specificity phosphatases that regulate cyclin-dependent kinases, the main gatekeepers of the eukaryotic cell division cycle. The three isoforms of Cdc25, including Cdc25A, Cdc25B and Cdc25C, appear to act on different cyclin-dependent kinase/cyclin complexes at different stages of the cell cycle. Overexpression of Cdc25A and/or Cdc25B, but not Cdc25C, has been detected in numerous cancers and is often correlated with a poor clinical prognosis. Thus, inhibition of these phosphatases may represent a promising therapeutic approach in oncology. AREAS COVERED IN THIS REVIEW The main focus of the present review is to describe the development of Cdc25 inhibitors over the years. We describe different compounds according to the decade of discovery and focus attention on molecules that were published in patents. WHAT THE READER WILL GAIN Insight into the most clinically relevant therapeutic Cdc25 analogues that have been published in over 40 patents over the past 19 years. TAKE HOME MESSAGE Some Cdc25 inhibitors have suppressed in vivo the growth of human tumor xenografts in animals; this confirmed the validity of using Cdc25 phosphatase inhibition as an anticancer strategy, but side effects and toxicity remain to be investigated.
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Affiliation(s)
- Antonio Lavecchia
- Università di Napoli Federico II, Facoltà di Farmacia, Dipartimento di Chimica Farmaceutica e Tossicologica, Drug Discovery Laboratory, Via D. Montesano 49, Napoli, 80131, Italy.
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1308
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Uhlenheuer DA, Petkau K, Brunsveld L. Combining supramolecular chemistry with biology. Chem Soc Rev 2010; 39:2817-26. [PMID: 20461247 DOI: 10.1039/b820283b] [Citation(s) in RCA: 287] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Supramolecular chemistry has primarily found its inspiration in biological molecules, such as proteins and lipids, and their interactions. Currently the supramolecular assembly of designed compounds can be controlled to great extent. This provides the opportunity to combine these synthetic supramolecular elements with biomolecules for the study of biological phenomena. This tutorial review focuses on the possibilities of the marriage of synthetic supramolecular architectures and biological systems. It highlights that synthetic supramolecular elements are for example ideal platforms for the recognition and modulation of proteins and cells. The unique features of synthetic supramolecular systems with control over size, shape, valency, and interaction strength allow the generation of structures fitting the demands to approach the biological problems at hand. Supramolecular chemistry has come full circle, studying the biology and its molecules which initially inspired its conception.
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Affiliation(s)
- Dana A Uhlenheuer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612AZ Eindhoven, The Netherlands
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1309
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Kota S, Scampavia L, Spicer T, Beeler AB, Takahashi V, Snyder JK, Porco JA, Hodder P, Strosberg AD. A time-resolved fluorescence-resonance energy transfer assay for identifying inhibitors of hepatitis C virus core dimerization. Assay Drug Dev Technol 2010; 8:96-105. [PMID: 20035614 DOI: 10.1089/adt.2009.0217] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Binding of hepatitis C virus (HCV) RNA to core, the capsid protein, results in the formation of the nucleocapsid, the first step in the assembly of the viral particle. A novel assay was developed to discover small molecule inhibitors of core dimerization. This assay is based on time-resolved fluorescence resonance energy transfer (TR-FRET) between anti-tag antibodies labeled with either europium cryptate (Eu) or allophycocyanin (XL-665). The N-terminal 106-residue portion of core protein (core106) was tagged with either glutathione-S-transferase (GST) or a Flag peptide. Tag-free core106 was selected as the reference inhibitor. The assay was used to screen the library of pharmacologically active compounds (LOPAC) consisting of 1,280 compounds and a 2,240-compound library from the Center for Chemical Methodology and Library Development at Boston University (CMLD-BU). Ten of the 28 hits from the primary TR-FRET run were confirmed in a secondary amplified luminescent proximity homogeneous assay (ALPHA screen). One hit was further characterized by dose-response analysis yielding an IC(50) of 9.3 microM. This 513 Da compound was shown to inhibit HCV production in cultured hepatoma cells.
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Affiliation(s)
- Smitha Kota
- Department of Infectology, The Scripps Research Institute-Scripps Florida, Jupiter, Florida 33458, USA
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1310
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Evolution: a guide to perturb protein function and networks. Curr Opin Struct Biol 2010; 20:351-9. [PMID: 20444593 DOI: 10.1016/j.sbi.2010.04.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 04/08/2010] [Indexed: 12/11/2022]
Abstract
Protein interactions give rise to networks that control cell fate in health and disease; selective means to probe these interactions are therefore of wide interest. We discuss here Evolutionary Tracing (ET), a comparative method to identify protein functional sites and to guide experiments that selectively block, recode, or mimic their amino acid determinants. These studies suggest, in principle, a scalable approach to perturb individual links in protein networks.
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1311
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Rose R, Erdmann S, Bovens S, Wolf A, Rose M, Hennig S, Waldmann H, Ottmann C. Identification and Structure of Small-Molecule Stabilizers of 14-3-3 Protein-Protein Interactions. Angew Chem Int Ed Engl 2010; 49:4129-32. [DOI: 10.1002/anie.200907203] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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1312
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Identifizierung und Struktur von niedermolekularen Substanzen als Stabilisatoren von 14-3-3-Protein-Protein-Wechselwirkungen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907203] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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1313
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Manolios N, Ali M, Bender V. T-cell antigen receptor (TCR) transmembrane peptides: A new paradigm for the treatment of autoimmune diseases. Cell Adh Migr 2010; 4:273-83. [PMID: 20431344 DOI: 10.4161/cam.4.2.11909] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cell surface membranes are generally considered as inert and hydrophobic providing a stable physical barrier that anchor proteins and maintain cellular homeostasis between the intra- and the extra-cellular environment. The integral proteins that transverse membranes do so once or multiple times and can function alone or as part of a larger complex. Far from being inert, there is a multiplicity of biophysical factors that drive protein-protein and protein-lipid interactions within membranes that are being increasingly recognised as very important for cellular function. Unravelling these "hot-spots" on the contact surface of transmembrane (TM) proteins and targeting peptides to these sites to interrupt the cohesive interaction between the proteins provides both an enormous challenge and a huge therapeutic potential that as yet remains unrecognized. Indeed, with biopharmaceutical research on the rise, TM peptides may prove a useful innovation. Using the T-cell antigen receptor (TCR) as a model system of multi-subunits interacting at the TM via electrostatic charges the potential for peptides as therapeutic agents to interfere with normal immune responses is discussed. The principles of such can be extended to other similar receptor systems including those involved in cancer or infection.
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Affiliation(s)
- Nicholas Manolios
- Department of Rheumatology, Westmead Hospital, Westmead, NSW, Australia.
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1314
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Izumikawa M, Hashimoto J, Hirokawa T, Sugimoto S, Kato T, Takagi M, Shin-Ya K. JBIR-22, an inhibitor for protein-protein interaction of the homodimer of proteasome assembly factor 3. JOURNAL OF NATURAL PRODUCTS 2010; 73:628-631. [PMID: 20180542 DOI: 10.1021/np900788e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Proteasome assembling chaperone (PAC) 3 acts as a homodimer and plays an important role in proteasome formation. We screened JBIR-22 (1) as an inhibitor for protein-protein interaction (PPI) of PAC3 homodimer from our natural product library using a protein fragment complementation assay (PCA) with monomeric Kusabira-Green fluorescent protein (mKG) in vitro and found that 1 exhibited potent inhibitory activity against PAC3 homodimerization. Compound 1 showed long-term cytotoxicity against the human cervical carcinoma cell line, HeLa. This is the first report of a PPI inhibitor for proteasome assembly factors.
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Affiliation(s)
- Miho Izumikawa
- Biomedicinal Information Research Center (BIRC), Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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1315
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Thrombospondin-1 as a Paradigm for the Development of Antiangiogenic Agents Endowed with Multiple Mechanisms of Action. Pharmaceuticals (Basel) 2010; 3:1241-1278. [PMID: 27713299 PMCID: PMC4034032 DOI: 10.3390/ph3041241] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2010] [Revised: 04/20/2010] [Accepted: 04/22/2010] [Indexed: 12/12/2022] Open
Abstract
Uncontrolled neovascularization occurs in several angiogenesis-dependent diseases, including cancer. Neovascularization is tightly controlled by the balance between angiogenic growth factors and antiangiogenic agents. The various natural angiogenesis inhibitors identified so far affect neovascularization by different mechanisms of action. Thrombospondin-1 (TSP-1) is a matricellular modular glycoprotein that acts as a powerful endogenous inhibitor of angiogenesis. It acts both indirectly, by sequestering angiogenic growth factors and effectors in the extracellular environment, and directly, by inducing an antiangiogenic program in endothelial cells following engagement of specific receptors including CD36, CD47, integrins and proteoglycans (all involved in angiogenesis ). In view of its central, multifaceted role in angiogenesis, TSP-1 has served as a source of antiangiogenic tools, including TSP-1 fragments, synthetic peptides and peptidomimetics, gene therapy strategies, and agents that up-regulate TSP-1 expression. This review discusses TSP-1-based inhibitors of angiogenesis, their mechanisms of action and therapeutic potential, drawing our experience with angiogenic growth factor-interacting TSP-1 peptides, and the possibility of exploiting them to design novel antiangiogenic agents.
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1316
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Drewry DH, Macarron R. Enhancements of screening collections to address areas of unmet medical need: an industry perspective. Curr Opin Chem Biol 2010; 14:289-98. [PMID: 20413343 DOI: 10.1016/j.cbpa.2010.03.024] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/19/2010] [Accepted: 03/24/2010] [Indexed: 01/31/2023]
Abstract
The past 20 years have witnessed an impressive expansion of the 'drug space'; defined as the intersection of the Medicinal Chemistry space and the Biologically Active space relevant in the quest for new treatments for disease. Despite the success of known lead discovery tactics, areas of unmet medical need are often linked to challenging or novel targets and are poorly served by current screening collections. A successful strategy to fill the gaps is to diversify the approaches taken in the enhancement of screening collections. Possible strategies include investments through proven methods, exploring areas of chemical space previously neglected (e.g. hydrophilic compounds, natural product mimics), and applying tactics to the lead discovery process that are complementary to HTS (e.g. fragment based screening or multidisciplinary team efforts to tackle new target classes).
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Affiliation(s)
- David H Drewry
- Molecular Discovery Research, GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, NC 27709, USA.
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1317
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Przybylo M, Borowik T, Langner M. Fluorescence Techniques for Determination of the Membrane Potentials in High Throughput Screening. J Fluoresc 2010; 20:1139-57. [DOI: 10.1007/s10895-010-0665-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 04/05/2010] [Indexed: 01/14/2023]
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1318
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Cerchietti LC, Ghetu AF, Zhu X, Da Silva GF, Shijun Z, Matthews M, Bunting KL, Polo JM, Farès C, Arrowsmith CH, Yang SN, Garcia M, Coop A, MacKerell AD, Privé GG, Melnick A. A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo. Cancer Cell 2010; 17:400-11. [PMID: 20385364 PMCID: PMC2858395 DOI: 10.1016/j.ccr.2009.12.050] [Citation(s) in RCA: 234] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 10/29/2009] [Accepted: 02/05/2010] [Indexed: 11/30/2022]
Abstract
The BCL6 transcriptional repressor is the most frequently involved oncogene in diffuse large B cell lymphoma (DLBCL). We combined computer-aided drug design with functional assays to identify low-molecular-weight compounds that bind to the corepressor binding groove of the BCL6 BTB domain. One such compound disrupted BCL6/corepressor complexes in vitro and in vivo, and was observed by X-ray crystallography and NMR to bind the critical site within the BTB groove. This compound could induce expression of BCL6 target genes and kill BCL6-positive DLBCL cell lines. In xenotransplantation experiments, the compound was nontoxic and potently suppressed DLBCL tumors in vivo. The compound also killed primary DLBCLs from human patients.
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Affiliation(s)
- Leandro C. Cerchietti
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY
| | | | - Xiao Zhu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD
| | - Gustavo F. Da Silva
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Zhong Shijun
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD
| | - Marilyn Matthews
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD
| | - Karen L. Bunting
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY
| | - Jose M. Polo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY
| | | | - Cheryl H. Arrowsmith
- Ontario Cancer Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Shao Ning Yang
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY
| | - Monica Garcia
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY
| | - Andrew Coop
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD
| | - Gilbert G. Privé
- Ontario Cancer Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Ari Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY
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1319
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Bevan DE, Martinko AJ, Loram LC, Stahl JA, Taylor FR, Joshee S, Watkins LR, Yin H. Selection, Preparation, and Evaluation of Small- Molecule Inhibitors of Toll-Like Receptor 4. ACS Med Chem Lett 2010; 1:194-198. [PMID: 20824192 DOI: 10.1021/ml100041f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Toll-like receptor 4 (TLR4), a membrane spanning receptor protein that functions in complex with its accessory protein MD-2, is an intriguing target for therapeutic development. Herein we report the identification of a series of novel TLR4 inhibitors and the development of a robust, enantioselective synthesis using an unprecedented Mannich-type reaction to functionalize a pyrazole ring. In silico and cellular assay results demonstrated that compound 1 and its analogues selectively block TLR4 activation in live cells. Animal model tests showed that 1 and its derivatives could potentiate morphine-induced analgesia in vivo, presumably by attenuating the opioid-induced TLR4 activation.
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Affiliation(s)
| | | | - Lisa C. Loram
- Department of Psychology and Neuroscience
- The Center for Neuroscience
| | | | | | | | - Linda R. Watkins
- Department of Psychology and Neuroscience
- The Center for Neuroscience
| | - Hang Yin
- Department of Chemistry and Biochemistry
- The Center for Neuroscience
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1320
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Abstract
The accurate prediction of protein druggability (propensity to bind high-affinity drug-like small molecules) would greatly benefit the fields of chemical genomics and drug discovery. We have developed a novel approach to quantitatively assess protein druggability by computationally screening a fragment-like compound library. In analogy to NMR-based fragment screening, we dock ∼11000 fragments against a given binding site and compute a computational hit rate based on the fraction of molecules that exceed an empirically chosen score cutoff. We perform a large-scale evaluation of the approach on four datasets, totaling 152 binding sites. We demonstrate that computed hit rates correlate with hit rates measured experimentally in a previously published NMR-based screening method. Secondly, we show that the in silico fragment screening method can be used to distinguish known druggable and non-druggable targets, including both enzymes and protein-protein interaction sites. Finally, we explore the sensitivity of the results to different receptor conformations, including flexible protein-protein interaction sites. Besides its original aim to assess druggability of different protein targets, this method could be used to identifying druggable conformations of flexible binding site for lead discovery, and suggesting strategies for growing or joining initial fragment hits to obtain more potent inhibitors.
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1321
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Jarvis A, Allerston CK, Jia H, Herzog B, Garza-Garcia A, Winfield N, Ellard K, Aqil R, Lynch R, Chapman C, Hartzoulakis B, Nally J, Stewart M, Cheng L, Menon M, Tickner M, Djordjevic S, Driscoll PC, Zachary I, Selwood DL. Small molecule inhibitors of the neuropilin-1 vascular endothelial growth factor A (VEGF-A) interaction. J Med Chem 2010; 53:2215-26. [PMID: 20151671 PMCID: PMC2841442 DOI: 10.1021/jm901755g] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the molecular design and synthesis of EG00229, 2, the first small molecule ligand for the VEGF-A receptor neuropilin 1 (NRP1) and the structural characterization of NRP1-ligand complexes by NMR spectroscopy and X-ray crystallography. Mutagenesis studies localized VEGF-A binding in the NRP1 b1 domain and a peptide fragment of VEGF-A was shown to bind at the same site by NMR, providing the basis for small molecule design. Compound 2 demonstrated inhibition of VEGF-A binding to NRP1 and attenuated VEGFR2 phosphorylation in endothelial cells. Inhibition of migration of endothelial cells was also observed. The viability of A549 lung carcinoma cells was reduced by 2, and it increased the potency of the cytotoxic agents paclitaxel and 5-fluorouracil when given in combination. These studies provide the basis for design of specific small molecule inhibitors of ligand binding to NRP1.
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Affiliation(s)
- Ashley Jarvis
- Domainex Ltd, NCE Discovery, 324 Cambridge Science Park, Cambridge CB4 0WG, UK
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1322
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Galzi JL, Hachet-Haas M, Bonnet D, Daubeuf F, Lecat S, Hibert M, Haiech J, Frossard N. Neutralizing endogenous chemokines with small molecules. Principles and potential therapeutic applications. Pharmacol Ther 2010; 126:39-55. [PMID: 20117133 PMCID: PMC7112609 DOI: 10.1016/j.pharmthera.2009.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 12/24/2009] [Indexed: 02/08/2023]
Abstract
Regulation of cellular responses to external stimuli such as hormones, neurotransmitters, or cytokines is achieved through the control of all steps of the complex cascade starting with synthesis, going through maturation steps, release, distribution, degradation and/or uptake of the signalling molecule interacting with the target protein. One possible way of regulation, referred to as scavenging or neutralization of the ligand, has been increasingly studied, especially for small protein ligands. It shows innovative potential in chemical biology approaches as well as in disease treatment. Neutralization of protein ligands, as for example cytokines or chemokines can lead to the validation of signalling pathways under physiological or pathophysiological conditions, and in certain cases, to the development of therapeutic molecules now used in autoimmune diseases, chronic inflammation and cancer treatment. This review explores the field of ligand neutralization and tries to determine to what extent small chemical molecules could substitute for neutralizing antibodies in therapeutic approaches.
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Affiliation(s)
- Jean-Luc Galzi
- IREBS, FRE3211, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67412 Illkirch, France.
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1323
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Co-expression of human malaria parasite Plasmodium falciparum orotate phosphoribosyltransferase and orotidine 5’-monophosphate decarboxylase as enzyme complex in Escherichia coli: a novel strategy for drug development. ASIAN BIOMED 2010. [DOI: 10.2478/abm-2010-0037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Background: Human malaria parasite Plasmodium falciparum operates de novo pyrimidine biosynthetic pathway. The fifth and sixth enzymes of the pathway form a heterotetrameric complex, containing two molecules each of orotate phosphoribosyltransferase (OPRT) and orotidine 5’-monophosphate decarboxylase (OMPDC). Objective: Define the function of OPRT-OMPDC enzyme complex of P. falciparum by co-expressing the enzymes in Escherichia coli. Methods: The constructed plasmids containing either P. falciparum OPRT or OMPDC were cloned in E. coli by co-transformation. Both genes were co-expressed as OPRT-OMPDC enzyme complex and the complex was purified by chromatographic techniques, including N2+-NTA affinity, Hi Trap Q HP anion-exchange, uridine 5’- monophosphate affinity, and Superose 12 gel-filtration columns. Physical and kinetic properties of the enzyme complex were analyzed for its molecular mass. Results: Co-transformation of PfOPRT and PfOMPDC plasmids in E. coli were achieved with a clone containing DNA ratio of 1:2, respectively. Both plasmids remained stable and were functionally expressed in the E. coli cell for at least 20 weeks. The P. falciparum OPRT-OMPDC enzyme complex were co-expressed and the complex was co-eluted in all chromatographic columns during purification and physical analysis. The molecular mass of the complex was 130 kDa, whereas the PfOPRT and PfOMPDC component were 35.6 and 41.5 kDa, respectively. The enzymatic activities of the complex were competitively inhibited by their products of each enzyme component. Conclusion: P. falciparum OPRT and OMPDC in E. coli as an enzyme complex were co-transformed and functionally co-expressed. These have similar properties to the native enzyme purified directly from P. falciparum, and this character is different from that of the human host organism. The enzyme complex would be suitable as new target to research selective inhibitors as suitable drugs to better control this disease.
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1324
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Assi SA, Tanaka T, Rabbitts TH, Fernandez-Fuentes N. PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces. Nucleic Acids Res 2010; 38:e86. [PMID: 20008102 PMCID: PMC2847225 DOI: 10.1093/nar/gkp1158] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 11/13/2009] [Accepted: 11/24/2009] [Indexed: 11/30/2022] Open
Abstract
Protein-protein interactions (PPIs) are ubiquitous in Biology, and thus offer an enormous potential for the discovery of novel therapeutics. Although protein interfaces are large and lack defining physiochemical traits, is well established that only a small portion of interface residues, the so-called hot spot residues, contribute the most to the binding energy of the protein complex. Moreover, recent successes in development of novel drugs aimed at disrupting PPIs rely on targeting such residues. Experimental methods for describing critical residues are lengthy and costly; therefore, there is a need for computational tools that can complement experimental efforts. Here, we describe a new computational approach to predict hot spot residues in protein interfaces. The method, called Presaging Critical Residues in Protein interfaces (PCRPi), depends on the integration of diverse metrics into a unique probabilistic measure by using Bayesian Networks. We have benchmarked our method using a large set of experimentally verified hot spot residues and on a blind prediction on the protein complex formed by HRAS protein and a single domain antibody. Under both scenarios, PCRPi delivered consistent and accurate predictions. Finally, PCRPi is able to handle cases where some of the input data is either missing or not reliable (e.g. evolutionary information).
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Affiliation(s)
| | | | | | - Narcis Fernandez-Fuentes
- Leeds Institute of Molecular Medicine, Section of Experimental Therapeutics, St James’s University Hospital, University of Leeds, Leeds, LS9 7TF, UK
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1325
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Henchey LK, Kushal S, Dubey R, Chapman RN, Olenyuk BZ, Arora PS. Inhibition of hypoxia inducible factor 1-transcription coactivator interaction by a hydrogen bond surrogate alpha-helix. J Am Chem Soc 2010; 132:941-3. [PMID: 20041650 DOI: 10.1021/ja9082864] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Designed ligands that inhibit hypoxia-inducible gene expression could offer new tools for genomic research and, potentially, drug discovery efforts for the treatment of neovascularization in cancers. We report a stabilized alpha-helix designed to target the binding interface between the C-terminal transactivation domain (C-TAD) of hypoxia-inducible factor 1alpha (HIF-1alpha) and cysteine-histidine rich region (CH1) of transcriptional coactivator CBP/p300. The synthetic helix disrupts the structure and function of this complex, resulting in a rapid downregulation of two hypoxia-inducible genes (VEGF and GLUT1) in cell culture.
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Affiliation(s)
- Laura K Henchey
- Department of Chemistry, New York University, New York, New York 10003, USA
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1326
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Bockaert J, Perroy J, Bécamel C, Marin P, Fagni L. GPCR interacting proteins (GIPs) in the nervous system: Roles in physiology and pathologies. Annu Rev Pharmacol Toxicol 2010; 50:89-109. [PMID: 20055699 DOI: 10.1146/annurev.pharmtox.010909.105705] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
G protein-coupled receptors (GPCRs) are key transmembrane recognition molecules for regulatory signals such as light, odors, taste hormones, and neurotransmitters. In addition to activating guanine nucleotide binding proteins (G proteins), GPCRs associate with a variety of GPCR-interacting proteins (GIPs). GIPs contain structural interacting domains that allow the formation of large functional complexes involved in G protein-dependent and -independent signaling. At the cellular level, other functions of GIPs include targeting of GPCRs to subcellular compartments and their trafficking to and from the plasma membrane. Recently, roles of GPCR-GIP interactions in central nervous system physiology and pathologies have been revealed. Here, we highlight the role of GIPs in some important neurological and psychiatric disorders, as well as their potential for the future development of therapeutic drugs.
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Affiliation(s)
- Joël Bockaert
- Centre National de la Recherche Scientifique, UMR, Institut de Génomique Fonctionnelle, Montpellier, France.
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1327
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Coyne AG, Scott DE, Abell C. Drugging challenging targets using fragment-based approaches. Curr Opin Chem Biol 2010; 14:299-307. [PMID: 20223699 DOI: 10.1016/j.cbpa.2010.02.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Revised: 02/08/2010] [Accepted: 02/15/2010] [Indexed: 02/02/2023]
Abstract
Fragment-based approaches have now become firmly established in the drug discovery armoury. After notable early successes against protein kinases, the versatility and power of fragment-based approaches are increasingly being demonstrated on more diverse and difficult protein targets. This review highlights seven examples including targeting protein-protein interactions, a RNA polymerase and a DNA-binding protein. It shows how fragment-based approaches using small libraries have been successful when large HTS screens have failed. It also highlights the range of biophysical approaches being used and the interplay between experimental and in silico screens. The examples all show the iterative way in which potency is built up by synthetic elaboration of the initial fragment hits.
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Affiliation(s)
- Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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1328
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Bourgeas R, Basse MJ, Morelli X, Roche P. Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. PLoS One 2010; 5:e9598. [PMID: 20231898 PMCID: PMC2834754 DOI: 10.1371/journal.pone.0009598] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Accepted: 02/15/2010] [Indexed: 11/19/2022] Open
Abstract
Background In the last decade, the inhibition of protein-protein interactions (PPIs) has emerged from both academic and private research as a new way to modulate the activity of proteins. Inhibitors of these original interactions are certainly the next generation of highly innovative drugs that will reach the market in the next decade. However, in silico design of such compounds still remains challenging. Methodology/Principal Findings Here we describe this particular PPI chemical space through the presentation of 2P2IDB, a hand-curated database dedicated to the structure of PPIs with known inhibitors. We have analyzed protein/protein and protein/inhibitor interfaces in terms of geometrical parameters, atom and residue properties, buried accessible surface area and other biophysical parameters. The interfaces found in 2P2IDB were then compared to those of representative datasets of heterodimeric complexes. We propose a new classification of PPIs with known inhibitors into two classes depending on the number of segments present at the interface and corresponding to either a single secondary structure element or to a more globular interacting domain. 2P2IDB complexes share global shape properties with standard transient heterodimer complexes, but their accessible surface areas are significantly smaller. No major conformational changes are seen between the different states of the proteins. The interfaces are more hydrophobic than general PPI's interfaces, with less charged residues and more non-polar atoms. Finally, fifty percent of the complexes in the 2P2IDB dataset possess more hydrogen bonds than typical protein-protein complexes. Potential areas of study for the future are proposed, which include a new classification system consisting of specific families and the identification of PPI targets with high druggability potential based on key descriptors of the interaction. Conclusions 2P2I database stores structural information about PPIs with known inhibitors and provides a useful tool for biologists to assess the potential druggability of their interfaces. The database can be accessed at http://2p2idb.cnrs-mrs.fr.
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Affiliation(s)
- Raphaël Bourgeas
- Laboratoire Interactions et Modulateurs de Réponses (UPR3243), Centre National de la Recherche Scientifique (CNRS) & Aix-Marseille Universités, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Marie-Jeanne Basse
- Laboratoire Interactions et Modulateurs de Réponses (UPR3243), Centre National de la Recherche Scientifique (CNRS) & Aix-Marseille Universités, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Xavier Morelli
- Laboratoire Interactions et Modulateurs de Réponses (UPR3243), Centre National de la Recherche Scientifique (CNRS) & Aix-Marseille Universités, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
- * E-mail: (XM); (PR)
| | - Philippe Roche
- Laboratoire Interactions et Modulateurs de Réponses (UPR3243), Centre National de la Recherche Scientifique (CNRS) & Aix-Marseille Universités, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
- * E-mail: (XM); (PR)
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1329
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Giménez-Oya V, Villacañas Ó, Obiol-Pardo C, Antolin-Llovera M, Rubio-Martinez J, Imperial S. Design of novel ligands of CDP-methylerythritol kinase by mimicking direct protein-protein and solvent-mediated interactions. J Mol Recognit 2010; 24:71-80. [DOI: 10.1002/jmr.1024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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1330
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Reynès C, Host H, Camproux AC, Laconde G, Leroux F, Mazars A, Deprez B, Fahraeus R, Villoutreix BO, Sperandio O. Designing focused chemical libraries enriched in protein-protein interaction inhibitors using machine-learning methods. PLoS Comput Biol 2010; 6:e1000695. [PMID: 20221258 PMCID: PMC2832677 DOI: 10.1371/journal.pcbi.1000695] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 01/30/2010] [Indexed: 12/27/2022] Open
Abstract
Protein-protein interactions (PPIs) may represent one of the next major classes of therapeutic targets. So far, only a minute fraction of the estimated 650,000 PPIs that comprise the human interactome are known with a tiny number of complexes being drugged. Such intricate biological systems cannot be cost-efficiently tackled using conventional high-throughput screening methods. Rather, time has come for designing new strategies that will maximize the chance for hit identification through a rationalization of the PPI inhibitor chemical space and the design of PPI-focused compound libraries (global or target-specific). Here, we train machine-learning-based models, mainly decision trees, using a dataset of known PPI inhibitors and of regular drugs in order to determine a global physico-chemical profile for putative PPI inhibitors. This statistical analysis unravels two important molecular descriptors for PPI inhibitors characterizing specific molecular shapes and the presence of a privileged number of aromatic bonds. The best model has been transposed into a computer program, PPI-HitProfiler, that can output from any drug-like compound collection a focused chemical library enriched in putative PPI inhibitors. Our PPI inhibitor profiler is challenged on the experimental screening results of 11 different PPIs among which the p53/MDM2 interaction screened within our own CDithem platform, that in addition to the validation of our concept led to the identification of 4 novel p53/MDM2 inhibitors. Collectively, our tool shows a robust behavior on the 11 experimental datasets by correctly profiling 70% of the experimentally identified hits while removing 52% of the inactive compounds from the initial compound collections. We strongly believe that this new tool can be used as a global PPI inhibitor profiler prior to screening assays to reduce the size of the compound collections to be experimentally screened while keeping most of the true PPI inhibitors. PPI-HitProfiler is freely available on request from our CDithem platform website, www.CDithem.com.
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Affiliation(s)
| | - Hélène Host
- CDithem Platform/IGM, Paris, France
- Inserm UMR-S 761, Institut Pasteur de Lille, Lille, France
- Université Lille 2, Faculté des Sciences Pharmaceutiques et Biologiques, Lille, France
| | | | - Guillaume Laconde
- CDithem Platform/IGM, Paris, France
- Inserm UMR-S 761, Institut Pasteur de Lille, Lille, France
- Université Lille 2, Faculté des Sciences Pharmaceutiques et Biologiques, Lille, France
| | - Florence Leroux
- CDithem Platform/IGM, Paris, France
- Inserm UMR-S 761, Institut Pasteur de Lille, Lille, France
- Université Lille 2, Faculté des Sciences Pharmaceutiques et Biologiques, Lille, France
| | - Anne Mazars
- CDithem Platform/IGM, Paris, France
- UMR-S940, Hôpital St Louis, Paris, France
| | - Benoit Deprez
- CDithem Platform/IGM, Paris, France
- Inserm UMR-S 761, Institut Pasteur de Lille, Lille, France
- Université Lille 2, Faculté des Sciences Pharmaceutiques et Biologiques, Lille, France
| | - Robin Fahraeus
- CDithem Platform/IGM, Paris, France
- UMR-S940, Hôpital St Louis, Paris, France
| | - Bruno O. Villoutreix
- Inserm UMR-S 973/MTi, University Paris Diderot, Paris, France
- CDithem Platform/IGM, Paris, France
| | - Olivier Sperandio
- Inserm UMR-S 973/MTi, University Paris Diderot, Paris, France
- CDithem Platform/IGM, Paris, France
- * E-mail:
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1331
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Meurice N, Wang L, Lipinski CA, Yang Z, Hulme C, Loftus JC. Structural conservation in band 4.1, ezrin, radixin, moesin (FERM) domains as a guide to identify inhibitors of the proline-rich tyrosine kinase 2. J Med Chem 2010; 53:669-77. [PMID: 20017492 DOI: 10.1021/jm901247a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The nonreceptor focal adhesion kinases FAK and Pyk2 play a central role in the regulation of glioma cell proliferation and migration, making them attractive targets to improve clinical outcome. Noncatalytic targeting represents a novel approach to regulate the activity of these tyrosine kinases. A combination of site directed mutagenesis and molecular modeling was used to identify compounds that target the F3 module of the Pyk2 FERM domain. A protein pharmacophore model for the Pyk2 FERM/F3 module, generated utilizing the structural conservation of ligand-bound FERM domains with known 3D structures, was used to search the LeadQuest compound library. Compounds compliant with the model were tested for their ability to inhibit the binding of a monoclonal antibody that maps to a functional site on the F3 module. The highest scoring compound bound directly to the Pyk2 FERM domain, inhibited Pyk2 stimulated glioma migration, and provides the framework for the development of novel therapeutic agents to target the activity of the focal adhesion kinases.
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Affiliation(s)
- Nathalie Meurice
- The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
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1332
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Buchwald P, Margolles-Clark E, Kenyon NS, Ricordi C. Organic dyes as small molecule protein-protein interaction inhibitors for the CD40-CD154 costimulatory interaction. J Mol Recognit 2010; 23:65-73. [PMID: 19621420 DOI: 10.1002/jmr.969] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
It is becoming increasingly clear that small molecules can often act as effective protein-protein interaction (PPI) inhibitors, an area of increasing interest for its many possible therapeutic applications. We have identified several organic dyes and related small molecules that (i) concentration-dependently inhibit the important CD40-CD154 costimulatory interaction with activities in the low micromolar (microM) range, (ii) show selectivity toward this particular PPI, (iii) seem to bind on the surface of CD154, and (iv) concentration-dependently inhibit the CD154-induced B cell proliferation. They were identified through an iterative activity screening/structural similarity search procedure starting with suramin as lead, and the best smaller compounds, the main focus of the present work, achieved an almost 3-fold increase in ligand efficiency (DeltaG(0)/nonhydrogen atom = 0.8 kJ/N(nHa)) approaching the average of known promising small-molecule PPI inhibitors (approximately 1.0 kJ/N(nHa)). Since CD154 is a member of the tumor necrosis factor (TNF) superfamily of cell surface interaction molecules, inhibitory activities on the TNF-R1-TNF-alpha interactions were also determined to test for specificity, and the compounds selected here all showed more than 30-fold selectivity toward the CD40-CD154 interaction. Because of their easy availability in various structural scaffolds and because of their good protein-binding ability, often explored for tissue-specific staining and other purposes, such organic dyes can provide a valuable addition to the chemical space searched to identify small molecule PPI inhibitors in general.
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Affiliation(s)
- Peter Buchwald
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA.
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1333
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Bauer RA, Wurst JM, Tan DS. Expanding the range of 'druggable' targets with natural product-based libraries: an academic perspective. Curr Opin Chem Biol 2010; 14:308-14. [PMID: 20202892 DOI: 10.1016/j.cbpa.2010.02.001] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 02/02/2010] [Indexed: 01/25/2023]
Abstract
Existing drugs address a relatively narrow range of biological targets. As a result, libraries of drug-like molecules have proven ineffective against a variety of challenging targets, such as protein-protein interactions, nucleic acid complexes, and antibacterial modalities. In contrast, natural products are known to be effective at modulating such targets, and new libraries are being developed based on underrepresented scaffolds and regions of chemical space associated with natural products. This has led to several recent successes in identifying new chemical probes that address these challenging targets.
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Affiliation(s)
- Renato A Bauer
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, Box 422, New York, NY 10065, USA
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1334
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Affiliation(s)
- Petra Tošovská
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003
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1335
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Muldoon J, Ashcroft AE, Wilson AJ. Selective protein-surface sensing using ruthenium(II) tris(bipyridine) complexes. Chemistry 2010; 16:100-3. [PMID: 19946912 DOI: 10.1002/chem.200902368] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- James Muldoon
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
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1336
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Chen JM, Pojer F, Blasco B, Cole ST. Towards anti-virulence drugs targeting ESX-1 mediated pathogenesis of Mycobacterium tuberculosis. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.ddmec.2010.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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1337
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Miyamoto-Sato E, Fujimori S, Ishizaka M, Hirai N, Masuoka K, Saito R, Ozawa Y, Hino K, Washio T, Tomita M, Yamashita T, Oshikubo T, Akasaka H, Sugiyama J, Matsumoto Y, Yanagawa H. A comprehensive resource of interacting protein regions for refining human transcription factor networks. PLoS One 2010; 5:e9289. [PMID: 20195357 PMCID: PMC2827538 DOI: 10.1371/journal.pone.0009289] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 01/05/2010] [Indexed: 11/24/2022] Open
Abstract
Large-scale data sets of protein-protein interactions (PPIs) are a valuable resource for mapping and analysis of the topological and dynamic features of interactome networks. The currently available large-scale PPI data sets only contain information on interaction partners. The data presented in this study also include the sequences involved in the interactions (i.e., the interacting regions, IRs) suggested to correspond to functional and structural domains. Here we present the first large-scale IR data set obtained using mRNA display for 50 human transcription factors (TFs), including 12 transcription-related proteins. The core data set (966 IRs; 943 PPIs) displays a verification rate of 70%. Analysis of the IR data set revealed the existence of IRs that interact with multiple partners. Furthermore, these IRs were preferentially associated with intrinsic disorder. This finding supports the hypothesis that intrinsically disordered regions play a major role in the dynamics and diversity of TF networks through their ability to structurally adapt to and bind with multiple partners. Accordingly, this domain-based interaction resource represents an important step in refining protein interactions and networks at the domain level and in associating network analysis with biological structure and function.
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Affiliation(s)
- Etsuko Miyamoto-Sato
- Advanced Research Centers, Keio University, Yokohama, Japan
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
- * E-mail: (HY); (EM-S)
| | | | - Masamichi Ishizaka
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Naoya Hirai
- Advanced Research Centers, Keio University, Yokohama, Japan
| | - Kazuyo Masuoka
- Advanced Research Centers, Keio University, Yokohama, Japan
| | - Rintaro Saito
- Department of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Yosuke Ozawa
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Katsuya Hino
- Advanced Research Centers, Keio University, Yokohama, Japan
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Takanori Washio
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Masaru Tomita
- Department of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Tatsuhiro Yamashita
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
- BioIT Business Development Unit, Fujitsu Limited, Chiba, Japan
| | - Tomohiro Oshikubo
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
- Production Solution Business Unit, Production Solution Division, Solutions and Services Department, Fujitsu Advanced Engineering Limited, Tokyo, Japan
| | - Hidetoshi Akasaka
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
- Production Solution Business Unit, Production Solution Division, Solutions and Services Department, Fujitsu Advanced Engineering Limited, Tokyo, Japan
| | - Jun Sugiyama
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
- Special Suite Team, Custom Primer Production Department, Haneda Laboratories, Invitrogen Japan K.K., Tokyo, Japan
| | - Yasuo Matsumoto
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
- Automation, QIAGEN K.K., Tokyo, Japan
| | - Hiroshi Yanagawa
- Advanced Research Centers, Keio University, Yokohama, Japan
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
- * E-mail: (HY); (EM-S)
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1338
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Stott KM, Yusof AM, Perham RN, Jones DD. A surface loop directs conformational switching of a lipoyl domain between a folded and a novel misfolded structure. Structure 2010; 17:1117-27. [PMID: 19679089 DOI: 10.1016/j.str.2009.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Revised: 06/30/2009] [Accepted: 07/02/2009] [Indexed: 10/20/2022]
Abstract
A prominent surface loop links the first two beta strands of the lipoyl domain (E2plip) from the pyruvate dehydrogenase multienzyme complex of Escherichia coli. We show here that shortening this loop by two residues generates a protein that populates two structurally distinct stable conformers: an active, native-like monomer (HM) and a functionally compromised misfolded dimer (LM). Conversion of LM to HM was observed after exposure to temperatures above 50 degrees C. Removal of two additional residues from the loop caused the protein to adopt exclusively the misfolded conformation. Detailed NMR structural studies of the misfolded dimer reveal that the N-terminal half of the domain was unfolded and dynamic, whereas the C-terminal halves of two monomers had associated to form a structure with two-fold symmetry and a topology mimicking that of the folded monomer. The surface loop is therefore a hitherto unsuspected determinant in the folding process that leads to a functional protein.
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1339
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García-Sosa AT, Hetényi C, Maran U. Drug efficiency indices for improvement of molecular docking scoring functions. J Comput Chem 2010; 31:174-84. [PMID: 19422000 DOI: 10.1002/jcc.21306] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A dataset of protein-drug complexes with experimental binding energy and crystal structure were analyzed and the performance of different docking engines and scoring functions (as well as components of these) for predicting the free energy of binding and several ligand efficiency indices were compared. The aim was not to evaluate the best docking method, but to determine the effect of different efficiency indices on the experimental and predicted free energy. Some ligand efficiency indices, such as DeltaG/W (Wiener index), DeltaG/NoC (number of carbons), and DeltaG/P (partition coefficient), improve the correlation between experimental and calculated values. This effect was shown to be valid across the different scoring functions and docking programs. It also removes the common bias of scoring functions in favor of larger ligands. For all scoring functions, the efficiency indices effectively normalize the free energy derived indices, to give values closer to experiment. Compound collection filtering can be done prior or after docking, using pharmacokinetic as well as pharmacodynamic profiles. Achieving these better correlations with experiment can improve the ability of docking scoring functions to predict active molecules in virtual screening.
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1340
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Bach A, Chi CN, Pang GF, Olsen L, Kristensen AS, Jemth P, Strømgaard K. Design and synthesis of highly potent and plasma-stable dimeric inhibitors of the PSD-95-NMDA receptor interaction. Angew Chem Int Ed Engl 2010; 48:9685-9. [PMID: 19937879 DOI: 10.1002/anie.200904741] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Anders Bach
- Department of Medicinal Chemistry, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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1341
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Davis FP, Sali A. The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comput Biol 2010; 6:e1000668. [PMID: 20140189 PMCID: PMC2816688 DOI: 10.1371/journal.pcbi.1000668] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 12/31/2009] [Indexed: 02/03/2023] Open
Abstract
Protein–protein interactions are challenging targets for modulation by small molecules. Here, we propose an approach that harnesses the increasing structural coverage of protein complexes to identify small molecules that may target protein interactions. Specifically, we identify ligand and protein binding sites that overlap upon alignment of homologous proteins. Of the 2,619 protein structure families observed to bind proteins, 1,028 also bind small molecules (250–1000 Da), and 197 exhibit a statistically significant (p<0.01) overlap between ligand and protein binding positions. These “bi-functional positions”, which bind both ligands and proteins, are particularly enriched in tyrosine and tryptophan residues, similar to “energetic hotspots” described previously, and are significantly less conserved than mono-functional and solvent exposed positions. Homology transfer identifies ligands whose binding sites overlap at least 20% of the protein interface for 35% of domain–domain and 45% of domain–peptide mediated interactions. The analysis recovered known small-molecule modulators of protein interactions as well as predicted new interaction targets based on the sequence similarity of ligand binding sites. We illustrate the predictive utility of the method by suggesting structural mechanisms for the effects of sanglifehrin A on HIV virion production, bepridil on the cellular entry of anthrax edema factor, and fusicoccin on vertebrate developmental pathways. The results, available at http://pibase.janelia.org, represent a comprehensive collection of structurally characterized modulators of protein interactions, and suggest that homologous structures are a useful resource for the rational design of interaction modulators. Proteins function through their interactions with other biological molecules, including other proteins. Often times, these interactions underlie cellular processes that go awry in disease. Therefore, modulating these interactions with small molecules is an active area of research for new drugs to treat diseases and new chemical tools to dissect cellular interaction networks. However, targeting protein–protein interactions has proven to be more challenging than the typical drug targets found on individual proteins. Here, we present a computational approach that aims to help in this challenge by identifying regions of protein–protein interfaces that may be amenable to targeting by small molecules. Through a comprehensive analysis of all known protein structures, we identify closely related proteins that in one case bind a protein and in another case bind a small molecule. We find that a significant number of protein–protein interactions occur through surface regions that bind small molecules in related proteins. These “bi-functional” positions, which can bind both proteins and ligands, will serve as an additional piece of structural information that can aid experimentalists in developing small molecules that modulate protein interactions.
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Affiliation(s)
- Fred P. Davis
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America
- * E-mail: (FPD); (AS)
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (FPD); (AS)
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1342
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Abstract
In the last decade, various target-guided synthesis (TGS) approaches have been developed in which a target protein is actively engaged in the assembly of its own bidentate ligand from a pool of smaller reactive fragments. Although TGS is relatively less explored, it demonstrates great promise to streamline drug discovery by combining screening and synthesis into a single step. Herein, we focus on the class of kinetic TGS approaches which utilize irreversible reactions to combine two reactive fragments into the inhibitory compound. These kinetic TGS applications have been successful due to the unique combination of the slow nature of the chemical reaction combining the two fragments into a single molecule and the use of reactive fragments displaying good affinities toward one of the binding sites. So far, kinetic TGS and especially in situ click chemistry, a kinetic TGS variant using the 1,3-dipolar cycloaddition of azides and alkynes, have led to the identification of highly potent inhibitors. This tutorial review focuses on kinetic TGS approaches aside from those employing the 1,3-dipolar cycloaddition of azides and alkynes, and discusses the features and advantages of these TGS approaches in detail.
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Affiliation(s)
- Xiangdong Hu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205 A, Tampa, FL 33620, USA
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1343
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Colombo G, Margosio B, Ragona L, Neves M, Bonifacio S, Annis DS, Stravalaci M, Tomaselli S, Giavazzi R, Rusnati M, Presta M, Zetta L, Mosher DF, Ribatti D, Gobbi M, Taraboletti G. Non-peptidic thrombospondin-1 mimics as fibroblast growth factor-2 inhibitors: an integrated strategy for the development of new antiangiogenic compounds. J Biol Chem 2010; 285:8733-42. [PMID: 20056600 DOI: 10.1074/jbc.m109.085605] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Endogenous inhibitors of angiogenesis, such as thrombospondin-1 (TSP-1), are promising sources of therapeutic agents to treat angiogenesis-driven diseases, including cancer. TSP-1 regulates angiogenesis through different mechanisms, including binding and sequestration of the angiogenic factor fibroblast growth factor-2 (FGF-2), through a site located in the calcium binding type III repeats. We hypothesized that the FGF-2 binding sequence of TSP-1 might serve as a template for the development of inhibitors of angiogenesis. Using a peptide array approach followed by binding assays with synthetic peptides and recombinant proteins, we identified a FGF-2 binding sequence of TSP-1 in the 15-mer sequence DDDDDNDKIPDDRDN. Molecular dynamics simulations, taking the full flexibility of the ligand and receptor into account, and nuclear magnetic resonance identified the relevant residues and conformational determinants for the peptide-FGF interaction. This information was translated into a pharmacophore model used to screen the NCI2003 small molecule databases, leading to the identification of three small molecules that bound FGF-2 with affinity in the submicromolar range. The lead compounds inhibited FGF-2-induced endothelial cell proliferation in vitro and affected angiogenesis induced by FGF-2 in the chicken chorioallantoic membrane assay. These small molecules, therefore, represent promising leads for the development of antiangiogenic agents. Altogether, this study demonstrates that new biological insights obtained by integrated multidisciplinary approaches can be used to develop small molecule mimics of endogenous proteins as therapeutic agents.
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Affiliation(s)
- Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milan 20131, Italy
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1344
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1345
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Ge J, Wu H, Yao SQ. An unnatural amino acid that mimics phosphotyrosine. Chem Commun (Camb) 2010; 46:2980-2. [DOI: 10.1039/c000283f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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1346
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Abstract
IMPORTANCE OF THE FIELD The focal adhesion tyrosine kinases FAK and Pyk2 are uniquely situated to act as critical mediators for the activation of signaling pathways that regulate cell migration, proliferation and survival. By coordinating adhesion and cytoskeletal dynamics with survival and growth signaling, FAK and Pyk2 represent molecular therapeutic targets in cancer as malignant cells often exhibit defects in these processes. AREAS COVERED IN THIS REVIEW This review examines the structure and function of the focal adhesion kinase Pyk2 and intends to provide a rationale for the employment of modulating strategies that include both catalytic and extra-catalytic approaches that have been developed in the last 3 - 5 years. WHAT THE READER WILL GAIN Targeting tyrosine kinases in oncology has focused on the ATP binding pocket as means to inhibit catalytic activity and downregulate pathways involved in tumor invasion. This review discusses the available catalytic inhibitors and compares them to the alternative approach of targeting protein-protein interactions that regulate kinase activity. TAKE HOME MESSAGE Development of specific catalytic inhibitors of the focal adhesion kinases has improved but significant challenges remain. Thus, approaches that inhibit the effector function of Pyk2 by targeting regulatory modules can increase specificity and will be a welcome asset to the therapeutic arena.
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Affiliation(s)
- Christopher A Lipinski
- Mayo Clinic Collaborative Research Building, Department of Biochemistry and Molecular Biology, Scottsdale, AZ 85259, USA
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1347
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Carr JL, Offermann DA, Holdom MD, Dusart P, White AJP, Beavil AJ, Leatherbarrow RJ, Lindell SD, Sutton BJ, Spivey AC. Total synthesis of (±)-aspercyclide A and its C19 methyl ether. Chem Commun (Camb) 2010; 46:1824-6. [DOI: 10.1039/b923528k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The total syntheses of (±)-aspercyclide A (1) and its C19 methyl ether derivative (15a) are described. ELISA studies show that both compounds display comparable antagonist activity against the IgE–FcεRI protein–protein interaction.
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Affiliation(s)
- James L. Carr
- Department of Chemistry
- South Kensington campus
- London
- UK
| | | | - Mary D. Holdom
- King's College London
- The Randall Division of Cell & Molecular Biophysics
- London
- UK
| | - Philip Dusart
- King's College London
- The Randall Division of Cell & Molecular Biophysics
- London
- UK
| | | | - Andrew J. Beavil
- King's College London
- The Randall Division of Cell & Molecular Biophysics
- London
- UK
| | | | | | - Brian J. Sutton
- King's College London
- The Randall Division of Cell & Molecular Biophysics
- London
- UK
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1348
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Janin J. Protein–protein docking tested in blind predictions: the CAPRI experiment. MOLECULAR BIOSYSTEMS 2010; 6:2351-62. [DOI: 10.1039/c005060c] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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1349
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Lunt B, Szurmant H, Procaccini A, Hoch JA, Hwa T, Weigt M. Inference of Direct Residue Contacts in Two-Component Signaling. Methods Enzymol 2010; 471:17-41. [DOI: 10.1016/s0076-6879(10)71002-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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1350
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Abstract
The transcription factor c-Myc is overexpressed in many tumors in human beings and has been identified as a highly promising target for cancer therapy. Most biological functions of c-Myc require heterodimerization with its activation partner Max. Inhibition of the protein-protein interactions between c-Myc and Max by small molecules has been shown to be a feasible and powerful approach toward the inhibition of c-Myc functions. More recently, stabilization of Max homodimers to reduce the amount of Max available for activating c-Myc has also been demonstrated to counteract Myc activity. This review summarizes our current knowledge on small organic molecules that inhibit c-Myc by modulating protein-protein interactions relevant for the biological function of this important oncoprotein.
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