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Previtali V, Bagnolini G, Ciamarone A, Ferrandi G, Rinaldi F, Myers SH, Roberti M, Cavalli A. New Horizons of Synthetic Lethality in Cancer: Current Development and Future Perspectives. J Med Chem 2024; 67:11488-11521. [PMID: 38955347 DOI: 10.1021/acs.jmedchem.4c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
In recent years, synthetic lethality has been recognized as a solid paradigm for anticancer therapies. The discovery of a growing number of synthetic lethal targets has led to a significant expansion in the use of synthetic lethality, far beyond poly(ADP-ribose) polymerase inhibitors used to treat BRCA1/2-defective tumors. In particular, molecular targets within DNA damage response have provided a source of inhibitors that have rapidly reached clinical trials. This Perspective focuses on the most recent progress in synthetic lethal targets and their inhibitors, within and beyond the DNA damage response, describing their design and associated therapeutic strategies. We will conclude by discussing the current challenges and new opportunities for this promising field of research, to stimulate discussion in the medicinal chemistry community, allowing the investigation of synthetic lethality to reach its full potential.
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Affiliation(s)
- Viola Previtali
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Greta Bagnolini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Ciamarone
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Giovanni Ferrandi
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Francesco Rinaldi
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Samuel Harry Myers
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Cavalli
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
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2
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Rinaldi F, Schipani F, Balboni B, Catalano F, Marotta R, Myers SH, Previtali V, Veronesi M, Scietti L, Cecatiello V, Pasqualato S, Ortega JA, Girotto S, Cavalli A. Isolation and Characterization of Monomeric Human RAD51: A Novel Tool for Investigating Homologous Recombination in Cancer. Angew Chem Int Ed Engl 2023; 62:e202312517. [PMID: 37924230 DOI: 10.1002/anie.202312517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/06/2023]
Abstract
DNA repair protein RAD51 is a key player in the homologous recombination pathway. Upon DNA damage, RAD51 is transported into the nucleus by BRCA2, where it can repair DNA double-strand breaks. Due to the structural complexity and dynamics, researchers have not yet clarified the mechanistic details of every step of RAD51 recruitment and DNA repair. RAD51 possesses an intrinsic tendency to form oligomeric structures, which make it challenging to conduct biochemical and biophysical investigations. Here, for the first time, we report on the isolation and characterization of a human monomeric RAD51 recombinant form, obtained through a double mutation, which preserves the protein's integrity and functionality. We investigated different buffers to identify the most suitable condition needed to definitively stabilize the monomer. The monomer of human RAD51 provides the community with a unique biological tool for investigating RAD51-mediated homologous recombination, and paves the way for more reliable structural, mechanistic, and drug discovery studies.
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Affiliation(s)
- Francesco Rinaldi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Fabrizio Schipani
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Beatrice Balboni
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Federico Catalano
- Electron Microscopy Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Roberto Marotta
- Electron Microscopy Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Samuel H Myers
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Viola Previtali
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marina Veronesi
- Structural Biophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Luigi Scietti
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Valentina Cecatiello
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Current address: Structural Biology Research Centre, Human Technopole Milan, Italy Palazzo Italia Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Sebastiano Pasqualato
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Current address: Structural Biology Research Centre, Human Technopole Milan, Italy Palazzo Italia Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Jose Antonio Ortega
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Stefania Girotto
- Structural Biophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Andrea Cavalli
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
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3
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Sutherland JH, Holloman WK. Determinants governing BRC function evaluated by mutational analysis of Brh2 in Ustilago maydis. DNA Repair (Amst) 2023; 127:103511. [PMID: 37141696 DOI: 10.1016/j.dnarep.2023.103511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/31/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023]
Abstract
BRC is a short evolutionarily conserved sequence motif generally arranged in multiple tandem repeats that is present as a defining feature in members of the BRCA2 tumor suppressor protein family. From crystallographic studies of a co-complex, the human BRC4 was found to form a structural element that interacts with RAD51, a key component in the DNA repair machinery directed by homologous recombination. The BRC is distinguished by two tetrameric sequence modules with characteristic hydrophobic residues separated by an intervening spacer region marked by certain highly conserved residues forming a hydrophobic surface for interaction with RAD51. It is present as a single copy in Brh2 of Ustilago maydis, the only reported example of a fungal BRCA2 ortholog. By comparative sequence analysis, examples of BRCA2 orthologs were identified in other fungal phyla, some of which featured multiple tandem repeats like those found in mammals. An expeditious biological assay system was developed for evaluating the two-tetramer module model and assessing the importance of particular conserved amino acid residues of BRC contributing to Brh2 functionality in DNA repair. This work was aided by the finding that the human BRC4 repeat could substitute completely for the endogenous BRC element in Brh2, while the human BRC5 repeat could not. In a survey of point mutations of certain residues, certain BRC mutant variants termed antimorphs were identified that caused a DNA repair phenotype more severe than the null.
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Affiliation(s)
- Jeanette H Sutherland
- Department of Microbiology and Immunology, Cornell University Weill Medical College, New York, NY 10065, USA; Department of Biology, Farmingdale State College, Farmingdale, NY 11735, USA.
| | - William K Holloman
- Department of Microbiology and Immunology, Cornell University Weill Medical College, New York, NY 10065, USA
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4
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BRCA2 C-Terminal RAD51-Binding Domain Confers Resistance to DNA-Damaging Agents. Int J Mol Sci 2022; 23:ijms23074060. [PMID: 35409418 PMCID: PMC9000072 DOI: 10.3390/ijms23074060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022] Open
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein is crucial for initiating DNA damage repair after chemotherapy with DNA interstrand crosslinking agents or X-ray irradiation, which induces DNA double-strand breaks. BRCA2 contains a C-terminal RAD51-binding domain (CTRBD) that interacts with RAD51 oligomer-containing nucleofilaments. In this study, we investigated CTRBD expression in cells exposed to X-ray irradiation and mitomycin C treatment. Surprisingly, BRCA2 CTRBD expression in HeLa cells increased their resistance to X-ray irradiation and mitomycin C. Under endogenous BRCA2 depletion using shRNA, the sensitivities of the BRCA2-depleted cells with and without the CTRBD did not significantly differ. Thus, the resistance to X-ray irradiation conferred by an exogenous CTRBD required endogenous BRCA2 expression. BRCA2 CTRBD-expressing cells demonstrated effective RAD51 foci formation and increased homologous recombination efficiency, but not nonhomologous end-joining efficiency. To the best of our knowledge, our study is the first to report the ability of the BRCA2 functional domain to confer resistance to X-ray irradiation and mitomycin C treatment by increased homologous recombination efficiency. Thus, this peptide may be useful for protecting cells against X-ray irradiation or chemotherapeutic agents.
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Delaunay M, Ha-Duong T. Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2405:205-230. [PMID: 35298816 DOI: 10.1007/978-1-0716-1855-4_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein-protein interactions play crucial and subtle roles in many biological processes and modifications of their fine mechanisms generally result in severe diseases. Peptide derivatives are very promising therapeutic agents for modulating protein-protein associations with sizes and specificities between those of small compounds and antibodies. For the same reasons, rational design of peptide-based inhibitors naturally borrows and combines computational methods from both protein-ligand and protein-protein research fields. In this chapter, we aim to provide an overview of computational tools and approaches used for identifying and optimizing peptides that target protein-protein interfaces with high affinity and specificity. We hope that this review will help to implement appropriate in silico strategies for peptide-based drug design that builds on available information for the systems of interest.
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Affiliation(s)
| | - Tâp Ha-Duong
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France.
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6
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Lindenburg LH, Pantelejevs T, Gielen F, Zuazua-Villar P, Butz M, Rees E, Kaminski CF, Downs JA, Hyvönen M, Hollfelder F. Improved RAD51 binders through motif shuffling based on the modularity of BRC repeats. Proc Natl Acad Sci U S A 2021; 118:e2017708118. [PMID: 34772801 PMCID: PMC8727024 DOI: 10.1073/pnas.2017708118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2021] [Indexed: 01/20/2023] Open
Abstract
Exchanges of protein sequence modules support leaps in function unavailable through point mutations during evolution. Here we study the role of the two RAD51-interacting modules within the eight binding BRC repeats of BRCA2. We created 64 chimeric repeats by shuffling these modules and measured their binding to RAD51. We found that certain shuffled module combinations were stronger binders than any of the module combinations in the natural repeats. Surprisingly, the contribution from the two modules was poorly correlated with affinities of natural repeats, with a weak BRC8 repeat containing the most effective N-terminal module. The binding of the strongest chimera, BRC8-2, to RAD51 was improved by -2.4 kCal/mol compared to the strongest natural repeat, BRC4. A crystal structure of RAD51:BRC8-2 complex shows an improved interface fit and an extended β-hairpin in this repeat. BRC8-2 was shown to function in human cells, preventing the formation of nuclear RAD51 foci after ionizing radiation.
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Affiliation(s)
- Laurens H Lindenburg
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Teodors Pantelejevs
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Fabrice Gielen
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Pedro Zuazua-Villar
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Maren Butz
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Eric Rees
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Jessica A Downs
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
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7
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Inhibiting homologous recombination by targeting RAD51 protein. Biochim Biophys Acta Rev Cancer 2021; 1876:188597. [PMID: 34332021 DOI: 10.1016/j.bbcan.2021.188597] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/09/2021] [Accepted: 07/24/2021] [Indexed: 02/06/2023]
Abstract
Homologous recombination (HR) is involved in repairing DNA double-strand breaks (DSB), the most harmful for the cell. Regulating HR is essential for maintaining genomic stability. In many forms of cancer, overactivation of HR increases tumor resistance to DNA-damaging treatments. RAD51, HR's core protein, is very often over-expressed in these cancers and plays a critical role in cancer cell development and survival. Targeting RAD51 directly to reduce its activity and its expression is therefore one strategy to sensitize and overcome resistance cancer cells to existing DNA-damaging therapies which remains the limiting factor for the success of targeted therapy. This review describes the structure and biological roles of RAD51, summarizes the different targeted sites of RAD51 and its inhibitory compounds discovered and described in the last decade.
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8
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Ray U, Raghavan SC. Understanding the DNA double-strand break repair and its therapeutic implications. DNA Repair (Amst) 2021; 106:103177. [PMID: 34325086 DOI: 10.1016/j.dnarep.2021.103177] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
Abstract
Repair of DNA double-strand breaks (DSBs) and its regulation are tightly integrated inside cells. Homologous recombination, nonhomologous end joining and microhomology mediated end joining are three major DSB repair pathways in mammalian cells. Targeting proteins associated with these repair pathways using small molecule inhibitors can prove effective in tumors, especially those with deregulated repair. Sensitization of cancer to current age therapy including radio and chemotherapy, using small molecule inhibitors is promising and warrant further development. Although several are under clinical trial, till date no repair inhibitor is approved for commercial use in cancer patients, with the exception of PARP inhibitors targeting single-strand break repair. Based on molecular profiling of repair proteins, better prognostic and therapeutic output can be achieved in patients. In the present review, we highlight the different mechanisms of DSB repair, chromatin dynamics to provide repair accessibility and modulation of inhibitors in association with molecular profiling and current gold standard treatment modalities for cancer.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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9
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Nordén B, Brown T, Feng B. Mismatch detection in homologous strand exchange amplified by hydrophobic effects. Biopolymers 2021; 112:e23426. [PMID: 33780001 PMCID: PMC11475334 DOI: 10.1002/bip.23426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/16/2021] [Accepted: 03/10/2021] [Indexed: 12/19/2022]
Abstract
In contrast to DNA replication and transcription where nucleotides are added and matched one by one, homologous recombination by DNA strand exchange tests whole sequences for complementarity, which requires elimination of mismatched yet thermodynamically stable intermediates. To understand the remarkable sequence specificity of homologous recombination, we have studied strand exchange between a 20-mer duplex containing one single mismatch (placed at varied positions) with the matching single strand in presence of poly(ethylene glycol) representing a semi-hydrophobic environment. A FRET-based assay shows that rates and yields of strand exchange from mismatched to matched strands rapidly increase with semi-hydrophobic co-solute concentration, contrasting previously observed general strand exchange accelerating effect of ethyl glycol ethers. We argue that this effect is not caused simply by DNA melting or solvent-induced changes of DNA conformation but is more complex involving several mechanisms. The catalytic effects, we propose, involve strand invasion facilitated by reduced duplex stability due to weakened base stacking ("longitudinal breathing"). Secondly, decreased water activity makes base-pair hydrogen bonds stronger, increasing the relative energy penalty per mismatch. Finally, unstacked mismatched bases (gaps) are stabilized through partly intercalated hydrophobic co-solvent molecules, assisting nucleation of strand invasion at the point of mismatch. We speculate that nature long ago discovered, and now exploits in various enzymes, that sequence recognition power of nucleic acids may be modulated in a hydrophobic environment.
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Affiliation(s)
- Bengt Nordén
- Department of Chemistry & Chemical EngineeringChalmers University of TechnologyGothenburgSweden
| | - Tom Brown
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUK
| | - Bobo Feng
- Department of Chemistry & Chemical EngineeringChalmers University of TechnologyGothenburgSweden
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10
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Scott DE, Francis-Newton NJ, Marsh ME, Coyne AG, Fischer G, Moschetti T, Bayly AR, Sharpe TD, Haas KT, Barber L, Valenzano CR, Srinivasan R, Huggins DJ, Lee M, Emery A, Hardwick B, Ehebauer M, Dagostin C, Esposito A, Pellegrini L, Perrior T, McKenzie G, Blundell TL, Hyvönen M, Skidmore J, Venkitaraman AR, Abell C. A small-molecule inhibitor of the BRCA2-RAD51 interaction modulates RAD51 assembly and potentiates DNA damage-induced cell death. Cell Chem Biol 2021; 28:835-847.e5. [PMID: 33662256 PMCID: PMC8219027 DOI: 10.1016/j.chembiol.2021.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/18/2020] [Accepted: 02/03/2021] [Indexed: 12/11/2022]
Abstract
BRCA2 controls RAD51 recombinase during homologous DNA recombination (HDR) through eight evolutionarily conserved BRC repeats, which individually engage RAD51 via the motif Phe-x-x-Ala. Using structure-guided molecular design, templated on a monomeric thermostable chimera between human RAD51 and archaeal RadA, we identify CAM833, a 529 Da orthosteric inhibitor of RAD51:BRC with a Kd of 366 nM. The quinoline of CAM833 occupies a hotspot, the Phe-binding pocket on RAD51 and the methyl of the substituted α-methylbenzyl group occupies the Ala-binding pocket. In cells, CAM833 diminishes formation of damage-induced RAD51 nuclear foci; inhibits RAD51 molecular clustering, suppressing extended RAD51 filament assembly; potentiates cytotoxicity by ionizing radiation, augmenting 4N cell-cycle arrest and apoptotic cell death and works with poly-ADP ribose polymerase (PARP)1 inhibitors to suppress growth in BRCA2-wildtype cells. Thus, chemical inhibition of the protein-protein interaction between BRCA2 and RAD51 disrupts HDR and potentiates DNA damage-induced cell death, with implications for cancer therapy.
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Affiliation(s)
- Duncan E Scott
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Nicola J Francis-Newton
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - May E Marsh
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Tommaso Moschetti
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Andrew R Bayly
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Timothy D Sharpe
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kalina T Haas
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Lorraine Barber
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Chiara R Valenzano
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Rajavel Srinivasan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - David J Huggins
- Yusuf Hamied 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
| | - Miyoung Lee
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Amy Emery
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Bryn Hardwick
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Matthias Ehebauer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Claudio Dagostin
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Alessandro Esposito
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Trevor Perrior
- Excellium Consulting, Brook Farm Barn, Lackford, Bury St Edmunds IP28 6HL, UK
| | - Grahame McKenzie
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
| | - John Skidmore
- Yusuf Hamied 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.
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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11
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Design of BRC analogous peptides based on the complex BRC8-RAD51 and the preliminary study on the peptide structures. Amino Acids 2020; 52:831-839. [PMID: 32417964 DOI: 10.1007/s00726-020-02856-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/30/2020] [Indexed: 10/24/2022]
Abstract
BRCA2 is an important tumor suppressor gene that plays a critical role in preserving the stability of cellular genetic information, participating in DNA repair by engaging in binding interactions with RAD51 proteins. However, the lack of structural data on BRCA2 and RAD51 makes the study of their interaction mechanism still a great challenge. We characterize the structure of the BRC8-RAD51 complex using ZDOCK protein docking software and identify the potential non-conserved active site of BRC8 via virtual alanine scanning, utilizing the obtained results to synthesize BRC8, its six analogous peptides (BRC8-1 to BRC8-6), and critical peptide fragment of RAD51 (RAD51(231-260)) by Fmoc solid-phase synthesis. The analogous peptides are found to exhibit a secondary structure significantly different from that of BRC8 by circular dichroism spectroscopy, which indicates that mutation sites determined by computer-aided simulation correspond to key amino acid residues substantially affecting polypeptide structure. On the other hand, the secondary structure of RAD51(231-260) was also considerably influenced by its interaction with BRC8 and analogs, e.g., the fraction of the α-helical structure in RAD51(231-260) increased to 23.6, 15.1, and 13.5% upon interaction with BRC8-1, BRC8-3, and BRC8-6, respectively. The results show that the properties of C-terminal amino acid residues significantly influence peptide-peptide interactions, in agreement with the results of virtual alanine scanning. Therefore, computer-aided simulation was confirmed to be a technique that is useful for narrowing down the range of sites responsible for interactions between peptides or proteins, and provides new inspirations for the design of peptides with strong interactions.
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12
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Bagnolini G, Milano D, Manerba M, Schipani F, Ortega JA, Gioia D, Falchi F, Balboni A, Farabegoli F, De Franco F, Robertson J, Pellicciari R, Pallavicini I, Peri S, Minucci S, Girotto S, Di Stefano G, Roberti M, Cavalli A. Synthetic Lethality in Pancreatic Cancer: Discovery of a New RAD51-BRCA2 Small Molecule Disruptor That Inhibits Homologous Recombination and Synergizes with Olaparib. J Med Chem 2020; 63:2588-2619. [PMID: 32037829 PMCID: PMC7997579 DOI: 10.1021/acs.jmedchem.9b01526] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Synthetic lethality
is an innovative framework for discovering
novel anticancer drug candidates. One example is the use of PARP inhibitors
(PARPi) in oncology patients with BRCA mutations.
Here, we exploit a new paradigm based on the possibility of triggering
synthetic lethality using only small organic molecules (dubbed “fully
small-molecule-induced synthetic lethality”). We exploited
this paradigm to target pancreatic cancer, one of the major unmet
needs in oncology. We discovered a dihydroquinolone pyrazoline-based
molecule (35d) that disrupts the RAD51-BRCA2 protein–protein
interaction, thus mimicking the effect of BRCA2 mutation. 35d inhibits the homologous recombination in a human pancreatic
adenocarcinoma cell line. In addition, it synergizes with olaparib
(a PARPi) to trigger synthetic lethality. This strategy aims to widen
the use of PARPi in BRCA-competent and olaparib-resistant
cancers, making fully small-molecule-induced synthetic lethality an
innovative approach toward unmet oncological needs.
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Affiliation(s)
- Greta Bagnolini
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Domenico Milano
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Marcella Manerba
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Fabrizio Schipani
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Jose Antonio Ortega
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Dario Gioia
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Federico Falchi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Andrea Balboni
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Fulvia Farabegoli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Francesca De Franco
- TES Pharma S.r.l., Via Palmiro Togliatti 22bis, I-06073 Corciano, Perugia, Italy
| | - Janet Robertson
- TES Pharma S.r.l., Via Palmiro Togliatti 22bis, I-06073 Corciano, Perugia, Italy
| | - Roberto Pellicciari
- TES Pharma S.r.l., Via Palmiro Togliatti 22bis, I-06073 Corciano, Perugia, Italy
| | - Isabella Pallavicini
- Department of Experimental Oncology at the IEO, European Institute of Oncology IRCCS, IFOM-IEO Campus, Via Adamello 16, 20100 Milan, Italy
| | - Sebastiano Peri
- Department of Experimental Oncology at the IEO, European Institute of Oncology IRCCS, IFOM-IEO Campus, Via Adamello 16, 20100 Milan, Italy
| | - Saverio Minucci
- Department of Biosciences, University of Milan, Via Celoria 26, 20100 Milan, Italy.,Department of Experimental Oncology at the IEO, European Institute of Oncology IRCCS, IFOM-IEO Campus, Via Adamello 16, 20100 Milan, Italy
| | - Stefania Girotto
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Giuseppina Di Stefano
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Andrea Cavalli
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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13
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Design, synthesis and interaction of BRC4 analogous peptides with RAD51(241–260). Amino Acids 2019; 52:361-369. [DOI: 10.1007/s00726-019-02813-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 12/12/2019] [Indexed: 02/05/2023]
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14
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Velic D, Charlier C, Popova M, Jaunet-Lahary T, Bouchouireb Z, Henry S, Weigel P, Masson JY, Laurent A, Nabiev I, Fleury F. Interactions of the Rad51 inhibitor DIDS with human and bovine serum albumins: Optical spectroscopy and isothermal calorimetry approaches. Biochimie 2019; 167:187-197. [PMID: 31562898 DOI: 10.1016/j.biochi.2019.09.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022]
Abstract
Rad51 is a key protein in DNA repair by homologous recombination and an important target for development of drugs in cancer therapy. 4'-diisothiocyanostilbene-2,2'-disulfonic acid (DIDS) has been used in clinic during the past 30 years as an inhibitor of anion transporters and channels. Recently DIDS has been demonstrated to affect Rad51-mediated homologous pairing and strand exchange, key processes in homologous recombination. Consequently, DIDS has been considered as a potential revertant of radio- and chemo-resistance of cancer cells, the major causes of therapy failure. Here, we have investigated the behavior of DIDS towards serum albumins. The effects of environmental factors, primarily, solvent polarity, on DIDS stability were evaluated, and the mechanisms of interaction of DIDS with human or bovine serum albumin were analyzed using isothermal calorimetry, circular dichroism and fluorescence spectroscopies. DIDS interaction with both serum albumins have been demonstrated, and the interaction characteristics have been determined. By comparing these characteristics for several DIDS derivatives, we have identified the DIDS moiety essential for the interaction. Furthermore, site competition data indicate that human albumin has two DIDS-binding sites: a high-affinity site in the IIIA subdomain and a low-affinity one in the IB subdomain. Molecular docking has revealed the key molecular moieties of DIDS responsible for its interactions in each site and shown that the IB site can bind two ligands. These findings show that binding of DIDS to serum albumin may change the balance between the free and bound DIDS forms, thereby affecting its bioavailability and efficacy against Rad51.
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Affiliation(s)
- Denis Velic
- Group of Mechanism and Regulation of DNA Repair and IMPACT Platform, UFIP UMR CNRS 6286, University of Nantes, 44322, Nantes, France; Centre de Recherche en Cancérologie de l'Université Laval, Laboratoire de Stabilité du Génome, 9, rue McMahon, G1R 3S3, Québec, Canada
| | - Cathy Charlier
- Group of Mechanism and Regulation of DNA Repair and IMPACT Platform, UFIP UMR CNRS 6286, University of Nantes, 44322, Nantes, France
| | - Milena Popova
- Group of Mechanism and Regulation of DNA Repair and IMPACT Platform, UFIP UMR CNRS 6286, University of Nantes, 44322, Nantes, France
| | - Titouan Jaunet-Lahary
- Laboratoire CEISAM - UMR CNR 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France
| | - Zakaria Bouchouireb
- Laboratoire CEISAM - UMR CNR 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France
| | - Sébastien Henry
- Group of Mechanism and Regulation of DNA Repair and IMPACT Platform, UFIP UMR CNRS 6286, University of Nantes, 44322, Nantes, France
| | - Pierre Weigel
- Group of Mechanism and Regulation of DNA Repair and IMPACT Platform, UFIP UMR CNRS 6286, University of Nantes, 44322, Nantes, France
| | - Jean-Yves Masson
- Centre de Recherche en Cancérologie de l'Université Laval, Laboratoire de Stabilité du Génome, 9, rue McMahon, G1R 3S3, Québec, Canada
| | - Adèle Laurent
- Laboratoire CEISAM - UMR CNR 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France
| | - Igor Nabiev
- Laboratoire de Recherche en Nanosciences EA4682-LRB, Université de Reims Champagne-Ardenne, 51100, Reims, France; National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe Shosse, 115522, Moscow, Russian Federation; Department of Clinical Immunology and Allergology, Sechenov First Moscow State Medical University, 119992, Moscow, Russian Federation
| | - Fabrice Fleury
- Group of Mechanism and Regulation of DNA Repair and IMPACT Platform, UFIP UMR CNRS 6286, University of Nantes, 44322, Nantes, France.
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15
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Chabot T, Defontaine A, Marquis D, Renodon-Corniere A, Courtois E, Fleury F, Cheraud Y. New Phosphorylation Sites of Rad51 by c-Met Modulates Presynaptic Filament Stability. Cancers (Basel) 2019; 11:cancers11030413. [PMID: 30909596 PMCID: PMC6468871 DOI: 10.3390/cancers11030413] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/10/2019] [Accepted: 03/20/2019] [Indexed: 11/25/2022] Open
Abstract
Genomic instability through deregulation of DNA repair pathways can initiate cancer and subsequently result in resistance to chemo and radiotherapy. Understanding these biological mechanisms is therefore essential to overcome cancer. RAD51 is the central protein of the Homologous Recombination (HR) DNA repair pathway, which leads to faithful DNA repair of DSBs. The recombinase activity of RAD51 requires nucleofilament formation and is regulated by post-translational modifications such as phosphorylation. In the last decade, studies have suggested the existence of a relationship between receptor tyrosine kinases (RTK) and Homologous Recombination DNA repair. Among these RTK the c-MET receptor is often overexpressed or constitutively activated in many cancer types and its inhibition induces the decrease of HR. In this study, we show for the first time that c-MET is able to phosphorylate the RAD51 protein. We demonstrate in vitro that c-MET phosphorylates four tyrosine residues localized mainly in the subunit-subunit interface of RAD51. Whereas these post-translational modifications do not affect the presynaptic filament formation, they strengthen its stability against the inhibitor effect of the BRC peptide obtained from BRCA2. Taken together, these results confirm the role of these modifications in the regulation of the BRCA2-RAD51 interaction and underline the importance of c-MET in DNA damage response.
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Affiliation(s)
- Thomas Chabot
- Group of Mechanism and Regulation of DNA Repair, UFIP UMR CNRS 6286/University of Nantes, 44322 Nantes, France.
| | - Alain Defontaine
- Group of Molecular Engineering and Glycobiology, UFIP UMR CNRS 6286/University of Nantes, 44322 Nantes, France.
| | - Damien Marquis
- Group of Mechanism and Regulation of DNA Repair, UFIP UMR CNRS 6286/University of Nantes, 44322 Nantes, France.
| | | | - Emmanuelle Courtois
- Group of Mechanism and Regulation of DNA Repair, UFIP UMR CNRS 6286/University of Nantes, 44322 Nantes, France.
| | - Fabrice Fleury
- Group of Mechanism and Regulation of DNA Repair, UFIP UMR CNRS 6286/University of Nantes, 44322 Nantes, France.
| | - Yvonnick Cheraud
- Group of Mechanism and Regulation of DNA Repair, UFIP UMR CNRS 6286/University of Nantes, 44322 Nantes, France.
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16
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Roberti M, Schipani F, Bagnolini G, Milano D, Giacomini E, Falchi F, Balboni A, Manerba M, Farabegoli F, De Franco F, Robertson J, Minucci S, Pallavicini I, Di Stefano G, Girotto S, Pellicciari R, Cavalli A. Rad51/BRCA2 disruptors inhibit homologous recombination and synergize with olaparib in pancreatic cancer cells. Eur J Med Chem 2019; 165:80-92. [DOI: 10.1016/j.ejmech.2019.01.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 10/27/2022]
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17
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Peterson LE. Small Molecule Docking of DNA Repair Proteins Associated with Cancer Survival Following PCNA Metagene Adjustment: A Potential Novel Class of Repair Inhibitors. Molecules 2019; 24:E645. [PMID: 30759820 PMCID: PMC6384788 DOI: 10.3390/molecules24030645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/05/2019] [Accepted: 02/11/2019] [Indexed: 11/16/2022] Open
Abstract
Natural and synthetic small molecules from the NCI Developmental Therapeutics Program (DTP) were employed in molecular dynamics-based docking with DNA repair proteins whose RNA-Seq based expression was associated with overall cancer survival (OS) after adjustment for the PCNA metagene. The compounds employed were required to elicit a sensitive response (vs. resistance) in more than half of the cell lines tested for each cancer. Methodological approaches included peptide sequence alignments and homology modeling for 3D protein structure determination, ligand preparation, docking, toxicity and ADME prediction. Docking was performed for unique lists of DNA repair proteins which predict OS for AML, cancers of the breast, lung, colon, and ovaries, GBM, melanoma, and renal papillary cancer. Results indicate hundreds of drug-like and lead-like ligands with best-pose binding energies less than -6 kcal/mol. Ligand solubility for the top 20 drug-like hits approached lower bounds, while lipophilicity was acceptable. Most ligands were also blood-brain barrier permeable with high intestinal absorption rates. While the majority of ligands lacked positive prediction for HERG channel blockage and Ames carcinogenicity, there was a considerable variation for predicted fathead minnow, honey bee, and Tetrahymena pyriformis toxicity. The computational results suggest the potential for new targets and mechanisms of repair inhibition and can be directly employed for in vitro and in vivo confirmatory laboratory experiments to identify new targets of therapy for cancer survival.
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Affiliation(s)
- Leif E Peterson
- Department of Healthcare Policy and Research, Weill Cornell Medical College, Cornell University, New York City, NY 10065, USA.
- Center for Biostatistics, Institute for Academic Medicine, Houston Methodist Research Institute, 6565 Fannin Street, Houston, TX 77030, USA.
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18
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Zhao D, Lu K, Liu G, Ma L, Zhu H, He J. Design and synthesis of
BRC
analogous peptides and their interactions with a key p53 peptide. FEBS Lett 2018; 592:3438-3445. [DOI: 10.1002/1873-3468.13256] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/03/2018] [Accepted: 09/17/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Dongxin Zhao
- College of Chemistry, Chemical and Environmental Engineering Henan University of Technology Zhengzhou China
| | - Kui Lu
- College of Chemistry, Chemical and Environmental Engineering Henan University of Technology Zhengzhou China
- School of Chemical Engineering and Food Science Zhengzhou Institute of Technology China
| | - Guangbin Liu
- College of Chemistry and Molecular Engineering Zhengzhou University China
| | - Li Ma
- College of Chemistry, Chemical and Environmental Engineering Henan University of Technology Zhengzhou China
| | - Hanjing Zhu
- College of Chemistry, Chemical and Environmental Engineering Henan University of Technology Zhengzhou China
| | - Juan He
- College of Chemistry, Chemical and Environmental Engineering Henan University of Technology Zhengzhou China
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19
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Falchi F, Giacomini E, Masini T, Boutard N, Di Ianni L, Manerba M, Farabegoli F, Rossini L, Robertson J, Minucci S, Pallavicini I, Di Stefano G, Roberti M, Pellicciari R, Cavalli A. Synthetic Lethality Triggered by Combining Olaparib with BRCA2-Rad51 Disruptors. ACS Chem Biol 2017; 12:2491-2497. [PMID: 28841282 DOI: 10.1021/acschembio.7b00707] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In BRCA2-defective cells, poly(adenosine diphosphate [ADP]-ribose) polymerase inhibitors can trigger synthetic lethality, as two independent DNA-repairing mechanisms are simultaneously impaired. Here, we have pharmacologically induced synthetic lethality, which was triggered by combining two different small organic molecules. When administered with a BRCA2-Rad51 disruptor in nonmutant cells, Olaparib showed anticancer activity comparable to that shown when administered alone in BRCA2-defective cells. This strategy could represent an innovative approach to anticancer drug discovery and could be extended to other synthetic lethality pathways.
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Affiliation(s)
- Federico Falchi
- CompuNet, Istituto Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
| | - Elisa Giacomini
- CompuNet, Istituto Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
| | - Tiziana Masini
- CompuNet, Istituto Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
| | - Nicolas Boutard
- CompuNet, Istituto Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
| | - Lorenza Di Ianni
- Department
of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via S. Giacomo 14, I-40126 Bologna, Italy
| | - Marcella Manerba
- Department
of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via S. Giacomo 14, I-40126 Bologna, Italy
| | - Fulvia Farabegoli
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
| | - Lara Rossini
- TES Pharma S.r.l., Via Palmiro Togliatti 22bis, I-06073 Loc. Terrioli, Corciano, Perugia, Italy
| | - Janet Robertson
- TES Pharma S.r.l., Via Palmiro Togliatti 22bis, I-06073 Loc. Terrioli, Corciano, Perugia, Italy
| | - Saverio Minucci
- Department
of Experimental Oncology at the European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, I-20100 Milan, Italy
- Department
of Biosciences, University of Milan, Via Celoria 26, I-20100 Milan, Italy
| | - Isabella Pallavicini
- Department
of Experimental Oncology at the European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, I-20100 Milan, Italy
| | - Giuseppina Di Stefano
- Department
of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via S. Giacomo 14, I-40126 Bologna, Italy
| | - Marinella Roberti
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
| | - Roberto Pellicciari
- TES Pharma S.r.l., Via Palmiro Togliatti 22bis, I-06073 Loc. Terrioli, Corciano, Perugia, Italy
| | - Andrea Cavalli
- CompuNet, Istituto Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
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20
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Fujii N. Potential Strategies to Target Protein-Protein Interactions in the DNA Damage Response and Repair Pathways. J Med Chem 2017; 60:9932-9959. [PMID: 28654754 DOI: 10.1021/acs.jmedchem.7b00358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review article discusses some insights about generating novel mechanistic inhibitors of the DNA damage response and repair (DDR) pathways by focusing on protein-protein interactions (PPIs) of the key DDR components. General requirements for PPI strategies, such as selecting the target PPI site on the basis of its functionality, are discussed first. Next, on the basis of functional rationale and biochemical feasibility to identify a PPI inhibitor, 26 PPIs in DDR pathways (BER, MMR, NER, NHEJ, HR, TLS, and ICL repair) are specifically discussed for inhibitor discovery to benefit cancer therapies using a DNA-damaging agent.
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Affiliation(s)
- Naoaki Fujii
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, MS1000, Memphis, Tennessee 38105, United States
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21
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Gielen F, Butz M, Rees EJ, Erdelyi M, Moschetti T, Hyvönen M, Edel JB, Kaminski CF, Hollfelder F. Quantitative Affinity Determination by Fluorescence Anisotropy Measurements of Individual Nanoliter Droplets. Anal Chem 2017; 89:1092-1101. [PMID: 28192993 PMCID: PMC5287478 DOI: 10.1021/acs.analchem.6b02528] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Fluorescence anisotropy measurements of reagents compartmentalized into individual nanoliter droplets are shown to yield high-resolution binding curves from which precise dissociation constants (Kd) for protein-peptide interactions can be inferred. With the current platform, four titrations can be obtained per minute (based on ∼100 data points each), with stoichiometries spanning more than 2 orders of magnitude and requiring only tens of microliters of reagents. In addition to affinity measurements with purified components, Kd values for unpurified proteins in crude cell lysates can be obtained without prior knowledge of the concentration of the expressed protein, so that protein purification can be avoided. Finally, we show how a competition assay can be set up to perform focused library screens, so that compound labeling is not required anymore. These data demonstrate the utility of droplet compartments for the quantitative characterization of biomolecular interactions and establish fluorescence anisotropy imaging as a quantitative technique in a miniaturized droplet format, which is shown to be as reliable as its macroscopic test tube equivalent.
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Affiliation(s)
- Fabrice Gielen
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.,Living Systems Institute, University of Exeter , Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Maren Butz
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Eric J Rees
- Department of Chemical Engineering and Biotechnology, New Museums Site , Pembroke Street, Cambridge, CB2 3RA, United Kingdom
| | - Miklos Erdelyi
- Department of Chemical Engineering and Biotechnology, New Museums Site , Pembroke Street, Cambridge, CB2 3RA, United Kingdom.,Department of Optics and Quantum Electronics, University of Szeged , Dom ter 9, Szeged, Hungary
| | - Tommaso Moschetti
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Joshua B Edel
- Department of Chemistry, Imperial College London , South Kensington, London, SW7 2AZ, United Kingdom
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, New Museums Site , Pembroke Street, Cambridge, CB2 3RA, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
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22
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Luo K, Li L, Li Y, Wu C, Yin Y, Chen Y, Deng M, Nowsheen S, Yuan J, Lou Z. A phosphorylation-deubiquitination cascade regulates the BRCA2-RAD51 axis in homologous recombination. Genes Dev 2016; 30:2581-2595. [PMID: 27941124 PMCID: PMC5204351 DOI: 10.1101/gad.289439.116] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/30/2016] [Indexed: 11/24/2022]
Abstract
Homologous recombination (HR) is one of the major DNA double-strand break (DSB) repair pathways in mammalian cells. Defects in HR trigger genomic instability and result in cancer predisposition. The defining step of HR is homologous strand exchange directed by the protein RAD51, which is recruited to DSBs by BRCA2. However, the regulation of the BRCA2-RAD51 axis remains unclear. Here we report that ubiquitination of RAD51 hinders RAD51-BRCA2 interaction, while deubiquitination of RAD51 facilitates RAD51-BRCA2 binding and RAD51 recruitment and thus is critical for proper HR. Mechanistically, in response to DNA damage, the deubiquitinase UCHL3 is phosphorylated and activated by ATM. UCHL3, in turn, deubiquitinates RAD51 and promotes the binding between RAD51 and BRCA2. Overexpression of UCHL3 renders breast cancer cells resistant to radiation and chemotherapy, while depletion of UCHL3 sensitizes cells to these treatments, suggesting a determinant role of UCHL3 in cancer therapy. Overall, we identify UCHL3 as a novel regulator of DNA repair and reveal a model in which a phosphorylation-deubiquitination cascade dynamically regulates the BRCA2-RAD51 pathway.
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Affiliation(s)
- Kuntian Luo
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Lei Li
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yunhui Li
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Chenming Wu
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yujiao Yin
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yuping Chen
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Somaira Nowsheen
- Medical Scientist Training Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic School of Medicine, Rochester, Minnesota 55905, USA
| | - Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
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23
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Scott DE, Marsh M, Blundell TL, Abell C, Hyvönen M. Structure-activity relationship of the peptide binding-motif mediating the BRCA2:RAD51 protein-protein interaction. FEBS Lett 2016; 590:1094-102. [PMID: 26992456 PMCID: PMC4855620 DOI: 10.1002/1873-3468.12139] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 02/25/2016] [Accepted: 03/14/2016] [Indexed: 12/18/2022]
Abstract
RAD51 is a recombinase involved in the homologous recombination of double‐strand breaks in DNA. RAD51 forms oligomers by binding to another molecule of RAD51 via an ‘FxxA’ motif, and the same recognition sequence is similarly utilised to bind BRCA2. We have tabulated the effects of mutation of this sequence, across a variety of experimental methods and from relevant mutations observed in the clinic. We use mutants of a tetrapeptide sequence to probe the binding interaction, using both isothermal titration calorimetry and X‐ray crystallography. Where possible, comparison between our tetrapeptide mutational study and the previously reported mutations is made, discrepancies are discussed and the importance of secondary structure in interpreting alanine scanning and mutational data of this nature is considered.
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Affiliation(s)
- Duncan E Scott
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - May Marsh
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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24
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Schay G, Borka B, Kernya L, Bulyáki É, Kardos J, Fekete M, Fidy J. Without Binding ATP, Human Rad51 Does Not Form Helical Filaments on ssDNA. J Phys Chem B 2016; 120:2165-78. [PMID: 26890079 DOI: 10.1021/acs.jpcb.5b12220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of the presynaptic filament (PSF) of proper helical structure by Rad51 recombinases is a prerequisite of the progress of homologous recombination repair. We studied the contribution of ATP-binding to this structure of wt human Rad51 (hRad51). We exploited the protein-dissociation effect of high hydrostatic pressure to determine the free energy of dissociation of the protomer interfaces in hRad51 oligomer states and used electron microscopy to obtain topological parameters. Without cofactors ATP and Ca(2+) and template DNA, hRad51 did not exist in monomer form, but it formed rodlike long filaments without helical order. ΔG(diss) indicated a strong inherent tendency of aggregation. Binding solely ssDNA left the filament unstructured with slightly increased ΔG(diss). Adding only ATP and Ca(2+) to the buffer disintegrated the self-associated rods into rings and short helices of further increased ΔG(diss). Rad51 binding to ssDNA only with ATP and Ca bound could lead to ordered helical filament formation of proper pitch size with interface contacts of K(d) ∼ 2 × 10(-11) M, indicating a structure of outstanding stability. ATP/Ca binding increased the ΔG(diss) of protomer contacts in the filament by 16 kJ/mol. The results emphasize that ATP-binding in the PSF of hRad51 has an essential, yet purely structural, role.
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Affiliation(s)
- Gusztáv Schay
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
| | - Bálint Borka
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
| | - Linda Kernya
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Pázmány P. sétány 1/C, Budapest H-1117, Hungary
| | - Éva Bulyáki
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Pázmány P. sétány 1/C, Budapest H-1117, Hungary
| | - József Kardos
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Pázmány P. sétány 1/C, Budapest H-1117, Hungary
| | - Melinda Fekete
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
| | - Judit Fidy
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
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Samadder P, Aithal R, Belan O, Krejci L. Cancer TARGETases: DSB repair as a pharmacological target. Pharmacol Ther 2016; 161:111-131. [PMID: 26899499 DOI: 10.1016/j.pharmthera.2016.02.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cancer is a disease attributed to the accumulation of DNA damages due to incapacitation of DNA repair pathways resulting in genomic instability and a mutator phenotype. Among the DNA lesions, double stranded breaks (DSBs) are the most toxic forms of DNA damage which may arise as a result of extrinsic DNA damaging agents or intrinsic replication stress in fast proliferating cancer cells. Accurate repair of DSBs is therefore paramount to the cell survival, and several classes of proteins such as kinases, nucleases, helicases or core recombinational proteins have pre-defined jobs in precise execution of DSB repair pathways. On one hand, the proper functioning of these proteins ensures maintenance of genomic stability in normal cells, and on the other hand results in resistance to various drugs employed in cancer therapy and therefore presents a suitable opportunity for therapeutic targeting. Higher relapse and resistance in cancer patients due to non-specific, cytotoxic therapies is an alarming situation and it is becoming more evident to employ personalized treatment based on the genetic landscape of the cancer cells. For the success of personalized treatment, it is of immense importance to identify more suitable targetable proteins in DSB repair pathways and also to explore new synthetic lethal interactions with these pathways. Here we review the various alternative approaches to target the various protein classes termed as cancer TARGETases in DSB repair pathway to obtain more beneficial and selective therapy.
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Affiliation(s)
- Pounami Samadder
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, 60200 Brno, Czech Republic
| | - Rakesh Aithal
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; Department of Biology, Masaryk University, 62500 Brno, Czech Republic
| | - Ondrej Belan
- Department of Biology, Masaryk University, 62500 Brno, Czech Republic
| | - Lumir Krejci
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, 60200 Brno, Czech Republic; Department of Biology, Masaryk University, 62500 Brno, Czech Republic.
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26
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Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. Molecules 2015; 20:11569-603. [PMID: 26111183 PMCID: PMC6272567 DOI: 10.3390/molecules200611569] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 06/02/2015] [Accepted: 06/15/2015] [Indexed: 02/06/2023] Open
Abstract
Blocking protein-protein interactions (PPI) using small molecules or peptides modulates biochemical pathways and has therapeutic significance. PPI inhibition for designing drug-like molecules is a new area that has been explored extensively during the last decade. Considering the number of available PPI inhibitor databases and the limited number of 3D structures available for proteins, docking and scoring methods play a major role in designing PPI inhibitors as well as stabilizers. Docking methods are used in the design of PPI inhibitors at several stages of finding a lead compound, including modeling the protein complex, screening for hot spots on the protein-protein interaction interface and screening small molecules or peptides that bind to the PPI interface. There are three major challenges to the use of docking on the relatively flat surfaces of PPI. In this review we will provide some examples of the use of docking in PPI inhibitor design as well as its limitations. The combination of experimental and docking methods with improved scoring function has thus far resulted in few success stories of PPI inhibitors for therapeutic purposes. Docking algorithms used for PPI are in the early stages, however, and as more data are available docking will become a highly promising area in the design of PPI inhibitors or stabilizers.
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Feng B, Westerlund F, Nordén B. Evidence for hydrophobic catalysis of DNA strand exchange. Chem Commun (Camb) 2015; 51:7390-2. [DOI: 10.1039/c5cc01515d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
DNA strand exchange is catalysed by a hydrophobic environment which destabilises base stacking and promotes DNA breathing.
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Affiliation(s)
- B. Feng
- Department of Chemistry and Chemical Engineering
- Chalmers University of Technology
- SE-412 96 Gothenburg
- Sweden
| | - F. Westerlund
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- SE-412 96 Gothenburg
- Sweden
| | - B. Nordén
- Department of Chemistry and Chemical Engineering
- Chalmers University of Technology
- SE-412 96 Gothenburg
- Sweden
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Abe T, Branzei D. High levels of BRC4 induced by a Tet-On 3G system suppress DNA repair and impair cell proliferation in vertebrate cells. DNA Repair (Amst) 2014; 22:153-64. [PMID: 25218467 PMCID: PMC4194320 DOI: 10.1016/j.dnarep.2014.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/01/2014] [Accepted: 08/21/2014] [Indexed: 12/27/2022]
Abstract
The Tet-On 3G system is useful for conditional gene overexpression studies in DT40. The Tet-On-I-SceI effectively induces DSB formation in vertebrate cells. BRC4 overexpression induces chromosomal breaks and G2-arrest. BRC4 cytotoxicity is mediated by endogenous BRCA2, but independent of NHEJ. BRC4 inhibits cancer cell proliferation and exacerbates the effects of chemotherapy.
Transient induction or suppression of target genes is useful to study the function of toxic or essential genes in cells. Here we apply a Tet-On 3G system to DT40 lymphoma B cell lines, validating it for three different genes. Using this tool, we then show that overexpression of the chicken BRC4 repeat of the tumor suppressor BRCA2 impairs cell proliferation and induces chromosomal breaks. Mechanistically, high levels of BRC4 suppress double strand break-induced homologous recombination, inhibit the formation of RAD51 recombination repair foci, reduce cellular resistance to DNA damaging agents and induce a G2 damage checkpoint-mediated cell-cycle arrest. The above phenotypes are mediated by BRC4 capability to bind and inhibit RAD51. The toxicity associated with BRC4 overexpression is exacerbated by chemotherapeutic agents and reversed by RAD51 overexpression, but it is neither aggravated nor suppressed by a deficit in the non-homologous end-joining pathway of double strand break repair. We further find that the endogenous BRCA2 mediates the cytotoxicity associated with BRC4 induction, thus underscoring the possibility that BRC4 or other domains of BRCA2 cooperate with ectopic BRC4 in regulating repair activities or mitotic cell division. In all, the results demonstrate the utility of the Tet-On 3G system in DT40 research and underpin a model in which BRC4 role on cell proliferation and chromosome repair arises primarily from its suppressive role on RAD51 functions.
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Affiliation(s)
- Takuya Abe
- IFOM, The FIRC Institute for Molecular Oncology Foundation, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy.
| | - Dana Branzei
- IFOM, The FIRC Institute for Molecular Oncology Foundation, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy.
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Normand A, Rivière E, Renodon-Cornière A. Identification and characterization of human Rad51 inhibitors by screening of an existing drug library. Biochem Pharmacol 2014; 91:293-300. [PMID: 25124703 DOI: 10.1016/j.bcp.2014.07.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/29/2014] [Accepted: 07/31/2014] [Indexed: 12/21/2022]
Abstract
Homologous Recombination (HR) plays an essential role in cellular proliferation and in maintaining genomic stability by repairing DNA double-stranded breaks that appear during replication. Rad51, a key protein of HR in eukaryotes, can have an elevated expression level in tumor cells, which correlates with their resistance to anticancer therapies. Therefore, targeted inhibition of Rad51 through inhibitor may improve the tumor response to these therapies. In order to identify small molecules that inhibit Rad51 activity, we screened the Prestwick Library (1120 molecules) for their effect on the strand exchange reaction catalyzed by Rad51. We found that Chicago Sky Blue (CSB) is a potent inhibitor of Rad51, showing IC₅₀ values in the low nanomolar range (400 nM). Biochemical analysis demonstrated that the inhibitory mechanism probably occurs by disrupting the Rad51 association with the single-stranded DNA, which prevents the nucleoprotein filament formation, the first step of the protein activity. Structure Activity Relationship analysis with a number of compounds that shared structure homology with CSB was also performed. The sensitivity of Rad51 inhibition to CSB modifications suggests specific interactions between the molecule and Rad51 nucleofilament. CSB and some of its analogs open up new perspectives in the search for agents capable of potentiating chemo- and radio-therapy treatments for cancer. Moreover, these compounds may be excellent tools to analyze Rad51 cellular functions. Our study also highlights how CSB and its analogs, which are frequently used in colorants, stains and markers, could be responsible of unwanted side effects by perturbing the DNA repair process.
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Affiliation(s)
- Anaïs Normand
- Research Unit UFIP UMR 6286, Centre National de la Recherche Scientifique & University of Nantes, F-44322 Nantes cedex 3, France
| | - Emmanuelle Rivière
- Research Unit UFIP UMR 6286, Centre National de la Recherche Scientifique & University of Nantes, F-44322 Nantes cedex 3, France
| | - Axelle Renodon-Cornière
- Research Unit UFIP UMR 6286, Centre National de la Recherche Scientifique & University of Nantes, F-44322 Nantes cedex 3, France.
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Jekimovs C, Bolderson E, Suraweera A, Adams M, O’Byrne KJ, Richard DJ. Chemotherapeutic compounds targeting the DNA double-strand break repair pathways: the good, the bad, and the promising. Front Oncol 2014; 4:86. [PMID: 24795863 PMCID: PMC4001069 DOI: 10.3389/fonc.2014.00086] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 04/08/2014] [Indexed: 01/09/2023] Open
Abstract
The repair of DNA double-strand breaks (DSBs) is a critical cellular mechanism that exists to ensure genomic stability. DNA DSBs are the most deleterious type of insult to a cell's genetic material and can lead to genomic instability, apoptosis, or senescence. Incorrectly repaired DNA DSBs have the potential to produce chromosomal translocations and genomic instability, potentially leading to cancer. The prevalence of DNA DSBs in cancer due to unregulated growth and errors in repair opens up a potential therapeutic window in the treatment of cancers. The cellular response to DNA DSBs is comprised of two pathways to ensure DNA breaks are repaired: homologous recombination and non-homologous end joining. Identifying chemotherapeutic compounds targeting proteins involved in these DNA repair pathways has shown promise as a cancer therapy for patients, either as a monotherapy or in combination with genotoxic drugs. From the beginning, there have been a number of chemotherapeutic compounds that have yielded successful responses in the clinic, a number that have failed (CGK-733 and iniparib), and a number of promising targets for future studies identified. This review looks in detail at how the cell responds to these DNA DSBs and investigates the chemotherapeutic avenues that have been and are currently being explored to target this repair process.
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Affiliation(s)
- Christian Jekimovs
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Emma Bolderson
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Amila Suraweera
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mark Adams
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kenneth J. O’Byrne
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Derek J. Richard
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
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Carvalho JFS, Kanaar R. Targeting homologous recombination-mediated DNA repair in cancer. Expert Opin Ther Targets 2014; 18:427-58. [PMID: 24491188 DOI: 10.1517/14728222.2014.882900] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION DNA is the target of many traditional non-specific chemotherapeutic drugs. New drugs or therapeutic approaches with a more rational and targeted component are mandatory to improve the success of cancer therapy. The homologous recombination (HR) pathway is an attractive target for the development of inhibitors because cancer cells rely heavily on HR for repair of DNA double-strand breaks resulting from chemotherapeutic treatments. Additionally, the discovery that poly(ADP)ribose polymerase-1 inhibitors selectively kill cells with genetic defects in HR has spurned an even greater interest in inhibitors of HR. AREAS COVERED HR drives the repair of broken DNA via numerous protein-mediated sequential DNA manipulations. Due to extensive number of steps and proteins involved, the HR pathway provides a rich pool of potential drug targets. This review discusses the latest developments concerning the strategies being explored to inhibit HR. Particular attention is given to the identification of small molecule inhibitors of key HR proteins, including the BRCA proteins and RAD51. EXPERT OPINION Current HR inhibitors are providing the basis for pharmaceutical development of more potent and specific inhibitors to be applied in mono- or combinatorial therapy regimes, while novel targets will be uncovered by experiments aimed to gain a deeper mechanistic understanding of HR and its subpathways.
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Affiliation(s)
- João F S Carvalho
- Erasmus MC Cancer Institute, Department of Genetics, Department of Radiation Oncology, Cancer Genomics Netherlands , PO Box 2040, 3000 CA Rotterdam , The Netherlands
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Subramanyam S, Jones WT, Spies M, Spies MA. Contributions of the RAD51 N-terminal domain to BRCA2-RAD51 interaction. Nucleic Acids Res 2013; 41:9020-32. [PMID: 23935068 PMCID: PMC3799448 DOI: 10.1093/nar/gkt691] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
RAD51 DNA strand exchange protein catalyzes the central step in homologous recombination, a cellular process fundamentally important for accurate repair of damaged chromosomes, preservation of the genetic integrity, restart of collapsed replication forks and telomere maintenance. BRCA2 protein, a product of the breast cancer susceptibility gene, is a key recombination mediator that interacts with RAD51 and facilitates RAD51 nucleoprotein filament formation on single-stranded DNA generated at the sites of DNA damage. An accurate atomistic level description of this interaction, however, is limited to a partial crystal structure of the RAD51 core fused to BRC4 peptide. Here, by integrating homology modeling and molecular dynamics, we generated a structure of the full-length RAD51 in complex with BRC4 peptide. Our model predicted previously unknown hydrogen bonding patterns involving the N-terminal domain (NTD) of RAD51. These interactions guide positioning of the BRC4 peptide within a cavity between the core and the NTDs; the peptide binding separates the two domains and restricts internal dynamics of RAD51 protomers. The model’s depiction of the RAD51-BRC4 complex was validated by free energy calculations and in vitro functional analysis of rationally designed mutants. All generated mutants, RAD51E42A, RAD51E59A, RAD51E237A, RAD51E59A/E237A and RAD51E42A/E59A/E237A maintained basic biochemical activities of the wild-type RAD51, but displayed reduced affinities for the BRC4 peptide. Strong correlation between the calculated and experimental binding energies confirmed the predicted structure of the RAD51-BRC4 complex and highlighted the importance of RAD51 NTD in RAD51-BRCA2 interaction.
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Affiliation(s)
- Shyamal Subramanyam
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA, Center for the Physics of Living Cells, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA, Department of Biochemistry, Carver College of Medicine, College of Pharmacy, University of Iowa, Iowa City, IA 52242, USA and Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA 52242, USA
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Budke B, Kalin JH, Pawlowski M, Zelivianskaia AS, Wu M, Kozikowski AP, Connell PP. An optimized RAD51 inhibitor that disrupts homologous recombination without requiring Michael acceptor reactivity. J Med Chem 2012; 56:254-63. [PMID: 23231413 DOI: 10.1021/jm301565b] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Homologous recombination (HR) is an essential process in cells that provides repair of DNA double-strand breaks and lesions that block DNA replication. RAD51 is an evolutionarily conserved protein that is central to HR. Overexpression of RAD51 protein is common in cancer cells and represents a potential therapeutic target in oncology. We previously described a chemical inhibitor of RAD51, called RI-1 (referred to as compound 1 in this report). The chloromaleimide group of this compound is thought to act as a Michael acceptor and react with the thiol group on C319 of RAD51, using a conjugate addition-elimination mechanism. In order to reduce the likelihood of off-target effects and to improve compound stability in biological systems, we developed an analogue of compound 1 that lacks maleimide-based reactivity but retains RAD51 inhibitory activity. This compound, 1-(3,4-dichlorophenyl)-3-(4-methoxyphenyl)-4-morpholino-1H-pyrrole-2,5-dione, named RI-2 (referred to as compound 7a in this report), appears to bind reversibly to the same site on the RAD51 protein as does compound 1. Like compound 1, compound 7a specifically inhibits HR repair in human cells.
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Affiliation(s)
- Brian Budke
- Department of Radiation and Cellular Oncology, University of Chicago, 5758 S. Maryland Avenue, Chicago, Illinois 60637, USA
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Budke B, Logan HL, Kalin JH, Zelivianskaia AS, Cameron McGuire W, Miller LL, Stark JM, Kozikowski AP, Bishop DK, Connell PP. RI-1: a chemical inhibitor of RAD51 that disrupts homologous recombination in human cells. Nucleic Acids Res 2012; 40:7347-57. [PMID: 22573178 PMCID: PMC3424541 DOI: 10.1093/nar/gks353] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Homologous recombination serves multiple roles in DNA repair that are essential for maintaining genomic stability. We here describe RI-1, a small molecule that inhibits the central recombination protein RAD51. RI-1 specifically reduces gene conversion in human cells while stimulating single strand annealing. RI-1 binds covalently to the surface of RAD51 protein at cysteine 319 that likely destabilizes an interface used by RAD51 monomers to oligomerize into filaments on DNA. Correspondingly, the molecule inhibits the formation of subnuclear RAD51 foci in cells following DNA damage, while leaving replication protein A focus formation unaffected. Finally, it potentiates the lethal effects of a DNA cross-linking drug in human cells. Given that this inhibitory activity is seen in multiple human tumor cell lines, RI-1 holds promise as an oncologic drug. Furthermore, RI-1 represents a unique tool to dissect the network of reaction pathways that contribute to DNA repair in cells.
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Affiliation(s)
- Brian Budke
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637, USA
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Ghai R, Falconer RJ, Collins BM. Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010. J Mol Recognit 2012; 25:32-52. [PMID: 22213449 DOI: 10.1002/jmr.1167] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.
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Affiliation(s)
- Rajesh Ghai
- Institute for Molecular Bioscience (IMB), University of Queensland, St. Lucia, Queensland, 4072, Australia
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Cole DJ, Rajendra E, Roberts-Thomson M, Hardwick B, McKenzie GJ, Payne MC, Venkitaraman AR, Skylaris CK. Interrogation of the protein-protein interactions between human BRCA2 BRC repeats and RAD51 reveals atomistic determinants of affinity. PLoS Comput Biol 2011; 7:e1002096. [PMID: 21789034 PMCID: PMC3136434 DOI: 10.1371/journal.pcbi.1002096] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Accepted: 05/04/2011] [Indexed: 11/23/2022] Open
Abstract
The breast cancer suppressor BRCA2 controls the recombinase RAD51 in the reactions that mediate homologous DNA recombination, an essential cellular process required for the error-free repair of DNA double-stranded breaks. The primary mode of interaction between BRCA2 and RAD51 is through the BRC repeats, which are ∼35 residue peptide motifs that interact directly with RAD51 in vitro. Human BRCA2, like its mammalian orthologues, contains 8 BRC repeats whose sequence and spacing are evolutionarily conserved. Despite their sequence conservation, there is evidence that the different human BRC repeats have distinct capacities to bind RAD51. A previously published crystal structure reports the structural basis of the interaction between human BRC4 and the catalytic core domain of RAD51. However, no structural information is available regarding the binding of the remaining seven BRC repeats to RAD51, nor is it known why the BRC repeats show marked variation in binding affinity to RAD51 despite only subtle sequence variation. To address these issues, we have performed fluorescence polarisation assays to indirectly measure relative binding affinity, and applied computational simulations to interrogate the behaviour of the eight human BRC-RAD51 complexes, as well as a suite of BRC cancer-associated mutations. Our computational approaches encompass a range of techniques designed to link sequence variation with binding free energy. They include MM-PBSA and thermodynamic integration, which are based on classical force fields, and a recently developed approach to computing binding free energies from large-scale quantum mechanical first principles calculations with the linear-scaling density functional code onetep. Our findings not only reveal how sequence variation in the BRC repeats directly affects affinity with RAD51 and provide significant new insights into the control of RAD51 by human BRCA2, but also exemplify a palette of computational and experimental tools for the analysis of protein-protein interactions for chemical biology and molecular therapeutics. The atomic scale interactions that occur at the interfaces between proteins are fundamental to all biological processes. One such critical interface is formed between the proteins, human BRCA2 and RAD51. BRCA2 binds to and delivers RAD51 to sites of DNA damage, where RAD51 mediates the error-free repair of double-stranded DNA breaks. Mutations in BRCA2 have been linked to breast cancer predisposition. Therefore, an accurate picture of the interactions between these two proteins is of great importance. BRCA2 interacts with RAD51 via eight “BRC repeats” that are similar, but not identical, in sequence. Due to lack of experimental structural information regarding the binding of seven of the eight BRC repeats to RAD51, it is unknown how subtle sequence variations in the repeats translate to measurable variations in their binding affinity. We have used a range of computational methods, firstly based on classical force fields, and secondly based on first principles quantum mechanical techniques whose computational cost scales linearly with the number of atoms, allowing us to perform calculations on the entire protein complex. This is the first study comparing all eight BRC repeats at the atomic scale and our results provide critical insights into the control of RAD51 by human BRCA2.
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Affiliation(s)
- Daniel J. Cole
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Eeson Rajendra
- MRC Cancer Cell Unit Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Meredith Roberts-Thomson
- Cambridge Molecular Therapeutics Programme, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Bryn Hardwick
- MRC Cancer Cell Unit Hutchison/MRC Research Centre, Cambridge, United Kingdom
- Cambridge Molecular Therapeutics Programme, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Grahame J. McKenzie
- MRC Cancer Cell Unit Hutchison/MRC Research Centre, Cambridge, United Kingdom
- Cambridge Molecular Therapeutics Programme, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Mike C. Payne
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Ashok R. Venkitaraman
- MRC Cancer Cell Unit Hutchison/MRC Research Centre, Cambridge, United Kingdom
- Cambridge Molecular Therapeutics Programme, Hutchison/MRC Research Centre, Cambridge, United Kingdom
- * E-mail: (ARV); (CKS)
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
- * E-mail: (ARV); (CKS)
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Ochiai K, Yoshikawa Y, Yoshimatsu K, Oonuma T, Tomioka Y, Takeda E, Arikawa J, Mominoki K, Omi T, Hashizume K, Morimatsu M. Valine 1532 of human BRC repeat 4 plays an important role in the interaction between BRCA2 and RAD51. FEBS Lett 2011; 585:1771-7. [PMID: 21601571 DOI: 10.1016/j.febslet.2011.05.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 05/06/2011] [Accepted: 05/06/2011] [Indexed: 11/17/2022]
Abstract
The breast cancer susceptibility protein BRCA2 is essential for recombinational DNA repair. BRCA2 specifically binds to RAD51 via eight BRC repeat motifs and delivers RAD51 to double-stranded DNA breaks. In this study, a mammalian two-hybrid assay and competitive ELISA showed that the interaction between BRC repeat 4 (BRC4) and RAD51 was strengthened by the substitution of a single BRC4 amino acid from valine to isoleucine (V1532I). However, the cancer-associated V1532F mutant exhibited very weak interaction with RAD51. This study used a comparative analysis of BRC4 between animal species to identify V1532 as an important residue that interacts with RAD51.
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Affiliation(s)
- Kazuhiko Ochiai
- Department of Basic Science, School of Veterinary Nursing and Technology, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Tokyo, Japan
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Ponomarev SY, Audie J. Computational prediction and analysis of the DR6-NAPP interaction. Proteins 2011; 79:1376-95. [DOI: 10.1002/prot.22962] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 11/02/2010] [Accepted: 11/24/2010] [Indexed: 01/14/2023]
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