1
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Picco G, Rao Y, Al Saedi A, Lee Y, Vieira SF, Bhosle S, May K, Herranz-Ors C, Walker SJ, Shenje R, Dincer C, Gibson F, Banerjee R, Hewitson Z, Werner T, Cottom JE, Peng Y, Deng N, Zhang Y, Nartey EN, Nickels L, Landis P, Conticelli D, McCarten K, Bush J, Sharma M, Lightfoot H, House D, Milford E, Grant EK, Glogowski MP, Wagner CD, Bantscheff M, Rutkowska-Klute A, Zappacosta F, Pettinger J, Barthorpe S, Eberl HC, Jones BT, Schneck JL, Murphy DJ, Voest EE, Taygerly JP, DeMartino MP, Coelho MA, Houseley J, Sharma G, Schwartz B, Garnett MJ. Novel WRN Helicase Inhibitors Selectively Target Microsatellite-Unstable Cancer Cells. Cancer Discov 2024; 14:1457-1475. [PMID: 38587317 DOI: 10.1158/2159-8290.cd-24-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 04/09/2024]
Abstract
Microsatellite-unstable (MSI) cancers require WRN helicase to resolve replication stress due to expanded DNA (TA)n dinucleotide repeats. WRN is a promising synthetic lethal target for MSI tumors, and WRN inhibitors are in development. In this study, we used CRISPR-Cas9 base editing to map WRN residues critical for MSI cells, validating the helicase domain as the primary drug target. Fragment-based screening led to the development of potent and highly selective WRN helicase covalent inhibitors. These compounds selectively suppressed MSI model growth in vitro and in vivo by mimicking WRN loss, inducing DNA double-strand breaks at expanded TA repeats and DNA damage. Assessment of biomarkers in preclinical models linked TA-repeat expansions and mismatch repair alterations to compound activity. Efficacy was confirmed in immunotherapy-resistant organoids and patient-derived xenograft models. The discovery of potent, selective covalent WRN inhibitors provides proof of concept for synthetic lethal targeting of WRN in MSI cancer and tools to dissect WRN biology. Significance: We report the discovery and characterization of potent, selective WRN helicase inhibitors for MSI cancer treatment, with biomarker analysis and evaluation of efficacy in vivo and in immunotherapy-refractory preclinical models. These findings pave the way to translate WRN inhibition into MSI cancer therapies and provide tools to investigate WRN biology. See related commentary by Wainberg, p. 1369.
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Affiliation(s)
| | | | | | - Yang Lee
- GSK, Upper Providence, Pennsylvania
| | | | | | - Kieron May
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Emile E Voest
- Netherlands Cancer Institute, Amsterdam, the Netherlands
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2
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Jiang T, Zhang Y, Yu S, Hu B. Discovering potential WRN inhibitors from natural product database through computational methods. J Mol Graph Model 2024; 129:108758. [PMID: 38507856 DOI: 10.1016/j.jmgm.2024.108758] [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: 11/15/2023] [Revised: 02/29/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
Microsatellite instability (MSI) is a relatively common feature associated with multiple cancers, and Werner syndrome (WRN) ATP-dependent helicase has been recognized as a novel target for treating MSI cancers, such as colorectal cancer. A small-molecule inhibitor targeting WRN would be a promising strategy for treating colorectal cancer with high MSI expression. In this study, we employed a computer-assisted drug discovery strategy to screen over 30,000 natural product molecules. By using a combination of docking, ligand efficiency, Molecular Mechanics/Generalized Born Surface Area (MM/GBSA), and thermodynamic integration (TI) calculations, we identified MOL008980, MOL010740, MOL011832, T4743, TN1166, and TNP-002173 as potential WRN inhibitors. Subsequent molecular dynamics simulation revealed that these screened natural products possessed better binding dynamic characteristics than ATP substrate and were capable of inhibiting the dynamic process of WRN, making them potential strong ATP competitive inhibitors. In conclusion, our computational approach revealed potential WRN inhibitors from a natural product database, providing a theoretical basis for future research.
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Affiliation(s)
| | | | - Shuihong Yu
- College of Pharmacy, Anqing Medical College, Anqing, China
| | - Bingde Hu
- Navy Anqing Hospital, Anqing, China.
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3
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Yoon JH, Sellamuthu K, Prakash L, Prakash S. WRN exonuclease imparts high fidelity on translesion synthesis by Y family DNA polymerases. Genes Dev 2024; 38:213-232. [PMID: 38503516 PMCID: PMC11065173 DOI: 10.1101/gad.351410.123] [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: 12/04/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024]
Abstract
Purified translesion synthesis (TLS) DNA polymerases (Pols) replicate through DNA lesions with a low fidelity; however, TLS operates in a predominantly error-free manner in normal human cells. To explain this incongruity, here we determine whether Y family Pols, which play an eminent role in replication through a diversity of DNA lesions, are incorporated into a multiprotein ensemble and whether the intrinsically high error rate of the TLS Pol is ameliorated by the components in the ensemble. To this end, we provide evidence for an indispensable role of Werner syndrome protein (WRN) and WRN-interacting protein 1 (WRNIP1) in Rev1-dependent TLS by Y family Polη, Polι, or Polκ and show that WRN, WRNIP1, and Rev1 assemble together with Y family Pols in response to DNA damage. Importantly, we identify a crucial role of WRN's 3' → 5' exonuclease activity in imparting high fidelity on TLS by Y family Pols in human cells, as the Y family Pols that accomplish TLS in an error-free manner manifest high mutagenicity in the absence of WRN's exonuclease function. Thus, by enforcing high fidelity on TLS Pols, TLS mechanisms have been adapted to safeguard against genome instability and tumorigenesis.
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Affiliation(s)
- Jung-Hoon Yoon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
| | - Karthi Sellamuthu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
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4
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Haggag HS, Aboukhatwa SM, Nafie MS, Paul A, Sharafeldin N, Oliver AW, El-Hamamsy MH. Design and synthesis of quinazolin-4-one derivatives as potential anticancer agents and investigation of their interaction with RecQ helicases. Bioorg Chem 2024; 144:107086. [PMID: 38219478 DOI: 10.1016/j.bioorg.2023.107086] [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: 07/17/2023] [Revised: 12/27/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024]
Abstract
The upregulation of RecQ helicases has been associated with cancer cell survival and resistance to chemotherapy, making them appealing targets for therapeutic intervention. In this study, twenty-nine novel quinazolinone derivatives were designed and synthesized. The anti-proliferative activity of all compounds was evaluated against 60 cancer cell lines at the National Cancer Institute Developmental Therapeutic Program, with six compounds (11f, 11g, 11k, 11n, 11p, and 11q) being promoted to a five-dose screen. Compound 11g demonstrated high cytotoxic activity against all examined cell lines. The compounds were further assayed for Bloom syndrome (BLM) helicase inhibition, where 11g, 11q, and 11u showed moderate activity. These compounds were counter-screened against WRN and RECQ1 helicases, where 11g moderately inhibited both enzymes. An ATP competition assay confirmed that the compounds bound to the ATP site of RecQ helicases, and molecular docking simulations were used to study the binding mode within the active site of BLM, WRN, and RECQ1 helicases. Compound 11g induced apoptosis in both HCT-116 and MDA-MB-231 cell lines, but also caused an G2/M phase cell cycle arrest in HCT-116 cells. This data revealed the potential of 11g as a modulator of cell cycle dynamics and supports its interaction with RecQ helicases. In addition, compound 11g displayed non-significant toxicity against FCH normal colon cells at doses up to 100 µM, which confirming its high safety margin and selectivity on cancer cells. Overall, these findings suggest compound 11g as a potential pan RecQ helicase inhibitor with high anticancer potency and a favorable safety margin and selectivity.
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Affiliation(s)
- Hanan S Haggag
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt
| | - Shaimaa M Aboukhatwa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt; Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago 60608, IL, USA
| | - Mohamed S Nafie
- Department of Chemistry, College of Sciences, University of Sharjah, (P. O. Box 27272), Sharjah, United Arab Emirates; Chemistry Department (Biochemistry Program), Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Anju Paul
- Genome Damage and Stability Centre, Science Park Road, University of Sussex Falmer, Brighton BN1 9RQ, UK
| | - Nabaweya Sharafeldin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt
| | - Antony W Oliver
- Genome Damage and Stability Centre, Science Park Road, University of Sussex Falmer, Brighton BN1 9RQ, UK
| | - Mervat H El-Hamamsy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt
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5
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Yang H, Kang M, Jang S, Baek SY, Kim J, Kim GU, Kim D, Ha J, Kim JS, Jung C, Kim NJ, Cho SY, Shin WH, Lee J, Ko J, Lee A, Keum G, Lee S, Kang T. Discovery of thiophen-2-ylmethylene bis-dimedone derivatives as novel WRN inhibitors for treating cancers with microsatellite instability. Bioorg Med Chem 2024; 100:117588. [PMID: 38295487 DOI: 10.1016/j.bmc.2024.117588] [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: 10/05/2023] [Revised: 11/23/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
Microsatellite instability (MSI) is a hypermutable condition caused by DNA mismatch repair system defects, contributing to the development of various cancer types. Recent research has identified Werner syndrome ATP-dependent helicase (WRN) as a promising synthetic lethal target for MSI cancers. Herein, we report the first discovery of thiophen-2-ylmethylene bis-dimedone derivatives as novel WRN inhibitors for MSI cancer therapy. Initial computational analysis and biological evaluation identified a new scaffold for a WRN inhibitor. Subsequent SAR study led to the discovery of a highly potent WRN inhibitor. Furthermore, we demonstrated that the optimal compound induced DNA damage and apoptotic cell death in MSI cancer cells by inhibiting WRN. This study provides a new pharmacophore for WRN inhibitors, emphasizing their therapeutic potential for MSI cancers.
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Affiliation(s)
- Hwasun Yang
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Miso Kang
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Fundamental Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Seonyeong Jang
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Soo Yeon Baek
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Jiwon Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Gyeong Un Kim
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Dongwoo Kim
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Junsu Ha
- Arontier Co., Ltd., Seoul 06735, Republic of Korea
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Nam-Jung Kim
- Department of Fundamental Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sung-Yup Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Medical Research Center, Genomic Medicine Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
| | - Woong-Hee Shin
- Arontier Co., Ltd., Seoul 06735, Republic of Korea; Department of Medicine, Korea University College of Medicine, Seoul 02708, Republic of Korea
| | - Juyong Lee
- Arontier Co., Ltd., Seoul 06735, Republic of Korea; Research Institute of Pharmaceutical Science, Seoul National University, Seoul 08826, Republic of Korea; Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea
| | - Junsu Ko
- Arontier Co., Ltd., Seoul 06735, Republic of Korea
| | - Ansoo Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Gyochang Keum
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Sanghee Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department for HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Republic of Korea.
| | - Taek Kang
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.
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6
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Le ST, Choi S, Lee SW, Kim H, Ahn B. ssDNA reeling is an intermediate step in the reiterative DNA unwinding activity of the WRN-1 helicase. J Biol Chem 2023; 299:105081. [PMID: 37495105 PMCID: PMC10480542 DOI: 10.1016/j.jbc.2023.105081] [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: 01/26/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
RecQ helicases are highly conserved between bacteria and humans. These helicases unwind various DNA structures in the 3' to 5'. Defective helicase activity elevates genomic instability and is associated with predisposition to cancer and/or premature aging. Recent single-molecule analyses have revealed the repetitive unwinding behavior of RecQ helicases from Escherichia coli to humans. However, the detailed mechanisms underlying this behavior are unclear. Here, we performed single-molecule studies of WRN-1 Caenorhabditis elegans RecQ helicase on various DNA constructs and characterized WRN-1 unwinding dynamics. We showed that WRN-1 persistently repeated cycles of DNA unwinding and rewinding with an unwinding limit of 25 to 31 bp per cycle. Furthermore, by monitoring the ends of the displaced strand during DNA unwinding we demonstrated that WRN-1 reels in the ssDNA overhang in an ATP-dependent manner. While WRN-1 reeling activity was inhibited by a C. elegans homolog of human replication protein A, we found that C. elegans replication protein A actually switched the reiterative unwinding activity of WRN-1 to unidirectional unwinding. These results reveal that reeling-in ssDNA is an intermediate step in the reiterative unwinding process for WRN-1 (i.e., the process proceeds via unwinding-reeling-rewinding). We propose that the reiterative unwinding activity of WRN-1 may prevent extensive unwinding, allow time for partner proteins to assemble on the active region, and permit additional modulation in vivo.
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Affiliation(s)
- Son Truong Le
- Department of Life Sciences, University of Ulsan, Ulsan, Republic of Korea
| | - Seoyun Choi
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington DC, USA
| | - Seung-Won Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hajin Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea; Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea.
| | - Byungchan Ahn
- Department of Life Sciences, University of Ulsan, Ulsan, Republic of Korea.
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7
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Parker MJ, Lee H, Yao S, Irwin S, Hwang S, Belanger K, de Mare SW, Surgenor R, Yan L, Gee P, Morla S, Puyang X, Hsiao P, Zeng H, Zhu P, Korpal M, Dransfield P, Bolduc DM, Larsen NA. Identification of 2-Sulfonyl/Sulfonamide Pyrimidines as Covalent Inhibitors of WRN Using a Multiplexed High-Throughput Screening Assay. Biochemistry 2023; 62:2147-2160. [PMID: 37403936 PMCID: PMC10358344 DOI: 10.1021/acs.biochem.2c00599] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/03/2023] [Indexed: 07/06/2023]
Abstract
Werner syndrome protein (WRN) is a multifunctional enzyme with helicase, ATPase, and exonuclease activities that are necessary for numerous DNA-related transactions in the human cell. Recent studies identified WRN as a synthetic lethal target in cancers characterized by genomic microsatellite instability resulting from defects in DNA mismatch repair pathways. WRN's helicase activity is essential for the viability of these high microsatellite instability (MSI-H) cancers and thus presents a therapeutic opportunity. To this end, we developed a multiplexed high-throughput screening assay that monitors exonuclease, ATPase, and helicase activities of full-length WRN. This screening campaign led to the discovery of 2-sulfonyl/sulfonamide pyrimidine derivatives as novel covalent inhibitors of WRN helicase activity. The compounds are specific for WRN versus other human RecQ family members and show competitive behavior with ATP. Examination of these novel chemical probes established the sulfonamide NH group as a key driver of compound potency. One of the leading compounds, H3B-960, showed consistent activities in a range of assays (IC50 = 22 nM, KD = 40 nM, KI = 32 nM), and the most potent compound identified, H3B-968, has inhibitory activity IC50 ∼ 10 nM. These kinetic properties trend toward other known covalent druglike molecules. Our work provides a new avenue for screening WRN for inhibitors that may be adaptable to different therapeutic modalities such as targeted protein degradation, as well as a proof of concept for the inhibition of WRN helicase activity by covalent molecules.
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Affiliation(s)
- Mackenzie J. Parker
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Hyelee Lee
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Shihua Yao
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Sean Irwin
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Sunil Hwang
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Kylie Belanger
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Sofia Woo de Mare
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Richard Surgenor
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Lu Yan
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Patricia Gee
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Shravan Morla
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Xiaoling Puyang
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Peng Hsiao
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Hao Zeng
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Ping Zhu
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Manav Korpal
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Paul Dransfield
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - David M. Bolduc
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
| | - Nicholas A. Larsen
- H3 Biomedicine, Inc., 300 Technology Square, Suite 5, Cambridge, Massachusetts 02139, United States
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8
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Chan EM, Foster KJ, Bass AJ. WRN Is a Promising Synthetic Lethal Target for Cancers with Microsatellite Instability (MSI). Cancer Treat Res 2023; 186:313-328. [PMID: 37978143 DOI: 10.1007/978-3-031-30065-3_17] [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] [Indexed: 11/19/2023]
Abstract
Microsatellite instability (MSI), a type of genetic hypermutability arising from impaired DNA mismatch repair (MMR), is observed in approximately 3% of all cancers. Preclinical work has identified the RecQ helicase WRN as a promising synthetic lethal target for patients with MSI cancers. WRN depletion substantially impairs the viability of MSI, but not microsatellite stable (MSS), cells. Experimental evidence suggests that this synthetic lethal phenotype is driven by numerous TA dinucleotide repeats that undergo expansion mutations in the setting of long-standing MMR deficiency. The lengthening of TA repeats increases their propensity to form secondary DNA structures that require WRN to resolve. In the absence of WRN helicase activity, these unresolved DNA secondary structures stall DNA replication forks and induce catastrophic DNA damage.
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Affiliation(s)
- Edmond M Chan
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, USA.
- Broad Institute of MIT and Harvard, Cambridge, USA.
- New York Genome Center, New York, USA.
| | | | - Adam J Bass
- Novartis Institutes for BioMedical Research, Cambridge, USA
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9
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Vanson S, Li Y, Wood RD, Doublié S. Probing the structure and function of polymerase θ helicase-like domain. DNA Repair (Amst) 2022; 116:103358. [PMID: 35753097 PMCID: PMC10329254 DOI: 10.1016/j.dnarep.2022.103358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/19/2022]
Abstract
DNA Polymerase θ is the key actuator of the recently identified double-strand break repair pathway, theta-mediated end joining (TMEJ). It is the only known polymerase to have a 3-domain architecture containing an independently functional family A DNA polymerase tethered by a long central region to an N-terminal helicase-like domain (HLD). Full-length polymerase θ and the isolated HLD hydrolyze ATP in the presence of DNA, but no processive DNA duplex unwinding has been observed. Based on sequence and structure conservation, the HLD is classified as a member of helicase superfamily II and, more specifically, the Ski2-like family. The specific subdomain composition and organization most closely resemble that of archaeal DNA repair helicases Hel308 and Hjm. The underlying structural basis as to why the HLD is not able to processively unwind duplex DNA, despite its similarity to bona fide helicases, remains elusive. Activities of the HLD include ATP hydrolysis, protein displacement, and annealing of complementary DNA. These observations have led to speculation about the role of the HLD within the context of double-strand break repair via TMEJ, such as removal of single-stranded DNA binding proteins like RPA and RAD51 and microhomology alignment. This review summarizes the structural classification and organization of the polymerase θ HLD and its homologs and explores emerging data on its biochemical activities. We conclude with a simple, speculative model for the HLD's role in TMEJ.
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Affiliation(s)
- Scott Vanson
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405, USA
| | - Yuzhen Li
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, TX 77230, USA
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, TX 77230, USA.
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405, USA.
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10
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Partial lipodystrophy, severe dyslipidaemia and insulin resistant diabetes as early signs of Werner syndrome. J Clin Lipidol 2022; 16:583-590. [DOI: 10.1016/j.jacl.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/02/2022] [Accepted: 06/13/2022] [Indexed: 11/19/2022]
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11
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Determining translocation orientations of nucleic acid helicases. Methods 2021; 204:160-171. [PMID: 34758393 PMCID: PMC9076756 DOI: 10.1016/j.ymeth.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
Helicase enzymes translocate along an RNA or DNA template with a defined polarity to unwind, separate, or remodel duplex strands for a variety of genome maintenance processes. Helicase mutations are commonly associated with a variety of diseases including aging, cancer, and neurodegeneration. Biochemical characterization of these enzymes has provided a wealth of information on the kinetics of unwinding and substrate preferences, and several high-resolution structures of helicases alone and bound to oligonucleotides have been solved. Together, they provide mechanistic insights into the structural translocation and unwinding orientations of helicases. However, these insights rely on structural inferences derived from static snapshots. Instead, continued efforts should be made to combine structure and kinetics to better define active translocation orientations of helicases. This review explores many of the biochemical and biophysical methods utilized to map helicase binding orientation to DNA or RNA substrates and includes several time-dependent methods to unequivocally map the active translocation orientation of these enzymes to better define the active leading and trailing faces.
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12
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Choi J, Lee J. V-Dock: Fast Generation of Novel Drug-like Molecules Using Machine-Learning-Based Docking Score and Molecular Optimization. Int J Mol Sci 2021; 22:11635. [PMID: 34769065 PMCID: PMC8584000 DOI: 10.3390/ijms222111635] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/13/2021] [Accepted: 10/24/2021] [Indexed: 02/06/2023] Open
Abstract
We propose a computational workflow to design novel drug-like molecules by combining the global optimization of molecular properties and protein-ligand docking with machine learning. However, most existing methods depend heavily on experimental data, and many targets do not have sufficient data to train reliable activity prediction models. To overcome this limitation, protein-ligand docking calculations must be performed using the limited data available. Such docking calculations during molecular generation require considerable computational time, preventing extensive exploration of the chemical space. To address this problem, we trained a machine-learning-based model that predicted the docking energy using SMILES to accelerate the molecular generation process. Docking scores could be accurately predicted using only a SMILES string. We combined this docking score prediction model with the global molecular property optimization approach, MolFinder, to find novel molecules exhibiting the desired properties with high values of predicted docking scores. We named this design approach V-dock. Using V-dock, we efficiently generated many novel molecules with high docking scores for a target protein, a similarity to the reference molecule, and desirable drug-like and bespoke properties, such as QED. The predicted docking scores of the generated molecules were verified by correlating them with the actual docking scores.
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Affiliation(s)
- Jieun Choi
- Department of Chemistry, Division of Chemistry and Biochemistry, Kangwon National University, Chuncheon 24341, Korea;
| | - Juyong Lee
- Department of Chemistry, Division of Chemistry and Biochemistry, Kangwon National University, Chuncheon 24341, Korea;
- Arontier Co., Seoul 06735, Korea
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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