101
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Norton RS, Leung EWW, Chandrashekaran IR, MacRaild CA. Applications of (19)F-NMR in Fragment-Based Drug Discovery. Molecules 2016; 21:molecules21070860. [PMID: 27438818 PMCID: PMC6273323 DOI: 10.3390/molecules21070860] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/21/2016] [Accepted: 06/21/2016] [Indexed: 11/16/2022] Open
Abstract
(19)F-NMR has proved to be a valuable tool in fragment-based drug discovery. Its applications include screening libraries of fluorinated fragments, assessing competition among elaborated fragments and identifying the binding poses of promising hits. By observing fluorine in both the ligand and the target protein, useful information can be obtained on not only the binding pose but also the dynamics of ligand-protein interactions. These applications of (19)F-NMR will be illustrated in this review with studies from our fragment-based drug discovery campaigns against protein targets in parasitic and infectious diseases.
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Affiliation(s)
- Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
| | - Eleanor W W Leung
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
| | - Indu R Chandrashekaran
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
| | - Christopher A MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
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102
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Modell AE, Blosser SL, Arora PS. Systematic Targeting of Protein-Protein Interactions. Trends Pharmacol Sci 2016; 37:702-713. [PMID: 27267699 DOI: 10.1016/j.tips.2016.05.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/14/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022]
Abstract
Over the past decade, protein-protein interactions (PPIs) have gone from being neglected as 'undruggable' to being considered attractive targets for the development of therapeutics. Recent advances in computational analysis, fragment-based screening, and molecular design have revealed promising strategies to address the basic molecular recognition challenge: how to target large protein surfaces with specificity. Several systematic and complementary workflows have been developed to yield successful inhibitors of PPIs. Here we review the major contemporary approaches utilized for the discovery of inhibitors and focus on a structure-based workflow, from the selection of a biological target to design.
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Affiliation(s)
- Ashley E Modell
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sarah L Blosser
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
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103
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Keserű GM, Erlanson DA, Ferenczy GG, Hann MM, Murray CW, Pickett SD. Design Principles for Fragment Libraries: Maximizing the Value of Learnings from Pharma Fragment-Based Drug Discovery (FBDD) Programs for Use in Academia. J Med Chem 2016; 59:8189-206. [DOI: 10.1021/acs.jmedchem.6b00197] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- György M. Keserű
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Daniel A. Erlanson
- Carmot Therapeutics, Inc. 409 Illinois Street, San Francisco, California 94158, United States
| | - György G. Ferenczy
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Michael M. Hann
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Stephen D. Pickett
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
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104
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Mamonov AB, Moghadasi M, Mirzaei H, Zarbafian S, Grove LE, Bohnuud T, Vakili P, Paschalidis IC, Vajda S, Kozakov D. Focused grid-based resampling for protein docking and mapping. J Comput Chem 2016; 37:961-70. [PMID: 26837000 PMCID: PMC4814242 DOI: 10.1002/jcc.24273] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 08/31/2015] [Accepted: 09/26/2015] [Indexed: 12/27/2022]
Abstract
The fast Fourier transform (FFT) sampling algorithm has been used with success in application to protein-protein docking and for protein mapping, the latter docking a variety of small organic molecules for the identification of binding hot spots on the target protein. Here we explore the local rather than global usage of the FFT sampling approach in docking applications. If the global FFT based search yields a near-native cluster of docked structures for a protein complex, then focused resampling of the cluster generally leads to a substantial increase in the number of conformations close to the native structure. In protein mapping, focused resampling of the selected hot spot regions generally reveals further hot spots that, while not as strong as the primary hot spots, also contribute to ligand binding. The detection of additional ligand binding regions is shown by the improved overlap between hot spots and bound ligands.
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Affiliation(s)
- Artem B. Mamonov
- Department of Biomedical Engineering, Boston University, Boston MA 02215
| | - Mohammad Moghadasi
- Center for Information and Systems Engineering, Boston University, Boston, MA 02215
| | - Hanieh Mirzaei
- Center for Information and Systems Engineering, Boston University, Boston, MA 02215
| | - Shahrooz Zarbafian
- Department of Mechanical Engineering, Boston University, Boston MA 02215
| | - Laurie E. Grove
- Department of Sciences, Wentworth Institute of Technology, Boston, MA 02115, USA
| | - Tanggis Bohnuud
- Department of Biomedical Engineering, Boston University, Boston MA 02215
| | - Pirooz Vakili
- Center for Information and Systems Engineering, Boston University, Boston, MA 02215
- Department of Mechanical Engineering, Boston University, Boston MA 02215
| | - Ioannis Ch. Paschalidis
- Center for Information and Systems Engineering, Boston University, Boston, MA 02215
- Department of Electrical and Computer Engineering, Boston University, Boston MA 02215
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston MA 02215
- Center for Information and Systems Engineering, Boston University, Boston, MA 02215
- Department of Chemistry, Boston University, Boston MA 02215
| | - Dima Kozakov
- Department of Biomedical Engineering, Boston University, Boston MA 02215
- Departemnt of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, 11790
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105
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Wilkins SE, Abboud MI, Hancock RL, Schofield CJ. Targeting Protein-Protein Interactions in the HIF System. ChemMedChem 2016; 11:773-86. [PMID: 26997519 PMCID: PMC4848768 DOI: 10.1002/cmdc.201600012] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/24/2016] [Indexed: 12/18/2022]
Abstract
Animals respond to chronic hypoxia by increasing the levels of a transcription factor known as the hypoxia-inducible factor (HIF). HIF upregulates multiple genes, the products of which work to ameliorate the effects of limited oxygen at cellular and systemic levels. Hypoxia sensing by the HIF system involves hydroxylase-catalysed post-translational modifications of the HIF α-subunits, which 1) signal for degradation of HIF-α and 2) limit binding of HIF to transcriptional coactivator proteins. Because the hypoxic response is relevant to multiple disease states, therapeutic manipulation of the HIF-mediated response has considerable medicinal potential. In addition to modulation of catalysis by the HIF hydroxylases, the HIF system manifests other possibilities for therapeutic intervention involving protein-protein and protein-nucleic acid interactions. Recent advances in our understanding of the structural biology and biochemistry of the HIF system are facilitating medicinal chemistry efforts. Herein we give an overview of the HIF system, focusing on structural knowledge of protein-protein interactions and how this might be used to modulate the hypoxic response for therapeutic benefit.
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Affiliation(s)
- Sarah E Wilkins
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Rebecca L Hancock
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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106
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Scott DE, Bayly AR, Abell C, Skidmore J. Small molecules, big targets: drug discovery faces the protein–protein interaction challenge. Nat Rev Drug Discov 2016; 15:533-50. [DOI: 10.1038/nrd.2016.29] [Citation(s) in RCA: 625] [Impact Index Per Article: 78.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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107
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Corbi-Verge C, Kim PM. Motif mediated protein-protein interactions as drug targets. Cell Commun Signal 2016; 14:8. [PMID: 26936767 PMCID: PMC4776425 DOI: 10.1186/s12964-016-0131-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/25/2016] [Indexed: 12/17/2022] Open
Abstract
Protein-protein interactions (PPI) are involved in virtually every cellular process and thus represent an attractive target for therapeutic interventions. A significant number of protein interactions are frequently formed between globular domains and short linear peptide motifs (DMI). Targeting these DMIs has proven challenging and classical approaches to inhibiting such interactions with small molecules have had limited success. However, recent new approaches have led to the discovery of potent inhibitors, some of them, such as Obatoclax, ABT-199, AEG-40826 and SAH-p53-8 are likely to become approved drugs. These novel inhibitors belong to a wide range of different molecule classes, ranging from small molecules to peptidomimetics and biologicals. This article reviews the main reasons for limited success in targeting PPIs, discusses how successful approaches overcome these obstacles to discovery promising inhibitors for human protein double minute 2 (HDM2), B-cell lymphoma 2 (Bcl-2), X-linked inhibitor of apoptosis protein (XIAP), and provides a summary of the promising approaches currently in development that indicate the future potential of PPI inhibitors in drug discovery.
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Affiliation(s)
- Carles Corbi-Verge
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada.
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108
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Toure M, Crews CM. Niedermolekulare PROTACs: neue Wege zum Abbau von Proteinen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201507978] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Momar Toure
- Departments of Chemistry; Molecular, Cellular & Developmental Biology; Pharmacology; Yale University; New Haven CT 06511 USA
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental Biology; Pharmacology; Yale University; New Haven CT 06511 USA
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109
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Toure M, Crews CM. Small-Molecule PROTACS: New Approaches to Protein Degradation. Angew Chem Int Ed Engl 2016; 55:1966-73. [DOI: 10.1002/anie.201507978] [Citation(s) in RCA: 379] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Momar Toure
- Departments of Chemistry; Molecular, Cellular & Developmental Biology, Pharmacology; Yale University; New Haven CT 06511 USA
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental Biology, Pharmacology; Yale University; New Haven CT 06511 USA
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110
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An Intriguing Correlation Based on the Superimposition of Residue Pairs with Inhibitors that Target Protein-Protein Interfaces. Sci Rep 2016; 6:18543. [PMID: 26730437 PMCID: PMC4698585 DOI: 10.1038/srep18543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/19/2015] [Indexed: 11/26/2022] Open
Abstract
Druggable sites on protein-protein interfaces are difficult to predict. To survey inhibitor-binding sites onto which residues are superimposed at protein-protein interfaces, we analyzed publicly available information for 39 inhibitors that target the protein-protein interfaces of 8 drug targets. By focusing on the differences between residues that were superimposed with inhibitors and non-superimposed residues, we observed clear differences in the distances and changes in the solvent-accessible surface areas (∆SASA). Based on the observation that two or more residues were superimposed onto inhibitors in 37 (95%) of 39 protein-inhibitor complexes, we focused on the two-residue relationships. Application of a cross-validation procedure confirmed a linear negative correlation between the absolute value of the dihedral angle and the sum of the ∆SASAs of the residues. Finally, we applied the regression equation of this correlation to four inhibitors that bind to new sites not bound by the 39 inhibitors as well as additional inhibitors of different targets. Our results shed light on the two-residue correlation between the absolute value of the dihedral angle and the sum of the ∆SASA, which may be a useful relationship for identifying the key two-residues as potential targets of protein-protein interfaces.
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111
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Cardote TAF, Ciulli A. Cyclic and Macrocyclic Peptides as Chemical Tools To Recognise Protein Surfaces and Probe Protein-Protein Interactions. ChemMedChem 2015; 11:787-94. [PMID: 26563831 PMCID: PMC4848765 DOI: 10.1002/cmdc.201500450] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Indexed: 01/25/2023]
Abstract
Targeting protein surfaces and protein-protein interactions (PPIs) with small molecules is a frontier goal of chemical biology and provides attractive therapeutic opportunities in drug discovery. The molecular properties of protein surfaces, including their shallow features and lack of deep binding pockets, pose significant challenges, and as a result have proved difficult to target. Peptides are ideal candidates for this mission due to their ability to closely mimic many structural features of protein interfaces. However, their inherently low intracellular stability and permeability and high in vivo clearance have thus far limited their biological applications. One way to improve these properties is to constrain the secondary structure of linear peptides by cyclisation. Herein we review various classes of cyclic and macrocyclic peptides as chemical probes of protein surfaces and modulators of PPIs. The growing interest in this area and recent advances provide evidence of the potential of developing peptide-like molecules that specifically target these interactions.
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Affiliation(s)
- Teresa A F Cardote
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK.
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112
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Hall DR, Kozakov D, Whitty A, Vajda S. Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery. Trends Pharmacol Sci 2015; 36:724-736. [PMID: 26538314 DOI: 10.1016/j.tips.2015.08.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 01/01/2023]
Abstract
Analysis of binding energy hot spots at protein surfaces can provide crucial insights into the prospects for successful application of fragment-based drug discovery (FBDD), and whether a fragment hit can be advanced into a high-affinity, drug-like ligand. The key factor is the strength of the top ranking hot spot, and how well a given fragment complements it. We show that published data are sufficient to provide a sophisticated and quantitative understanding of how hot spots derive from a protein 3D structure, and how their strength, number, and spatial arrangement govern the potential for a surface site to bind to fragment-sized and larger ligands. This improved understanding provides important guidance for the effective application of FBDD in drug discovery.
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Affiliation(s)
- David R Hall
- Acpharis Inc., 160 North Mill Street, Holliston, MA 01746, USA
| | - Dima Kozakov
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA, 02215, USA.
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA; Department of Chemistry, Boston University, Boston, MA, 02215, USA.
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113
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Hung AW, Silvestre HL, Wen S, George GPC, Boland J, Blundell TL, Ciulli A, Abell C. Optimization of Inhibitors of Mycobacterium tuberculosis Pantothenate Synthetase Based on Group Efficiency Analysis. ChemMedChem 2015; 11:38-42. [PMID: 26486566 PMCID: PMC4949533 DOI: 10.1002/cmdc.201500414] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Indexed: 11/06/2022]
Abstract
Ligand efficiency has proven to be a valuable concept for optimization of leads in the early stages of drug design. Taking this one step further, group efficiency (GE) evaluates the binding efficiency of each appendage of a molecule, further fine‐tuning the drug design process. Here, GE analysis is used to systematically improve the potency of inhibitors of Mycobacterium tuberculosis pantothenate synthetase, an important target in tuberculosis therapy. Binding efficiencies were found to be distributed unevenly within a lead molecule derived using a fragment‐based approach. Substitution of the less efficient parts of the molecule allowed systematic development of more potent compounds. This method of dissecting and analyzing different groups within a molecule offers a rational and general way of carrying out lead optimization, with potential broad application within drug discovery.
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Affiliation(s)
- Alvin W Hung
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK.,Experimental Therapeutic Centre, A-STAR, 11 Biopolis Way, Singapore, 138667, Singapore
| | - H Leonardo Silvestre
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, CB2 1GA, UK
| | - Shijun Wen
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Guillaume P C George
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Jennifer Boland
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, CB2 1GA, UK
| | - Alessio Ciulli
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK.,Division of Biological Chemistry & Drug Discovery, College of Life Sciences, James Black Centre, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK.
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114
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Abdelraheem EMM, Camacho CJ, Dömling A. Focusing on shared subpockets - new developments in fragment-based drug discovery. Expert Opin Drug Discov 2015; 10:1179-87. [PMID: 26296101 DOI: 10.1517/17460441.2015.1080684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Protein-protein interactions (PPIs) are important targets for understanding fundamental biology and for the development of therapeutic agents. Based on different physicochemical properties, numerous pieces of software (e.g., POCKETQUERY, ANCHORQUERY and FTMap) have been reported to find pockets on protein surfaces and have applications in facilitating the design and discovery of small-molecular-weight compounds that bind to these pockets. AREAS COVERED The authors discuss a pocket-centric method of analyzing PPI interfaces, which prioritize their pockets for small-molecule drug discovery and the importance of multicomponent reaction chemistry as starting points for undruggable targets. The authors also provide their perspectives on the field. EXPERT OPINION Only the tight interplay of efficient computational methods capable of screening a large chemical space and fast synthetic chemistry will lead to progress in the rational design of PPI antagonists in the future. Early drug discovery platforms will also benefit from efficient rapid feedback loops from early clinical research back to molecular design and the medicinal chemistry bench.
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Affiliation(s)
- Eman M M Abdelraheem
- a 1 University of Groningen, A. Deusinglaan, Department of Drug Design, 1, Groningen 9700 AD, The Netherlands .,b 2 Sohag University, Faculty of Science, Chemistry Department , Sohag 82524, Egypt
| | - Carlos J Camacho
- c 3 University of Pittsburgh, Department of Computational Biology, School of Medicine , 3501 Fifth Avenue, Suite 3064, Biomedical Science Tower 3 (BST3), Pittsburgh, PA 15260, USA
| | - Alexander Dömling
- a 1 University of Groningen, A. Deusinglaan, Department of Drug Design, 1, Groningen 9700 AD, The Netherlands .,b 2 Sohag University, Faculty of Science, Chemistry Department , Sohag 82524, Egypt
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115
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Buckley DL, Raina K, Darricarrere N, Hines J, Gustafson JL, Smith IE, Miah AH, Harling JD, Crews CM. HaloPROTACS: Use of Small Molecule PROTACs to Induce Degradation of HaloTag Fusion Proteins. ACS Chem Biol 2015; 10:1831-7. [PMID: 26070106 DOI: 10.1021/acschembio.5b00442] [Citation(s) in RCA: 280] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Small molecule-induced protein degradation is an attractive strategy for the development of chemical probes. One method for inducing targeted protein degradation involves the use of PROTACs, heterobifunctional molecules that can recruit specific E3 ligases to a desired protein of interest. PROTACs have been successfully used to degrade numerous proteins in cells, but the peptidic E3 ligase ligands used in previous PROTACs have hindered their development into more mature chemical probes or therapeutics. We report the design of a novel class of PROTACs that incorporate small molecule VHL ligands to successfully degrade HaloTag7 fusion proteins. These HaloPROTACs will inspire the development of future PROTACs with more drug-like properties. Additionally, these HaloPROTACs are useful chemical genetic tools, due to their ability to chemically knock down widely used HaloTag7 fusion proteins in a general fashion.
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Affiliation(s)
| | | | | | | | | | - Ian E. Smith
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline, Stevenage, SG1 2NY, United Kingdom
| | - Afjal H. Miah
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline, Stevenage, SG1 2NY, United Kingdom
| | - John D. Harling
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline, Stevenage, SG1 2NY, United Kingdom
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116
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Sheng C, Dong G, Miao Z, Zhang W, Wang W. State-of-the-art strategies for targeting protein-protein interactions by small-molecule inhibitors. Chem Soc Rev 2015; 44:8238-59. [PMID: 26248294 DOI: 10.1039/c5cs00252d] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Targeting protein-protein interactions (PPIs) has emerged as a viable approach in modern drug discovery. However, the identification of small molecules enabling us to effectively interrupt their interactions presents significant challenges. In the recent past, significant advances have been made in the development of new biological and chemical strategies to facilitate the discovery process of small-molecule PPI inhibitors. This review aims to highlight the state-of-the-art technologies and the achievements made recently in this field. The "hot spots" of PPIs have been proved to be critical for small molecules to bind. Three strategies including screening, designing, and synthetic approaches have been explored for discovering PPI inhibitors by targeting the "hot spots". Although the classic high throughput screening approach can be used, fragment screening, fragment-based drug design and newly improved virtual screening are demonstrated to be more effective in the discovery of PPI inhibitors. In addition to screening approaches, design strategies including anchor-based and small molecule mimetics of secondary structures involved in PPIs have become powerful tools as well. Finally, constructing new chemically spaced libraries with high diversity and complexity is becoming an important area of interest for PPI inhibitors. The successful cases from the recent five year studies are used to illustrate how these approaches are implemented to uncover and optimize small molecule PPI inhibitors and notably some of them have become promising therapeutics.
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Affiliation(s)
- Chunquan Sheng
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, P. R. China.
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117
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Targeting Cullin-RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation. Biochem J 2015; 467:365-86. [PMID: 25886174 PMCID: PMC4403949 DOI: 10.1042/bj20141450] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In the last decade, the ubiquitin–proteasome system has emerged as a valid target for the development of novel therapeutics. E3 ubiquitin ligases are particularly attractive targets because they confer substrate specificity on the ubiquitin system. CRLs [Cullin–RING (really interesting new gene) E3 ubiquitin ligases] draw particular attention, being the largest family of E3s. The CRLs assemble into functional multisubunit complexes using a repertoire of substrate receptors, adaptors, Cullin scaffolds and RING-box proteins. Drug discovery targeting CRLs is growing in importance due to mounting evidence pointing to significant roles of these enzymes in diverse biological processes and human diseases, including cancer, where CRLs and their substrates often function as tumour suppressors or oncogenes. In the present review, we provide an account of the assembly and structure of CRL complexes, and outline the current state of the field in terms of available knowledge of small-molecule inhibitors and modulators of CRL activity. A comprehensive overview of the reported crystal structures of CRL subunits, components and full-size complexes, alone or with bound small molecules and substrate peptides, is included. This information is providing increasing opportunities to aid the rational structure-based design of chemical probes and potential small-molecule therapeutics targeting CRLs.
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118
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Laraia L, McKenzie G, Spring DR, Venkitaraman AR, Huggins DJ. Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions. CHEMISTRY & BIOLOGY 2015; 22:689-703. [PMID: 26091166 PMCID: PMC4518475 DOI: 10.1016/j.chembiol.2015.04.019] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/01/2015] [Accepted: 04/08/2015] [Indexed: 01/19/2023]
Abstract
Protein-protein interactions (PPIs) underlie the majority of biological processes, signaling, and disease. Approaches to modulate PPIs with small molecules have therefore attracted increasing interest over the past decade. However, there are a number of challenges inherent in developing small-molecule PPI inhibitors that have prevented these approaches from reaching their full potential. From target validation to small-molecule screening and lead optimization, identifying therapeutically relevant PPIs that can be successfully modulated by small molecules is not a simple task. Following the recent review by Arkin et al., which summarized the lessons learnt from prior successes, we focus in this article on the specific challenges of developing PPI inhibitors and detail the recent advances in chemistry, biology, and computation that facilitate overcoming them. We conclude by providing a perspective on the field and outlining four innovations that we see as key enabling steps for successful development of small-molecule inhibitors targeting PPIs.
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Affiliation(s)
- Luca Laraia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Grahame McKenzie
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - David J Huggins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK; Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK.
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119
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Ligand deconstruction: Why some fragment binding positions are conserved and others are not. Proc Natl Acad Sci U S A 2015; 112:E2585-94. [PMID: 25918377 DOI: 10.1073/pnas.1501567112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fragment-based drug discovery (FBDD) relies on the premise that the fragment binding mode will be conserved on subsequent expansion to a larger ligand. However, no general condition has been established to explain when fragment binding modes will be conserved. We show that a remarkably simple condition can be developed in terms of how fragments coincide with binding energy hot spots--regions of the protein where interactions with a ligand contribute substantial binding free energy--the locations of which can easily be determined computationally. Because a substantial fraction of the free energy of ligand binding comes from interacting with the residues in the energetically most important hot spot, a ligand moiety that sufficiently overlaps with this region will retain its location even when other parts of the ligand are removed. This hypothesis is supported by eight case studies. The condition helps identify whether a protein is suitable for FBDD, predicts the size of fragments required for screening, and determines whether a fragment hit can be extended into a higher affinity ligand. Our results show that ligand binding sites can usefully be thought of in terms of an anchor site, which is the top-ranked hot spot and dominates the free energy of binding, surrounded by a number of weaker satellite sites that confer improved affinity and selectivity for a particular ligand and that it is the intrinsic binding potential of the protein surface that determines whether it can serve as a robust binding site for a suitably optimized ligand.
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120
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Cuchillo R, Pinto-Gil K, Michel J. A Collective Variable for the Rapid Exploration of Protein Druggability. J Chem Theory Comput 2015; 11:1292-307. [PMID: 26579775 DOI: 10.1021/ct501072t] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Rémi Cuchillo
- EaStCHEM School of Chemistry, Joseph Black Building, West Mains
Road, Edinburgh EH9 3JJ, United Kingdom
| | - Kevin Pinto-Gil
- EaStCHEM School of Chemistry, Joseph Black Building, West Mains
Road, Edinburgh EH9 3JJ, United Kingdom
| | - Julien Michel
- EaStCHEM School of Chemistry, Joseph Black Building, West Mains
Road, Edinburgh EH9 3JJ, United Kingdom
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121
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Nguyen HC, Yang H, Fribourgh JL, Wolfe LS, Xiong Y. Insights into Cullin-RING E3 ubiquitin ligase recruitment: structure of the VHL-EloBC-Cul2 complex. Structure 2015; 23:441-449. [PMID: 25661653 DOI: 10.1016/j.str.2014.12.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/03/2014] [Accepted: 12/11/2014] [Indexed: 01/24/2023]
Abstract
The von Hippel-Lindau tumor suppressor protein (VHL) recruits a Cullin 2 (Cul2) E3 ubiquitin ligase to downregulate HIF-1α, an essential transcription factor for the hypoxia response. Mutations in VHL lead to VHL disease and renal cell carcinomas. Inhibition of this pathway to upregulate erythropoietin production is a promising new therapy to treat ischemia and chronic anemia. Here, we report the crystal structure of VHL bound to a Cul2 N-terminal domain, Elongin B, and Elongin C (EloC). Cul2 interacts with both the VHL BC box and cullin box and a novel EloC site. Comparison with other cullin E3 ligase structures shows that there is a conserved, yet flexible, cullin recognition module and that cullin selectivity is influenced by distinct electrostatic interactions. Our structure provides a structural basis for the study of the pathogenesis of VHL disease and rationale for the design of novel compounds that may modulate cullin-substrate receptor interactions.
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Affiliation(s)
- Henry C Nguyen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Haitao Yang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Jennifer L Fribourgh
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Leslie S Wolfe
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
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122
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Douse CH, Vrielink N, Wenlin Z, Cota E, Tate EW. Targeting a dynamic protein-protein interaction: fragment screening against the malaria myosin A motor complex. ChemMedChem 2015; 10:134-43. [PMID: 25367834 PMCID: PMC4506568 DOI: 10.1002/cmdc.201402357] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Indexed: 01/13/2023]
Abstract
Motility is a vital feature of the complex life cycle of Plasmodium falciparum, the apicomplexan parasite that causes human malaria. Processes such as host cell invasion are thought to be powered by a conserved actomyosin motor (containing myosin A or myoA), correct localization of which is dependent on a tight interaction with myosin A tail domain interacting protein (MTIP) at the inner membrane of the parasite. Although disruption of this protein-protein interaction represents an attractive means to investigate the putative roles of myoA-based motility and to inhibit the parasitic life cycle, no small molecules have been identified that bind to MTIP. Furthermore, it has not been possible to obtain a crystal structure of the free protein, which is highly dynamic and unstable in the absence of its natural myoA tail partner. Herein we report the de novo identification of the first molecules that bind to and stabilize MTIP via a fragment-based, integrated biophysical approach and structural investigations to examine the binding modes of hit compounds. The challenges of targeting such a dynamic system with traditional fragment screening workflows are addressed throughout.
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Affiliation(s)
- Christopher H Douse
- Department of Chemistry, Imperial College London, South KensingtonLondon SW7 2AZ (UK) E-mail:
- Centre for Structural Biology, Department of Life Sciences, Imperial College LondonSouth Kensington, London SW7 2AZ (UK)
- Institute of Chemical Biology, Imperial College LondonSouth Kensington, London SW7 2AZ (UK)
| | - Nina Vrielink
- Department of Chemistry, Imperial College London, South KensingtonLondon SW7 2AZ (UK) E-mail:
| | - Zhang Wenlin
- Department of Chemistry, Imperial College London, South KensingtonLondon SW7 2AZ (UK) E-mail:
| | - Ernesto Cota
- Centre for Structural Biology, Department of Life Sciences, Imperial College LondonSouth Kensington, London SW7 2AZ (UK)
- Institute of Chemical Biology, Imperial College LondonSouth Kensington, London SW7 2AZ (UK)
| | - Edward W Tate
- Department of Chemistry, Imperial College London, South KensingtonLondon SW7 2AZ (UK) E-mail:
- Institute of Chemical Biology, Imperial College LondonSouth Kensington, London SW7 2AZ (UK)
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123
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Abstract
Fragment hopping is a fragment-based approach to designing biologically active small molecules. The key of this approach is the determination of the minimal pharmacophoric elements in the three-dimensional space. Based on the derived minimal pharmacophoric elements, new fragments with different chemotypes can be generated and positioned to the active site of the target protein. Herein, we detail a protocol for performing fragment hopping. This approach can not only explore a wide chemical space to produce new ligands with novel scaffolds but also characterize and utilize the delicate differences in the active sites between isofunctional proteins to produce new ligands with high target selectivity/specificity.
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Affiliation(s)
- Kevin B Teuscher
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, 315 South 1400 East, Salt Lake City, Utah, 84112-0850, USA
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124
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Scott DE, Coyne AG, Venkitaraman A, Blundell TL, Abell C, Hyvönen M. Small-molecule inhibitors that target protein-protein interactions in the RAD51 family of recombinases. ChemMedChem 2014; 10:296-303. [PMID: 25470112 PMCID: PMC4506530 DOI: 10.1002/cmdc.201402428] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Indexed: 11/13/2022]
Abstract
The development of small molecules that inhibit protein–protein interactions continues to be a challenge in chemical biology and drug discovery. Herein we report the development of indole-based fragments that bind in a shallow surface pocket of a humanised surrogate of RAD51. RAD51 is an ATP-dependent recombinase that plays a key role in the repair of double-strand DNA breaks. It both self-associates, forming filament structures with DNA, and interacts with the BRCA2 protein through a common “FxxA” tetrapeptide motif. We elaborated previously identified fragment hits that target the FxxA motif site and developed small-molecule inhibitors that are approximately 500-fold more potent than the initial fragments. The lead compounds were shown to compete with the BRCA2-derived Ac-FHTA-NH2 peptide and the self-association peptide of RAD51, but they had no effect on ATP binding. This study is the first reported elaboration of small-molecular-weight fragments against this challenging target.
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Affiliation(s)
- Duncan E Scott
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW (UK)
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125
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Galdeano C, Gadd MS, Soares P, Scaffidi S, Van Molle I, Birced I, Hewitt S, Dias DM, Ciulli A. Structure-guided design and optimization of small molecules targeting the protein-protein interaction between the von Hippel-Lindau (VHL) E3 ubiquitin ligase and the hypoxia inducible factor (HIF) alpha subunit with in vitro nanomolar affinities. J Med Chem 2014; 57:8657-63. [PMID: 25166285 PMCID: PMC4207132 DOI: 10.1021/jm5011258] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
E3 ubiquitin ligases are attractive targets in the ubiquitin-proteasome system, however, the development of small-molecule ligands has been rewarded with limited success. The von Hippel-Lindau protein (pVHL) is the substrate recognition subunit of the VHL E3 ligase that targets HIF-1α for degradation. We recently reported inhibitors of the pVHL:HIF-1α interaction, however they exhibited moderate potency. Herein, we report the design and optimization, guided by X-ray crystal structures, of a ligand series with nanomolar binding affinities.
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Affiliation(s)
- Carles Galdeano
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Dow Street, Dundee, DD1 5EH, Scotland, U.K
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126
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Dias DM, Ciulli A. NMR approaches in structure-based lead discovery: recent developments and new frontiers for targeting multi-protein complexes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:101-12. [PMID: 25175337 PMCID: PMC4261069 DOI: 10.1016/j.pbiomolbio.2014.08.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/06/2014] [Accepted: 08/19/2014] [Indexed: 01/08/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a pivotal method for structure-based and fragment-based lead discovery because it is one of the most robust techniques to provide information on protein structure, dynamics and interaction at an atomic level in solution. Nowadays, in most ligand screening cascades, NMR-based methods are applied to identify and structurally validate small molecule binding. These can be high-throughput and are often used synergistically with other biophysical assays. Here, we describe current state-of-the-art in the portfolio of available NMR-based experiments that are used to aid early-stage lead discovery. We then focus on multi-protein complexes as targets and how NMR spectroscopy allows studying of interactions within the high molecular weight assemblies that make up a vast fraction of the yet untargeted proteome. Finally, we give our perspective on how currently available methods could build an improved strategy for drug discovery against such challenging targets.
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Affiliation(s)
- David M Dias
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Alessio Ciulli
- College of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, DD1 5EH, Dundee, UK.
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127
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Ding Z, German P, Bai S, Reddy AS, Liu XD, Sun M, Zhou L, Chen X, Zhao X, Wu C, Zhang S, Mills GB, Jonasch E. Genetic and pharmacological strategies to refunctionalize the von Hippel Lindau R167Q mutant protein. Cancer Res 2014; 74:3127-36. [PMID: 24755468 DOI: 10.1158/0008-5472.can-13-3213] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aberrant von Hippel Lindau (VHL) protein function is the underlying driver of VHL-related diseases, including both sporadic and inherited clear cell renal cell carcinoma (ccRCC). About one third of VHL mutations are missense point mutations, with R167Q being the most common VHL point mutation in hereditary VHL disease. Although it has been studied extensively, the ability of VHL-R167Q to downregulate hypoxia-inducible factor 2α (HIF2α) is still controversial. In addition, the manner in which the mutation contributes to tumorigenesis is not fully understood. No therapeutic approach is available to target VHL-R167Q and similar missense point mutations. We analyzed VHL-R167Q proteostasis and function at normoxia, at hypoxia with different oxygen pressure, and in a xenograft mouse model. We showed that the protein levels of VHL-R167Q dictate its ability to downregulate HIF2α and suppress tumor growth. Strikingly, the proteasome inhibitors bortezomib and carfilzomib, which are currently in clinical use, stabilize VHL-R167Q and increase its ability to downregulate HIF2α. VHL-R167Q binds elongin C and elongin B with considerably less avidity than wild-type VHL does but retains residual capacity to generate a VHL-elongin C-elongin B complex, downregulate HIF2α, and suppress tumorigenesis, which could be rescued by increase of VHL-R167Q levels. Finally, we used in silico approaches and identified other missense VHL mutants in addition to VHL-R167Q that might be rescued by similar strategies. Thus, our studies revealed detailed information describing how VHL-R167Q contributes to tumorigenesis and identified a potential targeted therapy for ccRCC and other VHL-related disease in patients carrying VHL-R167Q or similar missense mutations.
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Affiliation(s)
- Zhiyong Ding
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Peter German
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Shanshan Bai
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - A Srinivas Reddy
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Xian-De Liu
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Mianen Sun
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Lijun Zhou
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Xiaohua Chen
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Xiaobei Zhao
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Chengbiao Wu
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Shuxing Zhang
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Gordon B Mills
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Eric Jonasch
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
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128
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Milroy LG, Grossmann TN, Hennig S, Brunsveld L, Ottmann C. Modulators of Protein–Protein Interactions. Chem Rev 2014; 114:4695-748. [DOI: 10.1021/cr400698c] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lech-Gustav Milroy
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
| | - Luc Brunsveld
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
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129
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Guo W, Wisniewski JA, Ji H. Hot spot-based design of small-molecule inhibitors for protein-protein interactions. Bioorg Med Chem Lett 2014; 24:2546-54. [PMID: 24751445 DOI: 10.1016/j.bmcl.2014.03.095] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 03/26/2014] [Accepted: 03/28/2014] [Indexed: 12/27/2022]
Abstract
Protein-protein interactions (PPIs) are important targets for the development of chemical probes and therapeutic agents. From the initial discovery of the existence of hot spots at PPI interfaces, it has been proposed that hot spots might provide the key for developing small-molecule PPI inhibitors. However, there has been no review on the ways in which the knowledge of hot spots can be used to achieve inhibitor design, nor critical examination of successful examples. This Digest discusses the characteristics of hot spots and the identification of druggable hot spot pockets. An analysis of four examples of hot spot-based design reveals the importance of this strategy in discovering potent and selective PPI inhibitors. A general procedure for hot spot-based design of PPI inhibitors is outlined.
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Affiliation(s)
- Wenxing Guo
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA
| | - John A Wisniewski
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA
| | - Haitao Ji
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
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130
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Buckley DL, Crews CM. Small-molecule control of intracellular protein levels through modulation of the ubiquitin proteasome system. Angew Chem Int Ed Engl 2014; 53:2312-30. [PMID: 24459094 PMCID: PMC4348030 DOI: 10.1002/anie.201307761] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Indexed: 12/25/2022]
Abstract
Traditionally, biological probes and drugs have targeted the activities of proteins (such as enzymes and receptors) that can be readily controlled by small molecules. The remaining majority of the proteome has been deemed "undruggable". By using small-molecule modulators of the ubiquitin proteasome, protein levels, rather than protein activity, can be targeted instead, thus increasing the number of druggable targets. Whereas targeting of the proteasome itself can lead to a global increase in protein levels, the targeting of other components of the UPS (e.g., the E3 ubiquitin ligases) can lead to an increase in protein levels in a more targeted fashion. Alternatively, multiple strategies for inducing protein degradation with small-molecule probes are emerging. With the ability to induce and inhibit the degradation of targeted proteins, small-molecule modulators of the UPS have the potential to significantly expand the druggable portion of the proteome beyond traditional targets, such as enzymes and receptors.
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Affiliation(s)
- Dennis L. Buckley
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
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131
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Buckley DL, Crews CM. Steuerung der intrazellulären Proteinmenge durch niedermolekulare Modulatoren des Ubiquitin-Proteasom-Systems. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307761] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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132
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Dias DM, Van Molle I, Baud MGJ, Galdeano C, Geraldes CFGC, Ciulli A. Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein-Protein Interactions? ACS Med Chem Lett 2014; 5:23-28. [PMID: 24436777 PMCID: PMC3891296 DOI: 10.1021/ml400296c] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 11/02/2013] [Indexed: 01/18/2023] Open
Abstract
Modulation of protein-protein interactions (PPIs) with small molecules has been hampered by a lack of lucid methods capable of reliably identifying high-quality hits. In fragment screening, the low ligand efficiencies associated with PPI target sites pose significant challenges to fragment binding detection. Here, we investigate the requirements for ligand-based NMR techniques to detect rule-of-three compliant fragments that form part of known high-affinity inhibitors of the PPI between the von Hippel-Lindau protein and the alpha subunit of hypoxia-inducible factor 1 (pVHL:HIF-1α). Careful triaging allowed rescuing weak but specific binding of fragments that would otherwise escape detection at this PPI. Further structural information provided by saturation transfer difference (STD) group epitope mapping, protein-based NMR, competitive isothermal titration calorimetry (ITC), and X-ray crystallography confirmed the binding mode of the rescued fragments. Our findings have important implications for PPI druggability assessment by fragment screening as they reveal an accessible threshold for fragment detection and validation.
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Affiliation(s)
- David M. Dias
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
- Department of Life Sciences, Faculty of
Science and Technology, Centre for Neurosciences and Cell Biology
and Chemistry Centre, University of Coimbra, Coimbra, Portugal
| | - Inge Van Molle
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | | | - Carles Galdeano
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Carlos F. G. C. Geraldes
- Department of Life Sciences, Faculty of
Science and Technology, Centre for Neurosciences and Cell Biology
and Chemistry Centre, University of Coimbra, Coimbra, Portugal
| | - Alessio Ciulli
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
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133
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Fry DC, Wartchow C, Graves B, Janson C, Lukacs C, Kammlott U, Belunis C, Palme S, Klein C, Vu B. Deconstruction of a nutlin: dissecting the binding determinants of a potent protein-protein interaction inhibitor. ACS Med Chem Lett 2013; 4:660-5. [PMID: 24900726 PMCID: PMC4027557 DOI: 10.1021/ml400062c] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 05/24/2013] [Indexed: 01/08/2023] Open
Abstract
Protein-protein interaction (PPI) systems represent a rich potential source of targets for drug discovery, but historically have proven to be difficult, particularly in the lead identification stage. Application of the fragment-based approach may help toward success with this target class. To provide an example toward understanding the potential issues associated with such an application, we have deconstructed one of the best established protein-protein inhibitors, the Nutlin series that inhibits the interaction between MDM2 and p53, into fragments, and surveyed the resulting binding properties using heteronuclear single quantum coherence nuclear magnetic resonance (HSQC NMR), surface plasmon resonance (SPR), and X-ray crystallography. We report the relative contributions toward binding affinity for each of the key substituents of the Nutlin molecule and show that this series could hypothetically have been discovered via a fragment approach. We find that the smallest fragment of Nutlin that retains binding accesses two subpockets of MDM2 and has a molecular weight at the high end of the range that normally defines fragments.
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Affiliation(s)
- David C. Fry
- Roche Research
Center, 340 Kingsland Street, Nutley, New Jersey 07110,
United States
| | - Charles Wartchow
- Roche Research
Center, 340 Kingsland Street, Nutley, New Jersey 07110,
United States
| | - Bradford Graves
- Roche Research
Center, 340 Kingsland Street, Nutley, New Jersey 07110,
United States
| | - Cheryl Janson
- Roche Research
Center, 340 Kingsland Street, Nutley, New Jersey 07110,
United States
| | - Christine Lukacs
- Roche Research
Center, 340 Kingsland Street, Nutley, New Jersey 07110,
United States
| | - Ursula Kammlott
- Roche Research
Center, 340 Kingsland Street, Nutley, New Jersey 07110,
United States
| | - Charles Belunis
- Roche Research
Center, 340 Kingsland Street, Nutley, New Jersey 07110,
United States
| | - Stefan Palme
- Roche Diagnostics
GmbH, Nonnenwald 2, Penzberg 82377, Germany
| | - Christian Klein
- Roche Glycart AG, Wagistrasse 18, Schlieren CH-8952, Switzerland
| | - Binh Vu
- Roche Research
Center, 340 Kingsland Street, Nutley, New Jersey 07110,
United States
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134
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Aguirre C, ten Brink T, Walker O, Guillière F, Davesne D, Krimm I. BcL-xL conformational changes upon fragment binding revealed by NMR. PLoS One 2013; 8:e64400. [PMID: 23717610 PMCID: PMC3662666 DOI: 10.1371/journal.pone.0064400] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 04/12/2013] [Indexed: 11/19/2022] Open
Abstract
Protein-protein interactions represent difficult but increasingly important targets for the design of therapeutic compounds able to interfere with biological processes. Recently, fragment-based strategies have been proposed as attractive approaches for the elaboration of protein-protein surface inhibitors from fragment-like molecules. One major challenge in targeting protein-protein interactions is related to the structural adaptation of the protein surface upon molecular recognition. Methods capable of identifying subtle conformational changes of proteins upon fragment binding are therefore required at the early steps of the drug design process. In this report we present a fast NMR method able to probe subtle conformational changes upon fragment binding. The approach relies on the comparison of experimental fragment-induced Chemical Shift Perturbation (CSP) of amine protons to CSP simulated for a set of docked fragment poses, considering the ring-current effect from fragment binding. We illustrate the method by the retrospective analysis of the complex between the anti-apoptotic Bcl-xL protein and the fragment 4′-fluoro-[1,1′-biphenyl]-4-carboxylic acid that was previously shown to bind one of the Bcl-xL hot spots. The CSP-based approach shows that the protein undergoes a subtle conformational rearrangement upon interaction, for residues located in helices 2, 3 and the very beginning of 5. Our observations are corroborated by residual dipolar coupling measurements performed on the free and fragment-bound forms of the Bcl-xL protein. These NMR-based results are in total agreement with previous molecular dynamic calculations that evidenced a high flexibility of Bcl-xL around the binding site. Here we show that CSP of protein amine protons are useful and reliable structural probes. Therefore, we propose to use CSP simulation to assess protein conformational changes upon ligand binding in the fragment-based drug design approach.
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Affiliation(s)
- Clémentine Aguirre
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Tim ten Brink
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Olivier Walker
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Florence Guillière
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Dany Davesne
- UMR5822/IN2P3/F-69622 Lyon, Université de Lyon, IPNL, Villeurbanne, France
| | - Isabelle Krimm
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
- * E-mail:
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135
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Buckley DL, Gustafson JL, Van Molle I, Roth AG, Tae HS, Gareiss PC, Jorgensen WL, Ciulli A, Crews CM. Small-molecule inhibitors of the interaction between the E3 ligase VHL and HIF1α. Angew Chem Int Ed Engl 2012; 51:11463-7. [PMID: 23065727 PMCID: PMC3519281 DOI: 10.1002/anie.201206231] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Indexed: 01/03/2023]
Abstract
E3 ubiquitin ligases, such as the therapeutically relevant VHL, are challenging targets for traditional medicinal chemistry, as their modulation requires targeting protein-protein interactions. We report novel small-molecule inhibitors of the interaction between VHL and its molecular target HIF1α, a transcription factor involved in oxygen sensing.
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Affiliation(s)
- Dennis L. Buckley
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
| | - Jeffrey L. Gustafson
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
| | - Inge Van Molle
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Anke G. Roth
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
| | - Hyun Seop Tae
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
| | - Peter C. Gareiss
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
| | - William L. Jorgensen
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
| | - Alessio Ciulli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Craig M. Crews
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
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136
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Buckley DL, Gustafson JL, Van Molle I, Roth AG, Tae HS, Gareiss PC, Jorgensen WL, Ciulli A, Crews CM. Niedermolekulare Inhibitoren der Wechselwirkung zwischen der E3-Ligase VHL und HIF1α. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206231] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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