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Kumar M, Dubey R, Kumar Shukla P, Dayal D, Kumar Chaubey K, Tsai LW, Kumar S. Identification of small molecule inhibitors of RAD52 for breast cancer therapy: in silico approach. J Biomol Struct Dyn 2024; 42:4605-4618. [PMID: 37288783 DOI: 10.1080/07391102.2023.2220822] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023]
Abstract
The breast cancer susceptibility gene 1/2 (BRCA1/2) are the key regulators in maintaining the genomic integrity and mutations in these genes have been associated with development of breast and ovarian cancers. Also, synthetic lethality has been shown in BRCA1/2 deficient cancers, when the RAD52 gene is silenced by shRNA or small molecules aptamers, suggesting a role for RAD52 in the breast cancers pathogenesis. Thus, to find the potential inhibitors of RAD52, a collection of 21,000 compounds from the ChemBridge screening library was screened to conduct molecular docking and molecular dynamics simulation (MD) against RAD52. Further, the results were validated by a density functional theory (DFT) analysis and using post-dynamics free energy calculations. Out of all screened molecules, the docking study revealed five compounds were found to have promising activities against RAD52. Moreover, the catalytic amino acid residues of RAD52 developed stable contacts with compound 8758 and 10593, as anticipated by DFT calculation, MD simulation, and post dynamics MM-GBSA energy calculation. It appears that compound 8758 is the best inhibitor against RAD52 followed by 10593 compared to the other top hits, in terms of the HOMO orbital energy (-1.0966 eV and -1.2136 eV) from DFT and the post dynamics binding free energy calculation (-54.71 and -52.43 Kcal/mol). Furthermore, a drug-like properties of lead molecules (8758 and 10593) were also seen via ADMET analysis. Based on our computational analysis, we hypothesize that a small molecule 8758 and 10593 possess the therapeutic potential in the management for breast cancer patients with a BRCA mutation via targeting RAD52.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mukesh Kumar
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Prakash Kumar Shukla
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Deen Dayal
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - Kundan Kumar Chaubey
- Division of Research and Innovation, School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Lung-Wen Tsai
- Department of Medicine Research, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Information Technology Office, Taipei Medical University Hospital, Taipei, Taiwan
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei, Taiwan
| | - Sanjay Kumar
- Biological and Bio-computational Lab, Department of Life Sciences, Sharda School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India
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Huang Y, Qiu Y, Ding L, Ren S, Jiang Y, Luo J, Huang J, Yin X, Fu S, Zhao J, Hu K, Liao J. Somatic mutations in four novel genes contribute to homologous recombination deficiency in breast cancer: a real-world clinical tumor sequencing study. J Pathol Clin Res 2024; 10:e12367. [PMID: 38504382 PMCID: PMC10951049 DOI: 10.1002/2056-4538.12367] [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: 08/08/2023] [Revised: 01/31/2024] [Accepted: 02/13/2024] [Indexed: 03/21/2024]
Abstract
Breast cancers involving mutations in homologous recombination (HR) genes, most commonly BRCA1 and BRCA2 (BRCA1/2), respond well to PARP inhibitors and platinum-based chemotherapy. However, except for these specific HR genes, it is not clear which other mutations contribute to homologous recombination defects (HRD). Here, we performed next-generation sequencing of tumor tissues and matched blood samples from 119 breast cancer patients using the OncoScreen Plus panel. Genomic mutation characteristics and HRD scores were analyzed. In the HR genes, we found that BRCA1/2 and PLAB2 mutations were related to HRD. HRD was also detected in a subset of patients without germline or somatic mutations in BRCA1/2, PLAB2, or other HR-related genes. Notably, LRP1B, NOTCH3, GATA2, and CARD11 (abbreviated as LNGC) mutations were associated with high HRD scores in breast cancer patients. Furthermore, functional experiments demonstrated that silencing CARD11 and GATA2 impairs HR repair efficiency and enhances the sensitivity of tumor cells to olaparib treatment. In summary, in the absence of mutations in the HR genes, the sensitivity of tumor cells to PARP inhibitors and platinum-based chemotherapy may be enhanced in a subset of breast cancer patients with LNGC somatic mutations.
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Affiliation(s)
- Yongsheng Huang
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationGuangzhouPR China
| | - Yuntan Qiu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationGuangzhouPR China
| | - Linxiaoxiao Ding
- Breast Tumor Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Shuwei Ren
- Department of Clinical LaboratoryThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Yuanling Jiang
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Jiahuan Luo
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Jinghua Huang
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Xinke Yin
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Sha Fu
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Jianli Zhao
- Breast Tumor Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
- Guangzhou Regenerative Medicine and Health, Guangdong Laboratory, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationGuangzhouPR China
| | - Jianwei Liao
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
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Li H, Zhuang H, Gu T, Li G, Jiang Y, Xu S, Zhou Q. RAD54L promotes progression of hepatocellular carcinoma via the homologous recombination repair pathway. Funct Integr Genomics 2023; 23:128. [PMID: 37071224 DOI: 10.1007/s10142-023-01060-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023]
Abstract
Hepatocellular carcinoma (HCC) is a malignant tumor with high incidence worldwide. The underlying mechanisms remain poorly understood. The DNA metabolic process of homologous recombination repair (HRR) has been linked to a high probability of tumorigenesis and drug resistance. This study aimed to determine the role of HRR in HCC and identify critical HRR-related genes that affect tumorigenesis and prognosis. A total of 613 tumor and 252 para-carcinoma tissue samples were collected from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) to obtain differentially expressed genes (DEGs). HRR-related genes were assessed using gene enrichment and pathway analyses. Survival analysis was performed using the Kaplan-Meier method in the Gene Expression Profiling Interactive Analysis portal. The levels of RAD54L in the HRR pathway were detected by RT-qPCR and western blotting in para-carcinoma and HCC tissues and in L02 normal human liver cells and Huh7 HCC cells. Immunohistochemistry (IHC) was performed on the clinical specimens to determine the connection between gene expression and clinical features. Bioinformatics analysis revealed that the HRR pathway was enriched in HCC tissues. Upregulation of HRR pathway DEGs in HCC tissues was positively correlated with tumor pathological staging and negatively associated with patient overall survival. RAD54B, RAD54L, and EME1 genes in the HRR pathway were screened as markers for predicting HCC prognosis. RT-qPCR identified RAD54L as the most significantly expressed of the three genes. Western blotting and IHC quantitative analyses further demonstrated that RAD54L protein levels were higher in HCC tissues. IHC analysis of 39 pairs of HCC and para-carcinoma tissue samples also revealed an association between RAD54L and Edmondson-Steiner grade and the proliferation-related gene Ki67. The collective findings positively correlate RAD54L in the HRR signaling pathway with HCC staging and implicate RAD54L as a marker to predict HCC progression.
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Affiliation(s)
- Hongda Li
- Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Haiwen Zhuang
- Division of Gastrointestinal Surgery, Department of General Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an Second People's Hospital, Huai'an, China
| | - Tengfei Gu
- Department of Anesthesiology, People's Hospital of Lianshui County, Huai'an, China
| | - Guangyu Li
- Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yuhang Jiang
- Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Sanrong Xu
- Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Qing Zhou
- Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China.
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Lee SY, Miller KM, Kim JJ. Clinical and Mechanistic Implications of R-Loops in Human Leukemias. Int J Mol Sci 2023; 24:ijms24065966. [PMID: 36983041 PMCID: PMC10052022 DOI: 10.3390/ijms24065966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Genetic mutations or environmental agents are major contributors to leukemia and are associated with genomic instability. R-loops are three-stranded nucleic acid structures consisting of an RNA-DNA hybrid and a non-template single-stranded DNA. These structures regulate various cellular processes, including transcription, replication, and DSB repair. However, unregulated R-loop formation can cause DNA damage and genomic instability, which are potential drivers of cancer including leukemia. In this review, we discuss the current understanding of aberrant R-loop formation and how it influences genomic instability and leukemia development. We also consider the possibility of R-loops as therapeutic targets for cancer treatment.
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Affiliation(s)
- Seo-Yun Lee
- Department of Life Science and Multidisciplinary, Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jae-Jin Kim
- Department of Life Science and Multidisciplinary, Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
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Selvaraj C. Therapeutic targets in cancer treatment: Cell cycle proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:313-342. [PMID: 37061336 DOI: 10.1016/bs.apcsb.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Cancer has been linked to the uncontrolled proliferation of cells and the overexpression of cell-cycle genes. The cell cycle machinery plays a crucial role in the regulation of the apoptosis to mitosis to growth phase progression. The mechanisms of the cell cycle also play an important role in preventing DNA damage. There are multiple members of the protein kinase family that are involved in the activities of the cell cycle. Essential cyclins effectively regulate cyclin-dependent kinases (CDKs), which are themselves adversely regulated by naturally occurring CDK inhibitors. Despite the fact that various compounds can effectively block the cell cycle kinases and being investigated for their potential to fight cancer. This chapter explains the detail of cell cycle and checkpoint regulators, that are crucial to the malignant cellular process. The known CDKs inhibitors and their mechanism of action in various cancers have also been addressed as a step toward the development of a possibly novel technique for the design of new drugs against cell cycle kinase proteins.
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Affiliation(s)
- Chandrabose Selvaraj
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, India.
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FOXO3a Mediates Homologous Recombination Repair (HRR) via Transcriptional Activation of MRE11, BRCA1, BRIP1, and RAD50. Molecules 2022; 27:molecules27238623. [PMID: 36500714 PMCID: PMC9741359 DOI: 10.3390/molecules27238623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
To test whether homologous recombination repair (HRR) depends on FOXO3a, a cellular aging model of human dermal fibroblast (HDF) and tet-on flag-h-FOXO3a transgenic mice were studied. HDF cells transfected with over-expression of wt-h-FOXO3a increased the protein levels of MRE11, BRCA1, BRIP1, and RAD50, while knock-down with siFOXO3a decreased them. The protein levels of MRE11, BRCA1, BRIP1, RAD50, and RAD51 decreased during cellular aging. Chromatin immunoprecipitation (ChIP) assay was performed on FOXO3a binding accessibility to FOXO consensus sites in human MRE11, BRCA1, BRIP1, and RAD50 promoters; the results showed FOXO3a binding decreased during cellular aging. When the tet-on flag-h-FOXO3a mice were administered doxycycline orally, the protein and mRNA levels of flag-h-FOXO3a, MRE11, BRCA1, BRIP1, and RAD50 increased in a doxycycline-dose-dependent manner. In vitro HRR assays were performed by transfection with an HR vector and I-SceI vector. The mRNA levels of the recombined GFP increased after doxycycline treatment in MEF but not in wt-MEF, and increased in young HDF comparing to old HDF, indicating that FOXO3a activates HRR. Overall, these results demonstrate that MRE11, BRCA1, BRIP1, and RAD50 are transcriptional target genes for FOXO3a, and HRR activity is increased via transcriptional activation of MRE11, BRCA1, BRIP1, and RAD50 by FOXO3a.
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Wnt antagonist as therapeutic targets in ovarian cancer. Int J Biochem Cell Biol 2022; 145:106191. [PMID: 35272015 DOI: 10.1016/j.biocel.2022.106191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 12/28/2022]
Abstract
Ovarian cancer is a fatal malignancy in women with a low survival rate that demands new therapeutic paradigms. Cancer cells acquire various exclusive alterations to proliferate, invade, metastasize, and escape cell death, acting independently of growth-inducing or growth-inhibiting signals. The nature of cellular signaling in tumorigenesis is interwoven. Wnt signaling is an evolutionarily conserved signaling cascade that has been shown to regulate ovarian cancer pathogenesis. The molecular mechanism of Wnt signaling underlying the development of ovarian cancer, drug resistance, and relapse is not completely understood. Extracellularly secreted Wnt signaling inhibitors are crucial regulators of ovarian cancer tumorigenesis and malignant properties of cancer stem cells. Wnt inhibitors arbitrated modifications affecting Wnt pathway proteins on the cell membranes, in the cytoplasm, and in the nucleus have been shown to span essential contributions in the initiation, progression, and chemoresistance of ovarian cancer. Although many extrinsic inhibitors developed targeting the downstream components of the Wnt signaling pathway, investigating the molecular mechanisms of endogenous secreted inhibitors might substantiate prognostic or therapeutic biomarkers development. Given the importance of Wnt signaling in ovarian cancer, more systematic studies combined with clinical studies are requisite to probe the precise mechanistic interactions of Wnt antagonists in ovarian cancer. This review outlines the latest progress on the Wnt antagonists and ovarian cancer-specific regulators such as micro-RNAs, small molecules, and drugs regulating these Wnt antagonists in ovarian tumourigenesis.
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