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Lukman S, Verma CS, Fuentes G. Exploiting Protein Intrinsic Flexibility in Drug Design. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 805:245-69. [DOI: 10.1007/978-3-319-02970-2_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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52
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Abstract
The design of a broad-spectrum cancer drug would provide enormous clinical benefits to treat cancer patients. Most of cancerous cells have a mutation in the p53 gene that results in an inactive mutant p53 protein. For this reason, p53 is a prime target for the development of a broad-spectrum cancer drug. To provide the atomic information to rationally design a drug to recover p53 activity is the main goal of the structural studies on mutant p53. We review three mechanisms that influence p53 activity and provide information about how reactivation of mutant p53 can be achieved: stabilization of the active conformation of the DNA-binding domain of the protein, suppression of missense mutations in the DNA-binding domain by a second-site mutation, and increased transactivation.
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Affiliation(s)
- Hector Viadiu
- Instituto de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City, D.F., Mexico,
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53
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Rouhana J, Hoh F, Estaran S, Henriquet C, Boublik Y, Kerkour A, Trouillard R, Martinez J, Pugnière M, Padilla A, Chavanieu A. Fragment-based identification of a locus in the Sec7 domain of Arno for the design of protein-protein interaction inhibitors. J Med Chem 2013; 56:8497-511. [PMID: 24112024 DOI: 10.1021/jm4009357] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
By virtual screening using a fragment-based drug design (FBDD) approach, 33 fragments were selected within small pockets around interaction hot spots on the Sec7 surface of the nucleotide exchange factor Arno, and then their ability to interfere with the Arno-catalyzed nucleotide exchange on the G-protein Arf1 was evaluated. By use of SPR, NMR, and fluorescence assays, the direct binding of three of the identified fragments to Arno Sec7 domain was demonstrated and the promiscuous aggregate behavior evaluated. Then the binding mode of one fragment and of a more active analogue was solved by X-ray crystallography. This highlighted the role of stable and transient pockets at the Sec7 domain surface in the discovery and binding of interfering compounds. These results provide structural information on how small organic compounds can interfere with the Arf1-Arno Sec7 domain interaction and may guide the rational drug design of competitive inhibitors of Arno enzymatic activity.
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Affiliation(s)
- Jad Rouhana
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Universités Montpellier 1 et 2, Faculté de Pharmacie, 15 Avenue Charles Flahault BP14491, 34093 Montpellier Cedex 5, France
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54
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Neklesa TK, Noblin DJ, Kuzin A, Lew S, Seetharaman J, Acton TB, Kornhaber G, Xiao R, Montelione GT, Tong L, Crews CM. A bidirectional system for the dynamic small molecule control of intracellular fusion proteins. ACS Chem Biol 2013; 8:2293-2300. [PMID: 23978068 DOI: 10.1021/cb400569k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Small molecule control of intracellular protein levels allows temporal and dose-dependent regulation of protein function. Recently, we developed a method to degrade proteins fused to a mutant dehalogenase (HaloTag2) using small molecule hydrophobic tags (HyTs). Here, we introduce a complementary method to stabilize the same HaloTag2 fusion proteins, resulting in a unified system allowing bidirectional control of cellular protein levels in a temporal and dose-dependent manner. From a small molecule screen, we identified N-(3,5-dichloro-2-ethoxybenzyl)-2H-tetrazol-5-amine as a nanomolar HALoTag2 Stabilizer (HALTS1) that reduces the Hsp70:HaloTag2 interaction, thereby preventing HaloTag2 ubiquitination. Finally, we demonstrate the utility of the HyT/HALTS system in probing the physiological role of therapeutic targets by modulating HaloTag2-fused oncogenic H-Ras, which resulted in either the cessation (HyT) or acceleration (HALTS) of cellular transformation. In sum, we present a general platform to study protein function, whereby any protein of interest fused to HaloTag2 can be either degraded 10-fold or stabilized 5-fold using two corresponding compounds.
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Affiliation(s)
- Taavi K. Neklesa
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 219
Prospect Street, New Haven, Connecticut 06511, United States
| | - Devin J. Noblin
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 219
Prospect Street, New Haven, Connecticut 06511, United States
| | - Alexander Kuzin
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Scott Lew
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Jayaraman Seetharaman
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Thomas B. Acton
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Gregory Kornhaber
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Rong Xiao
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Gaetano T. Montelione
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department
of Biochemistry and Molecular Biology, Robert Wood Johnson
Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Liang Tong
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Craig M. Crews
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 219
Prospect Street, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, United States
- Department
of Pharmacology, Yale University, 333 Cedar Street, New Haven, Connecticut 06511, United States
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55
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Magno A, Steiner S, Caflisch A. Mechanism and Kinetics of Acetyl-Lysine Binding to Bromodomains. J Chem Theory Comput 2013; 9:4225-32. [PMID: 26592411 DOI: 10.1021/ct400361k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bromodomains are four-helix bundle proteins that specifically recognize acetylation of lysine side chains on histones. The available X-ray structures of bromodomain/histone tail complexes show that the conserved Asn residue in the loop between helices B and C is involved in a hydrogen bond with the acetyl-lysine side chain. Here we analyze the spontaneous binding of acetyl-lysine to the bromodomain TAF1(2) by the first molecular dynamics simulations of histone mark binding to an epigenetic reader protein. Multiple events of reversible association sampled along the unbiased simulations allow us to determine the pathway and kinetics of binding. The simulations show that acetyl-lysine has two major binding modes in TAF1(2) one of which corresponds to the available crystal structures and is stabilized by a hydrogen bond to the conserved Asn side chain. The other major binding mode is more buried than in the crystal structures and is stabilized by two hydrogen bonds with conserved residues of the loop between helices Z and A. In the more buried binding conformation, three of the six structured water molecules at the bottom of the binding pocket are displaced by the acetyl-lysine side chain. The kinetic analysis shows that the two binding modes interconvert on a faster time scale with respect to the association/dissociation process. The atomic-level description of the binding pathway and binding modes is useful for the design of small molecule modulators of histone binding to bromodomains.
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Affiliation(s)
- A Magno
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190 CH-8057 Zurich, Switzerland
| | - S Steiner
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190 CH-8057 Zurich, Switzerland
| | - A Caflisch
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190 CH-8057 Zurich, Switzerland
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56
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Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery. Proc Natl Acad Sci U S A 2013; 110:12984-9. [PMID: 23872845 DOI: 10.1073/pnas.1304045110] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In fragment-based drug discovery, the weak affinities exhibited by fragments pose significant challenges for screening. Biophysical techniques are used to address this challenge, but there is no clear consensus on which cascade of methods is best suited to identify fragment hits that ultimately translate into bound X-ray structures and provide bona fide starting points for synthesis. We have benchmarked an integrated biophysical approach for fragment screening and validation against Mycobacterium tuberculosis pantothenate synthetase. A primary screen of 1,250 fragments library was performed by thermal shift, followed by secondary screen using one-dimensional NMR spectroscopy (water ligand observed gradient spectroscopy and saturation transfer difference binding experiments) and ultimate hit validation by isothermal titration calorimetry and X-ray crystallography. Our multibiophysical approach identified three distinct binding sites for fragments and laid a solid foundation for successful structure-based elaboration into potent inhibitors.
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57
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Huang D, Rossini E, Steiner S, Caflisch A. Structured water molecules in the binding site of bromodomains can be displaced by cosolvent. ChemMedChem 2013; 9:573-9. [PMID: 23804246 DOI: 10.1002/cmdc.201300156] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Indexed: 01/16/2023]
Abstract
Bromodomains are α-helical bundles of approximately 110 residues that recognize acetylated lysine side chains mainly on histone tails. Bromodomains are known to play an important role in cancer and inflammation, and as such, significant efforts are being made to identify small-molecule inhibitors of these epigenetic reader proteins. Here, explicit solvent molecular dynamics (MD) simulations of two bromodomains (BAZ2B and CREBBP) are used to analyze the water molecules that seem to be conserved at the bottom of the acetyl-lysine binding site in most crystal structures of bromodomains. The MD runs suggest that the occupancy of the structured water molecules is influenced by conformational transitions of the loop that connects helices Z and A. Additional simulations in the presence of 50 molecules of cosolvent (i.e., 440 mM of dimethylsulfoxide, methanol, or ethanol) indicate that some of the structured water molecules can be displaced transiently. The residence time in the acetyl-lysine binding site is calculated to be about 1 ns, 2-5 ns, and 10-30 ns for methanol, ethanol, and dimethylsulfoxide, respectively, while the affinity of the three cosolvents for BAZ2B and CREBBP is in the range of 50-500 mM. The results described have implications for ligand design, suggesting that only structured water molecules that do not exchange with cosolvent should be maintained in crystal structures used for docking campaigns, and that hydroxy substituents should be incorporated in the ligand so as to map the structured water molecules replaced by (m)ethanol.
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Affiliation(s)
- Danzhi Huang
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland).
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58
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Van Molle I, Thomann A, Buckley DL, So EC, Lang S, Crews CM, Ciulli A. Dissecting fragment-based lead discovery at the von Hippel-Lindau protein:hypoxia inducible factor 1α protein-protein interface. ACTA ACUST UNITED AC 2013; 19:1300-12. [PMID: 23102223 DOI: 10.1016/j.chembiol.2012.08.015] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/10/2012] [Accepted: 08/16/2012] [Indexed: 01/06/2023]
Abstract
Fragment screening is widely used to identify attractive starting points for drug design. However, its potential and limitations to assess the tractability of often challenging protein:protein interfaces have been underexplored. Here, we address this question by means of a systematic deconstruction of lead-like inhibitors of the pVHL:HIF-1α interaction into their component fragments. Using biophysical techniques commonly employed for screening, we could only detect binding of fragments that violate the Rule of Three, are more complex than those typically screened against classical druggable targets, and occupy two adjacent binding subsites at the interface rather than just one. Analyses based on ligand and group lipophilicity efficiency of anchored fragments were applied to dissect the individual subsites and probe for binding hot spots. The implications of our findings for targeting protein interfaces by fragment-based approaches are discussed.
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Affiliation(s)
- Inge Van Molle
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
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59
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Davis BJ, Erlanson DA. Learning from our mistakes: the 'unknown knowns' in fragment screening. Bioorg Med Chem Lett 2013; 23:2844-52. [PMID: 23562240 DOI: 10.1016/j.bmcl.2013.03.028] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 03/01/2013] [Accepted: 03/08/2013] [Indexed: 12/27/2022]
Abstract
In the past 15 years, fragment-based lead discovery (FBLD) has been adopted widely throughout academia and industry. The approach entails discovering very small molecular fragments and growing, merging, or linking them to produce drug leads. Because the affinities of the initial fragments are often low, detection methods are pushed to their limits, leading to a variety of artifacts, false positives, and false negatives that too often go unrecognized. This Digest discusses some of these problems and offers suggestions to avoid them. Although the primary focus is on FBLD, many of the lessons also apply to more established approaches such as high-throughput screening.
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Affiliation(s)
- Ben J Davis
- Vernalis Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, UK.
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60
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Wang N, Majmudar CY, Pomerantz WC, Gagnon JK, Sadowsky JD, Meagher JL, Johnson TK, Stuckey JA, Brooks CL, Wells JA, Mapp AK. Ordering a dynamic protein via a small-molecule stabilizer. J Am Chem Soc 2013; 135:3363-6. [PMID: 23384013 PMCID: PMC3607081 DOI: 10.1021/ja3122334] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Like many coactivators, the GACKIX domain of the master coactivator CBP/p300 recognizes transcriptional activators of diverse sequence composition via dynamic binding surfaces. The conformational dynamics of GACKIX that underlie its function also render it especially challenging for structural characterization. We have found that the ligand discovery strategy of Tethering is an effective method for identifying small-molecule fragments that stabilize the GACKIX domain, enabling for the first time the crystallographic characterization of this important motif. The 2.0 Å resolution structure of GACKIX complexed to a small molecule was further analyzed by molecular dynamics simulations, which revealed the importance of specific side-chain motions that remodel the activator binding site in order to accommodate binding partners of distinct sequence and size. More broadly, these results suggest that Tethering can be a powerful strategy for identifying small-molecule stabilizers of conformationally malleable proteins, thus facilitating their structural characterization and accelerating the discovery of small-molecule modulators.
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Affiliation(s)
- Ningkun Wang
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | | | | | - Jessica K. Gagnon
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Jack D. Sadowsky
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
| | | | - Taylor K. Johnson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Jeanne A. Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Charles L. Brooks
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - James A. Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
| | - Anna K. Mapp
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
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61
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Scott DE, Ehebauer MT, Pukala T, Marsh M, Blundell TL, Venkitaraman AR, Abell C, Hyvönen M. Using a fragment-based approach to target protein-protein interactions. Chembiochem 2013; 14:332-42. [PMID: 23344974 PMCID: PMC3594973 DOI: 10.1002/cbic.201200521] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Indexed: 02/02/2023]
Abstract
The ability to identify inhibitors of protein-protein interactions represents a major challenge in modern drug discovery and in the development of tools for chemical biology. In recent years, fragment-based approaches have emerged as a new methodology in drug discovery; however, few examples of small molecules that are active against chemotherapeutic targets have been published. Herein, we describe the fragment-based approach of targeting the interaction between the tumour suppressor BRCA2 and the recombination enzyme RAD51; it makes use of a screening pipeline of biophysical techniques that we expect to be more generally applicable to similar targets. Disruption of this interaction in vivo is hypothesised to give rise to cellular hypersensitivity to radiation and genotoxic drugs. We have used protein engineering to create a monomeric form of RAD51 by humanising a thermostable archaeal orthologue, RadA, and used this protein for fragment screening. The initial fragment hits were thoroughly validated biophysically by isothermal titration calorimetry (ITC) and NMR techniques and observed by X-ray crystallography to bind in a shallow surface pocket that is occupied in the native complex by the side chain of a phenylalanine from the conserved FxxA interaction motif found in BRCA2. This represents the first report of fragments or any small molecule binding at this protein-protein interaction site.
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Affiliation(s)
- Duncan E Scott
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Matthias T Ehebauer
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Old Addenbrooke's Site, Cambridge, CB2 1GA (UK) E-mail:
| | - Tara Pukala
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - May Marsh
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Old Addenbrooke's Site, Cambridge, CB2 1GA (UK) E-mail:
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Old Addenbrooke's Site, Cambridge, CB2 1GA (UK) E-mail:
| | - Ashok R Venkitaraman
- Hutchison/MRC Research Centre, University of CambridgeHills Road, Cambridge, CB2 0XZ (UK)
| | - Chris Abell
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Old Addenbrooke's Site, Cambridge, CB2 1GA (UK) E-mail:
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Zak K, Pecak A, Rys B, Wladyka B, Dömling A, Weber L, Holak TA, Dubin G. Mdm2 and MdmX inhibitors for the treatment of cancer: a patent review (2011-present). Expert Opin Ther Pat 2013; 23:425-48. [PMID: 23374098 DOI: 10.1517/13543776.2013.765405] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION One of the hallmarks of cancer cells is the inactivation of the p53 pathway either due to mutations in the p53 gene or over-expression of negative regulators, Mdm2 and/or MdmX. Pharmacological disruption of the Mdm2/X-p53 interaction to restore p53 activity is an attractive concept, aiming at a targeted and non-toxic cancer treatment. AREAS COVERED The introduction covers the biological role of p53 pathway and its regulation by Mdm2 and MdmX in normal and cancer cells and the current repertoire and development status of inhibitors of the Mdm2/X-p53 interaction for the treatment of cancer. The main part of the article covers patents and patent applications describing small molecule inhibitors of the Mdm2/X-p53 interaction published from 2011 until 2012. EXPERT OPINION The area of small molecule Mdm2/X-p53 interaction inhibitor development is progressing fast. Several Phase I clinical studies and preclinical programs are now in progress, however, the clinical proof concept has yet to be demonstrated. Multiple available compounds inhibit Mdm2-p53 interaction with nanomolar affinities, but MdmX is still missing such potent binders. Since research points to a complementary mode of Mdm2 and MdmX action, the future compound classes will possibly want to include dual actions versus Mdm2 and MdmX.
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Affiliation(s)
- Krzysztof Zak
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Kraków, Poland
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63
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Accordino SR, Rodríguez Fris JA, Appignanesi GA. Wrapping effects within a proposed function-rescue strategy for the Y220C oncogenic mutation of protein p53. PLoS One 2013; 8:e55123. [PMID: 23365691 PMCID: PMC3554699 DOI: 10.1371/journal.pone.0055123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 12/18/2012] [Indexed: 11/30/2022] Open
Abstract
Soluble proteins must protect their structural integrity from water attack by wrapping interactions which imply the clustering of nonpolar residues around the backbone hydrogen bonds. Thus, poorly wrapped hydrogen bonds constitute defects which have been identified as promoters of protein associations since they favor the removal of hydrating molecules. More specifically, a recent study of our group has shown that wrapping interactions allow the successful identification of protein binding hot spots. Additionally, we have also shown that drugs disruptive of protein-protein interfaces tend to mimic the wrapping behavior of the protein they replace. Within this context, in this work we study wrapping three body interactions related to the oncogenic Y220C mutation of the tumor suppressor protein p53. Our computational results rationalize the oncogenic nature of the Y220C mutation, explain the binding of a drug-like molecule already designed to restore the function of p53 and provide clues to help improve this function-rescue strategy and to apply in other drug design or re-engineering techniques.
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Affiliation(s)
- Sebastián R. Accordino
- Sección Fisicoquímica, INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - J. Ariel Rodríguez Fris
- Sección Fisicoquímica, INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Gustavo A. Appignanesi
- Sección Fisicoquímica, INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Bahía Blanca, Argentina
- * E-mail:
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64
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Dong J, Qiu J, Zhang Y, Lu C, Dai X, Wang J, Li H, Wang X, Tan W, Luo M, Niu X, Deng X. Oroxylin A inhibits hemolysis via hindering the self-assembly of α-hemolysin heptameric transmembrane pore. PLoS Comput Biol 2013; 9:e1002869. [PMID: 23349625 PMCID: PMC3547825 DOI: 10.1371/journal.pcbi.1002869] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 11/16/2012] [Indexed: 02/06/2023] Open
Abstract
Alpha-hemolysin (α-HL) is a self-assembling, channel-forming toxin produced by most Staphylococcus aureus strains as a 33.2-kDa soluble monomer. Upon binding to a susceptible cell membrane, the monomer self-assembles to form a 232.4-kDa heptamer that ultimately causes host cell lysis and death. Consequently, α-HL plays a significant role in the pathogenesis of S. aureus infections, such as pneumonia, mastitis, keratitis and arthritis. In this paper, experimental studies show that oroxylin A (ORO), a natural compound without anti-S. aureus activity, can inhibit the hemolytic activity of α-HL. Molecular dynamics simulations, free energy calculations, and mutagenesis assays were performed to understand the formation of the α-HL-ORO complex. This combined approach revealed that the catalytic mechanism of inhibition involves the direct binding of ORO to α-HL, which blocks the conformational transition of the critical “Loop” region of the α-HL protein thereby inhibiting its hemolytic activity. This mechanism was confirmed by experimental data obtained from a deoxycholate-induced oligomerization assay. It was also found that, in a co-culture system with S. aureus and human alveolar epithelial (A549) cells, ORO could protect against α-HL-mediated injury. These findings indicate that ORO hinders the lytic activity of α-HL through a novel mechanism, which should facilitate the design of new and more effective antibacterial agents against S. aureus. The mechanism controlling protein-ligand interactions is one of the most important processes in rational drug design. X-ray crystallography is a traditional tool used to investigate the interaction of ligands and proteins in a complex. However, protein crystallography is inefficient, and the development of crystal technology and research remains unequally distributed. Thus, it seems impractical to explore the structure of the α-hemolysin-ORO monomer complex by crystallography. Therefore, we used molecular dynamics simulations to investigate the receptor-ligand interaction in the α-HL-ORO monomer complex. In this study, we found that oroxylin A (ORO), a natural compound with little anti-S. aureus activity, can inhibit the hemolytic activity of α-HL at low concentrations. Through molecular docking and molecular dynamics simulations, we determined the potential binding mode of the protein-ligand interaction. The data revealed that ORO directly binds to α-HL, an interaction that blacks the conformational transition of the critical “Loop” region in α-HL and thus prevents the formation of the α-HL heptameric transmembrane pore, which ultimately inhibits the hemolytic activity of α-HL. This mechanism was confirmed by experimental data. Furthermore, we demonstrated that ORO could protect against α-HL-mediated injury in human alveolar epithelial (A549) cells.
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Affiliation(s)
- Jing Dong
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
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65
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McMahon RM, Scanlon MJ, Martin JL. Interrogating Fragments Using a Protein Thermal Shift Assay. Aust J Chem 2013. [DOI: 10.1071/ch13279] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein thermal shift is a relatively rapid and inexpensive technique for the identification of low molecular weight compound interactions with protein targets. An increase in the melting temperature of the target protein in the presence of a test ligand is indicative of a promising ligand–protein interaction. Due to its simplicity, protein thermal shift is an attractive method for screening libraries and validating hits in drug discovery programs. The methodology has been used successfully in high throughput screens of small molecule libraries, and its application has been extended to report on protein–drug-like-fragment interactions. Here, we review how protein thermal shift has been employed recently in fragment-based drug discovery (FBDD) efforts, and highlight its application to protein–protein interaction targets. Multiple validation of fragment hits by independent means is paramount to ensure efficient and economical progress in a FBDD campaign. We discuss the applicability of thermal shift assays in this light, and discuss more generally what one does when orthogonal approaches disagree.
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66
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Gavrin LK, Denny RA, Saiah E. Small Molecules That Target Protein Misfolding. J Med Chem 2012; 55:10823-43. [DOI: 10.1021/jm301182j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lori Krim Gavrin
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge,
Massachusetts 02140, United States
| | - Rajiah Aldrin Denny
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge,
Massachusetts 02140, United States
| | - Eddine Saiah
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge,
Massachusetts 02140, United States
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67
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Scott DE, Coyne AG, Hudson SA, Abell C. Fragment-Based Approaches in Drug Discovery and Chemical Biology. Biochemistry 2012; 51:4990-5003. [DOI: 10.1021/bi3005126] [Citation(s) in RCA: 324] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Duncan E. Scott
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Anthony G. Coyne
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Sean A. Hudson
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Chris Abell
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
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68
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Lahti JL, Tang GW, Capriotti E, Liu T, Altman RB. Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface 2012; 9:1409-37. [PMID: 22552919 DOI: 10.1098/rsif.2011.0843] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Marketed drugs frequently perform worse in clinical practice than in the clinical trials on which their approval is based. Many therapeutic compounds are ineffective for a large subpopulation of patients to whom they are prescribed; worse, a significant fraction of patients experience adverse effects more severe than anticipated. The unacceptable risk-benefit profile for many drugs mandates a paradigm shift towards personalized medicine. However, prior to adoption of patient-specific approaches, it is useful to understand the molecular details underlying variable drug response among diverse patient populations. Over the past decade, progress in structural genomics led to an explosion of available three-dimensional structures of drug target proteins while efforts in pharmacogenetics offered insights into polymorphisms correlated with differential therapeutic outcomes. Together these advances provide the opportunity to examine how altered protein structures arising from genetic differences affect protein-drug interactions and, ultimately, drug response. In this review, we first summarize structural characteristics of protein targets and common mechanisms of drug interactions. Next, we describe the impact of coding mutations on protein structures and drug response. Finally, we highlight tools for analysing protein structures and protein-drug interactions and discuss their application for understanding altered drug responses associated with protein structural variants.
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Affiliation(s)
- Jennifer L Lahti
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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69
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Wilcken R, Liu X, Zimmermann MO, Rutherford TJ, Fersht AR, Joerger AC, Boeckler FM. Halogen-enriched fragment libraries as leads for drug rescue of mutant p53. J Am Chem Soc 2012; 134:6810-8. [PMID: 22439615 PMCID: PMC3789257 DOI: 10.1021/ja301056a] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Indexed: 12/14/2022]
Abstract
The destabilizing p53 cancer mutation Y220C creates a druggable surface crevice. We developed a strategy exploiting halogen bonding for lead discovery to stabilize the mutant with small molecules. We designed halogen-enriched fragment libraries (HEFLibs) as starting points to complement classical approaches. From screening of HEFLibs and subsequent structure-guided design, we developed substituted 2-(aminomethyl)-4-ethynyl-6-iodophenols as p53-Y220C stabilizers. Crystal structures of their complexes highlight two key features: (i) a central scaffold with a robust binding mode anchored by halogen bonding of an iodine with a main-chain carbonyl and (ii) an acetylene linker, enabling the targeting of an additional subsite in the crevice. The best binders showed induction of apoptosis in a human cancer cell line with homozygous Y220C mutation. Our structural and biophysical data suggest a more widespread applicability of HEFLibs in drug discovery.
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Affiliation(s)
- Rainer Wilcken
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard-Karls-University
Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
- MRC
Laboratory
of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Xiangrui Liu
- MRC
Laboratory
of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Markus O. Zimmermann
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard-Karls-University
Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
| | - Trevor J. Rutherford
- MRC
Laboratory
of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Alan R. Fersht
- MRC
Laboratory
of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Andreas C. Joerger
- MRC
Laboratory
of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Frank M. Boeckler
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard-Karls-University
Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
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70
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Murray CW, Verdonk ML, Rees DC. Experiences in fragment-based drug discovery. Trends Pharmacol Sci 2012; 33:224-32. [PMID: 22459076 DOI: 10.1016/j.tips.2012.02.006] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 02/28/2012] [Accepted: 02/28/2012] [Indexed: 11/17/2022]
Abstract
Fragment-based drug discovery (FBDD) has become established in both industry and academia as an alternative approach to high-throughput screening for the generation of chemical leads for drug targets. In FBDD, specialised detection methods are used to identify small chemical compounds (fragments) that bind to the drug target, and structural biology is usually employed to establish their binding mode and to facilitate their optimisation. In this article, we present three recent and successful case histories in FBDD. We then re-examine the key concepts and challenges of FBDD with particular emphasis on recent literature and our own experience from a substantial number of FBDD applications. Our opinion is that careful application of FBDD is living up to its promise of delivering high quality leads with good physical properties and that in future many drug molecules will be derived from fragment-based approaches.
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Affiliation(s)
- Christopher W Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK.
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71
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Xu X, Ma Z, Wang X, Xiao ZT, Li Y, Xue ZH, Wang YH. Water's potential role: Insights from studies of the p53 core domain. J Struct Biol 2011; 177:358-66. [PMID: 22197648 DOI: 10.1016/j.jsb.2011.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2011] [Revised: 12/06/2011] [Accepted: 12/06/2011] [Indexed: 01/19/2023]
Abstract
Soluble proteins with amyloidogenic propensity such as the tumor suppressor protein p53 have high proportion of incompletely desolvated backbone H bonds (HB). Such bonds are vulnerable to water attack, thus potentially leading to the misfolding of these proteins. However, it is still not clear how the surrounding solvent influences the protein native states. To address this, systematic surveys by molecular dynamics simulations and entropy analysis were performed on the p53 core domain in this work. We examined seven wild/mutant X-ray structures and observed two types of water-network hydration in three "hot hydration centers" (DNA- or small molecule- binding surfaces of the p53 core domain). The "tight" water, resulting from the local collective hydrogen-bond interactions, is probably fundamental to the protein structural stability. The second type of water is highly "dynamical" and exchanges very fast within the bulk solution, which is unambiguously assisted by the local protein motions. An entropy mapping of the solvent around the protein and a temperature perturbation analysis further present the main features of the p53 hydration network. The particular environment created by different water molecules around the p53 core domain also partly explains the structural vulnerabilities of this protein.
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Affiliation(s)
- X Xu
- Center of Bioinformatics, Northwest A&F University, Yangling, 712100 Shaanxi, China
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72
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Larsson A, Jansson A, Åberg A, Nordlund P. Efficiency of hit generation and structural characterization in fragment-based ligand discovery. Curr Opin Chem Biol 2011; 15:482-8. [PMID: 21724447 DOI: 10.1016/j.cbpa.2011.06.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 06/07/2011] [Accepted: 06/07/2011] [Indexed: 12/21/2022]
Abstract
Fragment-based ligand discovery constitutes a useful strategy for the generation of high affinity ligands with suitable physico-chemical properties to serve as drug leads. There is an increasing number of generic biophysical screening strategies established with the potential for accelerating the generation of useful fragment hits. Crystal structures of these hits can subsequently be used as starting points for fragment evolution to high affinity ligands. Emerging understanding of the efficiency and operative aspects of hit generation and structural characterization in FBLD suggests that this method should be well suited for academic ligand development of chemical tools and experimental therapeutics.
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Affiliation(s)
- Andreas Larsson
- School of Biological Sciences, Nanyang Technological University, 61 Nanyang Drive, Singapore 639798, Singapore
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73
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[Recent advances in mutant p53 and novel personalized strategies for cancer therapy]. YI CHUAN = HEREDITAS 2011; 33:539-48. [PMID: 21684858 DOI: 10.3724/sp.j.1005.2011.00539] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Protein p53 is the most intensively studied tumor suppressor protein. Recent studies keep revealing its new function in metabolism and reproduction. At the same time, it is also found that varieties of p53 mutant gained new function in promoting tumorigenesis. These studies provide the basis for understanding the personalized gain of function of p53 mu-tants and help us searching for the new strategies for reactivation of wild-type p53 and correction of the function of p53 mutants. The personalized treatment targeting different p53 mutants will be the focus for cancer treatment. Here, we re-viewed the discovered gain of function of some p53 mutants and the molecular strategies for reactivating wild type p53 function: by use of small molecules or polypeptides to reactivate the wild type function of p53 mutants in tumor cells; by exogenous expression of wild type p53 carried by recombinant adenovirus in tumor cells; and by inhibition the interaction between p53 and mdm2 to stabilize wild type p53 proteins. Further study of variety of p53 point mutations farcilitates de-signing more effectively personalized strategies in the cancer therapy.
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74
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Huang D, Caflisch A. Small Molecule Binding to Proteins: Affinity and Binding/Unbinding Dynamics from Atomistic Simulations. ChemMedChem 2011; 6:1578-80. [DOI: 10.1002/cmdc.201100237] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Indexed: 11/08/2022]
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75
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Interaction of the p53 DNA-binding domain with its n-terminal extension modulates the stability of the p53 tetramer. J Mol Biol 2011; 409:358-68. [PMID: 21457718 PMCID: PMC3176915 DOI: 10.1016/j.jmb.2011.03.047] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 03/22/2011] [Accepted: 03/23/2011] [Indexed: 12/30/2022]
Abstract
The tetrameric tumor suppressor p53 plays a pivotal role in the control of the cell cycle and provides a paradigm for an emerging class of oligomeric, multidomain proteins with structured and intrinsically disordered regions. Many of its biophysical and functional properties have been extrapolated from truncated variants, yet the exact structural and functional role of certain segments of the protein is unclear. We found from NMR and X-ray crystallography that the DNA-binding domain (DBD) of human p53, usually defined as residues 94-292, extends beyond these domain boundaries. Trp91, in the hinge region between the disordered proline-rich N-terminal domain and the DBD, folds back onto the latter and has a cation-π interaction with Arg174. These additional interactions increase the melting temperature of the DBD by up to 2 °C and inhibit aggregation of the p53 tetramer. They also modulate the dissociation of the p53 tetramer. The absence of the Trp91/Arg174 packing presumably allows nonnative DBD-DBD interactions that both nucleate aggregation and stabilize the interface. These data have important implications for studies of multidomain proteins in general, highlighting the fact that weak ordered-disordered domain interactions can modulate the properties of proteins of complex structure.
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76
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Calhoun S, Daggett V. Structural effects of the L145Q, V157F, and R282W cancer-associated mutations in the p53 DNA-binding core domain. Biochemistry 2011; 50:5345-53. [PMID: 21561095 DOI: 10.1021/bi200192j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The p53 tumor suppressor is a transcription factor involved in many important signaling pathways, such as apoptosis and cell-cycle arrest. In over half of human cancers, p53 function is compromised by a mutation in its gene. Mutations in the p53 DNA-binding core domain destabilize the structure and reduce DNA-binding activity. We performed molecular dynamics simulations at physiological temperature to study the structural and dynamic effects of the L145Q, V157F, and R282W cancer-associated mutations in comparison to the wild-type protein. While there were common regions of destabilization in the mutant simulations, structural changes particular to individual mutations were also observed. Significant backbone deviations of the H2 helix and S7-S8 loop were observed in all mutant simulations; the H2 helix binds to DNA. In addition, the L145Q and V157F mutations, which are located in the β-sandwich core of the domain, disrupted the β-sheet structure and the loop-sheet-helix motif. The R282W mutation caused distortion of the loop-sheet-helix motif, but otherwise this mutant was similar to the wild-type structure. The introduction of these mutations caused rearrangement of the DNA-binding surface, consistent with their reduced DNA-binding activity. The simulations reveal detailed effects of the mutations on the stability and dynamics of p53 that may provide insight for therapeutic approaches.
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Affiliation(s)
- Sara Calhoun
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
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77
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Scarsdale JN, Webb HD, Ginder GD, Williams DC. Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence. Nucleic Acids Res 2011; 39:6741-52. [PMID: 21531701 PMCID: PMC3159451 DOI: 10.1093/nar/gkr262] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The epigenetic code of DNA methylation is interpreted chiefly by methyl cytosine binding domain (MBD) proteins which in turn recruit multiprotein co-repressor complexes. We previously isolated one such complex, MBD2-NuRD, from primary erythroid cells and have shown it contributes to embryonic/fetal β-type globin gene silencing during development. This complex has been implicated in silencing tumor suppressor genes in a variety of human tumor cell types. Here we present structural details of chicken MBD2 bound to a methylated DNA sequence from the ρ-globin promoter to which it binds in vivo and mediates developmental transcriptional silencing in normal erythroid cells. While previous studies have failed to show sequence specificity for MBD2 outside of the symmetric mCpG, we find that this domain binds in a single orientation on the ρ-globin target DNA sequence. Further, we show that the orientation and affinity depends on guanine immediately following the mCpG dinucleotide. Dynamic analyses show that DNA binding stabilizes the central β-sheet, while the N- and C-terminal regions of the protein maintain mobility. Taken together, these data lead to a model in which DNA binding stabilizes the MBD2 structure and that binding orientation and affinity is influenced by the DNA sequence surrounding the central mCpG.
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Affiliation(s)
- J Neel Scarsdale
- Institute of Structural Biology and Drug Design, Virginia Commonwealth University, Richmond, VA 23298-0035, USA
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78
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Kaar JL, Basse N, Joerger AC, Stephens E, Rutherford TJ, Fersht AR. Stabilization of mutant p53 via alkylation of cysteines and effects on DNA binding. Protein Sci 2011; 19:2267-78. [PMID: 20878668 DOI: 10.1002/pro.507] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Oncogenic mutations inactivate the tumor suppressor p53 by lowering its stability or by weakening its binding to DNA. Alkylating agents that reactivate mutant p53 are currently being explored for cancer therapy. We have discovered ligands containing an α,β-unsaturated double bond, characteristic of Michael acceptors, that bind covalently to generic cysteine sites in the p53 core domain. They raised the melting temperature of the core domain of wild-type p53 and the hotspot mutants R175H, Y220C, G245S, R249S, and R282 by up to 3°C. Analysis of the relative reactivity of the cysteines in p53 by mass spectrometry found that C124 and C141 react first, followed by C135, C182, and C277, and eventually C176 and C275. Post-translational modifications of cysteines are known to be involved in regulation of other transcription factors. Modification of C277, which sits on the DNA-binding surface, may, for example, play a role in regulating p53 activity in cells in response to environmental cues. We found that the modifications progressively reduced DNA-binding activity of full-length p53. In light of these results, it is likely that the anticancer activity of the alkylating drugs works via a nontranscriptional activity of p53.
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Affiliation(s)
- Joel L Kaar
- Medical Research Council Centre for Protein Engineering, Cambridge CB2 0QH, United Kingdom
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79
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Huang D, Caflisch A. The free energy landscape of small molecule unbinding. PLoS Comput Biol 2011; 7:e1002002. [PMID: 21390201 PMCID: PMC3033371 DOI: 10.1371/journal.pcbi.1002002] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 11/18/2010] [Indexed: 11/18/2022] Open
Abstract
The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein) is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide) and eleven (5-diethylamino-2-pentanone) non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand) are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential) time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance) are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics) of ligand unbinding.
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Affiliation(s)
- Danzhi Huang
- Department of Biochemistry, University of Zürich, Zürich,
Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich,
Switzerland
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80
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Khoury K, Popowicz GM, Holak TA, Dömling A. The p53-MDM2/MDMX axis - A chemotype perspective. MEDCHEMCOMM 2011; 2:246-260. [PMID: 24466404 PMCID: PMC3898590 DOI: 10.1039/c0md00248h] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The protein-protein interaction (PPI) of the tumor suppressor p53 and its negative regulator MDM2 consists of the most intense studied PPI with a group of small molecular weight antagonists described and many more disclosed in patent literature. Due to the Å-level structural insight into p53 interaction with MDM2 there is a reasonable understanding of the requirements of the molecules to bind. In contrast and despite the very close homology and 3-D similarity no potent MDMX antagonist has been disclosed up to date. The current review summarizes the different disclosed chemotypes for MDM2 including a discussion of the cocrystal structures. Structures and approaches to reconstitute functional p53 from mutated p53 are presented. Finally new screening methods and recent biotech deals based on p53 are discussed.
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Affiliation(s)
- Kareem Khoury
- University of Pittsburgh, Department of Pharmaceutical Science, Drug Discovery Institute, Pittsburgh, PA, USA
| | | | - Tad A. Holak
- Max Planck Institut für Biochemie, München, Germany
| | - Alexander Dömling
- University of Pittsburgh, Department of Pharmaceutical Science, Drug Discovery Institute, Pittsburgh, PA, USA
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81
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82
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Alibés A, Nadra AD, De Masi F, Bulyk ML, Serrano L, Stricher F. Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example. Nucleic Acids Res 2010; 38:7422-31. [PMID: 20685816 PMCID: PMC2995082 DOI: 10.1093/nar/gkq683] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Quite often a single or a combination of protein mutations is linked to specific diseases. However, distinguishing from sequence information which mutations have real effects in the protein’s function is not trivial. Protein design tools are commonly used to explain mutations that affect protein stability, or protein–protein interaction, but not for mutations that could affect protein–DNA binding. Here, we used the protein design algorithm FoldX to model all known missense mutations in the paired box domain of Pax6, a highly conserved transcription factor involved in eye development and in several diseases such as aniridia. The validity of FoldX to deal with protein–DNA interactions was demonstrated by showing that high levels of accuracy can be achieved for mutations affecting these interactions. Also we showed that protein-design algorithms can accurately reproduce experimental DNA-binding logos. We conclude that 88% of the Pax6 mutations can be linked to changes in intrinsic stability (77%) and/or to its capabilities to bind DNA (30%). Our study emphasizes the importance of structure-based analysis to understand the molecular basis of diseases and shows that protein–DNA interactions can be analyzed to the same level of accuracy as protein stability, or protein–protein interactions.
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Affiliation(s)
- Andreu Alibés
- EMBL/CRG Systems Biology Research Unit, Center for Genomic Regulation, UPF, Barcelona, Spain.
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83
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Maslon MM, Hupp TR. Drug discovery and mutant p53. Trends Cell Biol 2010; 20:542-55. [PMID: 20656489 DOI: 10.1016/j.tcb.2010.06.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/14/2010] [Accepted: 06/15/2010] [Indexed: 12/24/2022]
Abstract
Missense mutations in the p53 gene are commonly selected for in developing human cancer cells. These diverse mutations in p53 can inactivate its normal sequence-specific DNA-binding and transactivation function, but these mutations can also stabilize a mutant form of p53 with pro-oncogenic potential. Recent multi-disciplinary advances have demonstrated exciting and unexpected potential in therapeutically targeting the mutant p53 pathway, including: the development of biophysical models to explain how mutations inactivate p53 and strategies for refolding and reactivation of mutant p53, the ability of mutant p53 protein to escape MDM2-mediated degradation in human cancers, and the growing 'interactome' of mutant p53 that begins to explain how the mutant p53 protein can contribute to diverse oncogenic and pro-metastatic signaling. Our rapidly accumulating knowledge on mutant p53-signaling pathways will facilitate drug discovery programmes in the challenging area of protein-protein interactions and mutant protein conformational control.
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Affiliation(s)
- Magda M Maslon
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Cell Signalling Unit, Cancer Research UK p53 Signal Transduction Group, Edinburgh EH4 2XR, UK
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84
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Huang R, Martinez-Ferrando I, Cole PA. Enhanced interrogation: emerging strategies for cell signaling inhibition. Nat Struct Mol Biol 2010; 17:646-9. [PMID: 20520657 DOI: 10.1038/nsmb0610-646] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Here we summarize recent and developing chemical approaches for modulating signaling pathways. In particular, we discuss targeting mutant signaling proteins, disrupting protein-protein interactions in cellular signaling networks, designing bivalent inhibitors of signaling proteins and identifying allosteric regulators of signaling enzymes. Over the past decade, great progress in the harvesting of chemical tools for basic research and clinical medicine has been made, but many challenges remain, and examples of exciting future targets are highlighted.
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Affiliation(s)
- Rong Huang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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