Abstract
Cancer occurs when a portion of the body's cells begin to divide uncontrollably and spread into surrounding tissues. Most common reason for growth is genetic mutations. DNA Double Strand Breaks (DSB) brought about by ionizing radiation or other cancer-causing chemicals are one of the unavoidable changes bringing about carcinogenesis. Efficient DNA repair is generally gainful for living beings but in cancer therapy efficient DNA repair challenges the activity of radio and chemotherapies based on DNA damaging agents with cells becoming resistant to drugs. DSB repair pathways therefore serve as critical components for tumor suppression. Cells accomplish error-free repair of DNA DSBs by homologous recombination (HR) repair pathway. Mammalian proteins involved in HR include BRCA1, BRCA2, RAD51 and the RAD51 paralogs. Targeting the function of these proteins can, therefore, offer solution to resistance to anti-cancer treatment, thereby improving the efficiency of chemotherapy and preventing reoccurrence of tumors. RAD51 and its paralogs are central players of the pathway and are targeted for functional disruption. Sequence analysis of RAD51 proteins demonstrates regions within the ATPase domain that are conserved across species and amongst various paralogs. Multiple CHK1/CHK2 phosphorylation sites are present in all the paralogs with at least one of the site in close proximity to the ATPase domain. Inhibitors are identified that bind to the ATP-binding pocket of RAD51 paralogs thereby affecting its hydrolysis. The RAD51 protein interaction with BRCA2 protein is another important target through peptides designed against evolutionarily conserved regions of BRCA2, BRC4. Combinatorial targeting of the function of proteins involved in HR in combination with DNA damaging agents can, therefore, offer solution to radio and chemoresistance, thereby improving the efficiency of chemotherapy and preventing re-occurrence of tumors.
Similar content being viewed by others
Data availability
All data generated or analysed during this study are included in this published article. However, any data or analysis from the current study can be made available from the corresponding author upon reasonable request.
References
Amunugama, R., & Fishel, R. (2011). Subunit interface residues F129 and H294 of human RAD51 are essential for recombinase function. PLoS ONE, 6(8), e23071. https://doi.org/10.1371/journal.pone.0023071.
Aparicio, T., Baer, R., & Gautier, J. (2014). DNA double-strand break repair pathway choice and cancer. DNA Repair, 19, 169–175. https://doi.org/10.1016/j.dnarep.2014.03.014.
Bahassi, E. M., Ovesen, J. L., Riesenberg, A. L., Bernstein, W. Z., Hasty, P. E., & Stambrook, P. J. (2008). The checkpoint kinases Chk1 and Chk2 regulate the functional associations between hBRCA2 and Rad51 in response to DNA damage. Oncogene, 27(28), 3977–3985. https://doi.org/10.1038/onc.2008.17.
Begg, A. C., Stewart, F. A., & Vens, C. (2011). Strategies to improve radiotherapy with targeted drugs. Nature Reviews Cancer, 11(4), 239–253. https://doi.org/10.1038/nrc3007.
Chen, C. F., Chen, P. L., Zhong, Q., Sharp, Z. D., & Lee, W. H. (1999a). Expression of BRC repeats in breast cancer cells disrupts the BRCA2-Rad51 complex and leads to radiation hypersensitivity and loss of G(2)/M checkpoint control. The Journal of Biological Chemistry, 274(46), 32931–32935. https://doi.org/10.1074/jbc.274.46.32931.
Chen, G., Yuan, S. S., Liu, W., Xu, Y., Trujillo, K., Song, B., Cong, F., Goff, S. P., Wu, Y., Arlinghaus, R., Baltimore, D., Gasser, P. J., Park, M. S., Sung, P., & Lee, E. Y. (1999b). Radiation-induced assembly of Rad51 and Rad52 recombination complex requires ATM and c-Abl. The Journal of Biological Chemistry, 274(18), 12748–12752. https://doi.org/10.1074/jbc.274.18.12748.
Christodoulopoulos, G., Malapetsa, A., Schipper, H., Golub, E., Radding, C., & Panasci, L. C. (1999). Chlorambucil induction of HsRad51 in B-cell chronic lymphocytic leukemia. Clinical Cancer Research, 5(8), 2178–2184.
Davies, A. A., Masson, J. Y., McIlwraith, M. J., Stasiak, A. Z., Stasiak, A., Venkitaraman, A. R., & West, S. C. (2001). Role of BRCA2 in control of the RAD51 recombination and DNA repair protein. Molecular Cell, 7(2), 273–282. https://doi.org/10.1016/s1097-2765(01)00175-7.
Dean, M., Fojo, T., & Bates, S. (2005). Tumour stem cells and drug resistance. Nature Reviews Cancer, 5(4), 275–284. https://doi.org/10.1038/nrc1590.
delToro, D., Ortiz, D., Ordyan, M., Sippy, J., Oh, C.-S., Keller, N., Feiss, M., Catalano, C. E., & Smith, D. E. (2016). Walker-A motif acts to coordinate ATP hydrolysis with motor output in viral DNA packaging. Journal of Molecular Biology, 428(13), 2709–2729. https://doi.org/10.1016/j.jmb.2016.04.029.
Donnenberg, V. S., & Donnenberg, A. D. (2005). Multiple drug resistance in cancer revisited: The cancer stem cell hypothesis. Journal of Clinical Pharmacology, 45(8), 872–877. https://doi.org/10.1177/0091270005276905.
Friedberg, E. C., & Friedberg, E. C. (Eds.). (2006). DNA repair and mutagenesis (2nd ed.). ASM Press.
Gruver, A. M., Miller, K. A., Rajesh, C., Smiraldo, P. G., Kaliyaperumal, S., Balder, R., Stiles, K. M., Albala, J. S., & Pittman, D. L. (2005). The ATPase motif in RAD51D is required for resistance to DNA interstrand crosslinking agents and interaction with RAD51C. Mutagenesis, 20(6), 433–440. https://doi.org/10.1093/mutage/gei059.
Hannay, J. A. F., Liu, J., Zhu, Q.-S., Bolshakov, S. V., Li, L., Pisters, P. W. T., Lazar, A. J. F., Yu, D., Pollock, R. E., & Lev, D. (2007). Rad51 overexpression contributes to chemoresistance in human soft tissue sarcoma cells: A role for p53/activator protein 2 transcriptional regulation. Molecular Cancer Therapeutics, 6(5), 1650–1660. https://doi.org/10.1158/1535-7163.MCT-06-0636.
Hengel, S. R., Spies, M. A., & Spies, M. (2017). Small-molecule inhibitors targeting DNA repair and DNA repair deficiency in research and cancer therapy. Cell Chemical Biology, 24(9), 1101–1119. https://doi.org/10.1016/j.chembiol.2017.08.027.
Hoeijmakers, J. H. (2001). Genome maintenance mechanisms for preventing cancer. Nature, 411(6835), 366–374. https://doi.org/10.1038/35077232.
Indran, I. R., Tufo, G., Pervaiz, S., & Brenner, C. (2011). Recent advances in apoptosis, mitochondria and drug resistance in cancer cells. Biochimica Et Biophysica Acta, 1807(6), 735–745. https://doi.org/10.1016/j.bbabio.2011.03.010.
Jackson, S. P., & Bartek, J. (2009). The DNA-damage response in human biology and disease. Nature, 461(7267), 1071–1078. https://doi.org/10.1038/nature08467.
Källberg, M., Wang, H., Wang, S., Peng, J., Wang, Z., Lu, H., & Xu, J. (2012). Template-based protein structure modeling using the RaptorX web server. Nature Protocols, 7(8), 1511–1522. https://doi.org/10.1038/nprot.2012.085.
Kanaar, R., Hoeijmakers, J. H., & van Gent, D. C. (1998). Molecular mechanisms of DNA double strand break repair. Trends in Cell Biology, 8(12), 483–489. https://doi.org/10.1016/s0962-8924(98)01383-x.
Kaur, H., & Rajesh, C. (2016). Identification of conserved domains of proteins involved in homologous recombination repair. Recent Advances in Emerging Technologies, 39–51.
Kaur, H., Kaur, H., Rajesh, P., & Rajesh, C. (2019). Nanotechnology based drug delivery system for cancer therapy. International Journal of Nanobiotechnology, 5(2), 8–36.
Kelley, M. R., & Fishel, M. L. (2008). DNA repair proteins as molecular targets for cancer therapeutics. Anti-Cancer Agents in Medicinal Chemistry, 8(4), 417–425. https://doi.org/10.2174/187152008784220294.
Klein, H. L. (2008). The consequences of Rad51 overexpression for normal and tumor cells. DNA Repair, 7(5), 686–693. https://doi.org/10.1016/j.dnarep.2007.12.008.
Lamiable, A., Thévenet, P., Rey, J., Vavrusa, M., Derreumaux, P., & Tufféry, P. (2016). PEP-FOLD3: Faster de novo structure prediction for linear peptides in solution and in complex. Nucleic Acids Research, 44(W1), W449-454. https://doi.org/10.1093/nar/gkw329.
Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/10.1021/ci200227u.
Lee, M., Sadowska, A., Bekere, I., Ho, D., Gully, B. S., Lu, Y., Iyer, K. S., Trewhella, J., Fox, A. H., & Bond, C. S. (2015). The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation. Nucleic Acids Research, 43(7), 3826–3840. https://doi.org/10.1093/nar/gkv156.
Masson, J. Y., Tarsounas, M. C., Stasiak, A. Z., Stasiak, A., Shah, R., McIlwraith, M. J., Benson, F. E., & West, S. C. (2001). Identification and purification of two distinct complexes containing the five RAD51 paralogs. Genes & Development, 15(24), 3296–3307. https://doi.org/10.1101/gad.947001.
National Cancer Institute (NCI) (2018). https://www.Cancer.Gov/about-Cancer/Understanding/Statistics.
Nickoloff, J. A., Jones, D., Lee, S.-H., Williamson, E. A., & Hromas, R. (2017). Drugging the cancers addicted to DNA repair. Journal of the National Cancer Institute. https://doi.org/10.1093/jnci/djx059.
Obenauer, J. C., Cantley, L. C., & Yaffe, M. B. (2003). Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Research, 31(13), 3635–3641. https://doi.org/10.1093/nar/gkg584.
Park, N. H., Cheng, W., Lai, F., Yang, C., Florez de Sessions, P., Periaswamy, B., Wenhan Chu, C., Bianco, S., Liu, S., Venkataraman, S., Chen, Q., Yang, Y. Y., & Hedrick, J. L. (2018). Addressing drug resistance in cancer with macromolecular chemotherapeutic agents. Journal of the American Chemical Society, 140(12), 4244–4252. https://doi.org/10.1021/jacs.7b11468.
Pellegrini, L., Yu, D. S., Lo, T., Anand, S., Lee, M., Blundell, T. L., & Venkitaraman, A. R. (2002). Insights into DNA recombination from the structure of a RAD51-BRCA2 complex. Nature, 420(6913), 287–293. https://doi.org/10.1038/nature01230.
Rajendra, E., & Venkitaraman, A. R. (2010). Two modules in the BRC repeats of BRCA2 mediate structural and functional interactions with the RAD51 recombinase. Nucleic Acids Research, 38(1), 82–96. https://doi.org/10.1093/nar/gkp873.
Rajesh, C., Baker, D. K., Pierce, A. J., & Pittman, D. L. (2011a). The splicing-factor related protein SFPQ/PSF interacts with RAD51D and is necessary for homology-directed repair and sister chromatid cohesion. Nucleic Acids Research, 39(1), 132–145. https://doi.org/10.1093/nar/gkq738.
Rajesh, C., Gruver, A. M., Basrur, V., & Pittman, D. L. (2009). The interaction profile of homologous recombination repair proteins RAD51C, RAD51D and XRCC2 as determined by proteomic analysis. Proteomics, 9(16), 4071–4086. https://doi.org/10.1002/pmic.200800977.
Rajesh, P., Litvinchuk, A. V., Pittman, D. L., & Wyatt, M. D. (2011b). The homologous recombination protein RAD51D mediates the processing of 6-thioguanine lesions downstream of mismatch repair. Molecular Cancer Research MCR, 9(2), 206–214. https://doi.org/10.1158/1541-7786.MCR-10-0451.
Rajesh, P., Rajesh, C., Wyatt, M. D., & Pittman, D. L. (2010). RAD51D protects against MLH1-dependent cytotoxic responses to O(6)-methylguanine. DNA Repair, 9(4), 458–467. https://doi.org/10.1016/j.dnarep.2010.01.009.
Scott, D. E., Marsh, M., Blundell, T. L., Abell, C., & Hyvönen, M. (2016). Structure-activity relationship of the peptide binding-motif mediating the BRCA2:RAD51 protein-protein interaction. FEBS Letters, 590(8), 1094–1102. https://doi.org/10.1002/1873-3468.12139.
Scully, R., & Livingston, D. M. (2000). In search of the tumour-suppressor functions of BRCA1 and BRCA2. Nature, 408(6811), 429–432. https://doi.org/10.1038/35044000.
Short, J. M., Liu, Y., Chen, S., Soni, N., Madhusudhan, M. S., Shivji, M. K. K., & Venkitaraman, A. R. (2016). High-resolution structure of the presynaptic RAD51 filament on single-stranded DNA by electron cryo-microscopy. Nucleic Acids Research, 44(19), 9017–9030. https://doi.org/10.1093/nar/gkw783.
Smiraldo, P. G., Gruver, A. M., Osborn, J. C., & Pittman, D. L. (2005). Extensive chromosomal instability in Rad51d-deficient mouse cells. Cancer Research, 65(6), 2089–2096. https://doi.org/10.1158/0008-5472.CAN-04-2079.
Sørensen, C. S., Hansen, L. T., Dziegielewski, J., Syljuåsen, R. G., Lundin, C., Bartek, J., & Helleday, T. (2005). The cell-cycle checkpoint kinase Chk1 is required for mammalian homologous recombination repair. Nature Cell Biology, 7(2), 195–201. https://doi.org/10.1038/ncb1212.
Story, R. M., & Steitz, T. A. (1992). Structure of the recA protein-ADP complex. Nature, 355(6358), 374–376. https://doi.org/10.1038/355374a0.
Stothard, P. (2000). The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. BioTechniques, 28(6), 1102–1104. https://doi.org/10.2144/00286ir01.
Tang, W. K., Odzorig, T., Jin, W., & Xia, D. (2019). Structural basis of p97 inhibition by the site-selective anticancer compound CB-5083. Molecular Pharmacology, 95(3), 286–293. https://doi.org/10.1124/mol.118.114256.
Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334.
Vanneman, M., & Dranoff, G. (2012). Combining immunotherapy and targeted therapies in cancer treatment. Nature Reviews Cancer, 12(4), 237–251. https://doi.org/10.1038/nrc3237.
Venkitaraman, A. R. (2002). Cancer susceptibility and the functions of BRCA1 and BRCA2. Cell, 108(2), 171–182. https://doi.org/10.1016/s0092-8674(02)00615-3.
Wallner, B., & Elofsson, A. (2003). Can correct protein models be identified? Protein Science A Publication of the Protein Society, 12(5), 1073–1086. https://doi.org/10.1110/ps.0236803.
Wass, M. N., Kelley, L. A., & Sternberg, M. J. E. (2010). 3DLigandSite: Predicting ligand-binding sites using similar structures. Nucleic Acids Research. https://doi.org/10.1093/nar/gkq406.
Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research. https://doi.org/10.1093/nar/gkm290.
Wyatt, M. D., Reilly, N. M., Patel, S., Rajesh, P., Schools, G. P., Smiraldo, P. G., & Pittman, D. L. (2018). Thiopurine-induced mitotic catastrophe in Rad51d-deficient mammalian cells. Environmental and Molecular Mutagenesis, 59(1), 38–48. https://doi.org/10.1002/em.22138.
Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER suite: Protein structure and function prediction. Nature Methods, 12(1), 7–8. https://doi.org/10.1038/nmeth.3213.
Yu, V. P., Koehler, M., Steinlein, C., Schmid, M., Hanakahi, L. A., van Gool, A. J., West, S. C., & Venkitaraman, A. R. (2000). Gross chromosomal rearrangements and genetic exchange between nonhomologous chromosomes following BRCA2 inactivation. Genes & Development, 14(11), 1400–1406.
Zamarin, D., & Postow, M. A. (2015). Immune checkpoint modulation: Rational design of combination strategies. Pharmacology & Therapeutics, 150, 23–32. https://doi.org/10.1016/j.pharmthera.2015.01.003.
Funding
This study was supported by the Department of Science Technology-Science and Engineering Research Board (DST-SERB), Govt. of India, YSS/2015/001281, Preeti Rajesh, SB/YS/LS-168/2013, Harsimran Kaur.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare no conflict of interest with respect to research, authorship and /or publication of this manuscript.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Kaur, H., Kaur, H., Rajesh, P. et al. In Silico design and characterization of RAD51 protein inhibitors targeting homologous recombination repair for cancer therapy. GENOME INSTAB. DIS. 4, 289–302 (2023). https://doi.org/10.1007/s42764-023-00106-4
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s42764-023-00106-4