1
|
Ning K, Kuz CA, Cheng F, Feng Z, Yan Z, Qiu J. Adeno-Associated Virus Monoinfection Induces a DNA Damage Response and DNA Repair That Contributes to Viral DNA Replication. mBio 2023; 14:e0352822. [PMID: 36719192 PMCID: PMC9973366 DOI: 10.1128/mbio.03528-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 02/01/2023] Open
Abstract
Adeno-associated virus (AAV) belongs to the Dependoparvovirus genus of the Parvoviridae family. AAV replication relies on a helper virus, such as adenovirus (Ad). Co-infection of AAV and Ad induces a DNA damage response (DDR), although its function in AAV DNA replication remains unknown. In this study, monoinfection of AAV2 in HEK293T cells expressing a minimal set of Ad helper genes was used to investigate the role of the DDR solely induced by AAV. We found that AAV2 DNA replication, but not single stranded (ss)DNA genome accumulation and Rep expression only, induced a robust DDR in HEK293T cells. The induced DDR featured the phosphorylation of replication protein A32 (RPA32), histone variant H2AX (H2A histone family member X), and all 3 phosphatidylinositol 3-kinase-related kinases (PIKKs). We also found that the kinase ataxia telangiectasia and Rad3-related protein (ATR) plays a major role in AAV2 DNA replication and that Y family DNA repair DNA polymerases η (Pol η) and Pol κ contribute to AAV2 DNA replication both in vitro and in HEK293T cells. Knockout of Pol η and Pol κ in HEK293T cells significantly decreased wild-type AAV2 replication and recombinant AAV2 production. Thus, our study has proven that AAV2 DNA replication induces a DDR, which in turn initiates a DNA repairing process that partially contributes to the viral genome amplification in HEK293T cells. IMPORTANCE Recombinant AAV (rAAV) has emerged as one of the preferred delivery vectors for clinical gene therapy. rAAV production in HEK293 cells by transfection of a rAAV transgene plasmid, an AAV Rep and Cap expression packaging plasmid, and an Ad helper plasmid remains the popular method. Here, we demonstrated that the high fidelity Y family DNA repair DNA polymerase, Pol η, and Pol κ, plays a significant role in AAV DNA replication and rAAV production in HEK293T cells. Understanding the AAV DNA replication mechanism in HEK293T cells could provide clues to increase rAAV vector yield produced from the transfection method. We also provide evidence that the ATR-mediated DNA repair process through Pol η and Pol κ is one of the mechanisms to amplify AAV genome, which could explain AAV replication and rAAV ssDNA genome conversion in mitotic quiescent cells.
Collapse
Affiliation(s)
- Kang Ning
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cagla Aksu Kuz
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Fang Cheng
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Zehua Feng
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, USA
| | - Ziying Yan
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, USA
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| |
Collapse
|
2
|
McPherson KS, Korzhnev DM. Targeting protein-protein interactions in the DNA damage response pathways for cancer chemotherapy. RSC Chem Biol 2021; 2:1167-1195. [PMID: 34458830 PMCID: PMC8342002 DOI: 10.1039/d1cb00101a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/20/2021] [Indexed: 12/11/2022] Open
Abstract
Cellular DNA damage response (DDR) is an extensive signaling network that orchestrates DNA damage recognition, repair and avoidance, cell cycle progression and cell death. DDR alteration is a hallmark of cancer, with the deficiency in one DDR capability often compensated by a dependency on alternative pathways endowing cancer cells with survival and growth advantage. Targeting these DDR pathways has provided multiple opportunities for the development of cancer therapies. Traditional drug discovery has mainly focused on catalytic inhibitors that block enzyme active sites, which limits the number of potential drug targets within the DDR pathways. This review article describes the emerging approach to the development of cancer therapeutics targeting essential protein-protein interactions (PPIs) in the DDR network. The overall strategy for the structure-based design of small molecule PPI inhibitors is discussed, followed by an overview of the major DNA damage sensing, DNA repair, and DNA damage tolerance pathways with a specific focus on PPI targets for anti-cancer drug design. The existing small molecule inhibitors of DDR PPIs are summarized that selectively kill cancer cells and/or sensitize cancers to front-line genotoxic therapies, and a range of new PPI targets are proposed that may lead to the development of novel chemotherapeutics.
Collapse
Affiliation(s)
- Kerry Silva McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center Farmington CT 06030 USA +1 860 679 3408 +1 860 679 2849
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center Farmington CT 06030 USA +1 860 679 3408 +1 860 679 2849
| |
Collapse
|
3
|
Martin LJ, Cairns EA, Heblinski M, Fletcher C, Krycer JR, Arnold JC, McGregor IS, Bowen MT, Anderson LL. Cannabichromene and Δ 9-Tetrahydrocannabinolic Acid Identified as Lactate Dehydrogenase-A Inhibitors by in Silico and in Vitro Screening. JOURNAL OF NATURAL PRODUCTS 2021; 84:1469-1477. [PMID: 33887133 DOI: 10.1021/acs.jnatprod.0c01281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cannabis sativa contains >120 phytocannabinoids, but our understanding of these compounds is limited. Determining the molecular modes of action of the phytocannabinoids may assist in their therapeutic development. Ligand-based virtual screening was used to suggest novel protein targets for phytocannabinoids. The similarity ensemble approach, a virtual screening tool, was applied to target identification for the phytocannabinoids as a class and predicted a possible interaction with the lactate dehydrogenase (LDH) family of enzymes. In order to evaluate this in silico prediction, a panel of 18 phytocannabinoids was screened against two LDH isozymes (LDHA and LDHB) in vitro. Cannabichromene (CBC) and Δ9-tetrahydrocannabinolic acid (Δ9-THCA) inhibited LDHA via a noncompetitive mode of inhibition with respect to pyruvate, with Ki values of 8.5 and 6.5 μM, respectively. In silico modeling was then used to predict the binding site for CBC and Δ9-THCA. Both were proposed to bind within the nicotinamide pocket, overlapping the binding site of the cofactor NADH, which is consistent with the noncompetitive modes of inhibition. Stemming from our in silico screen, CBC and Δ9-THCA were identified as inhibitors of LDHA, a novel molecular target that may contribute to their therapeutic effects.
Collapse
Affiliation(s)
- Lewis J Martin
- Brain and Mind Centre, The Lambert Initiative for Cannabinoid Therapeutics, The University of Sydney, Sydney, NSW 2006, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Faculty of Science, School of Psychology, The University of Sydney, Sydney, NSW 2006, Australia
| | - Elizabeth A Cairns
- Brain and Mind Centre, The Lambert Initiative for Cannabinoid Therapeutics, The University of Sydney, Sydney, NSW 2006, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Faculty of Science, School of Psychology, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marika Heblinski
- Brain and Mind Centre, The Lambert Initiative for Cannabinoid Therapeutics, The University of Sydney, Sydney, NSW 2006, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Faculty of Medicine and Health, Discipline of Pharmacology, The University of Sydney, Sydney, NSW 2006, Australia
| | - Charlotte Fletcher
- Brain and Mind Centre, The Lambert Initiative for Cannabinoid Therapeutics, The University of Sydney, Sydney, NSW 2006, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Faculty of Medicine and Health, Discipline of Pharmacology, The University of Sydney, Sydney, NSW 2006, Australia
| | - James R Krycer
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Jonathon C Arnold
- Brain and Mind Centre, The Lambert Initiative for Cannabinoid Therapeutics, The University of Sydney, Sydney, NSW 2006, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Faculty of Medicine and Health, Discipline of Pharmacology, The University of Sydney, Sydney, NSW 2006, Australia
| | - Iain S McGregor
- Brain and Mind Centre, The Lambert Initiative for Cannabinoid Therapeutics, The University of Sydney, Sydney, NSW 2006, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Faculty of Science, School of Psychology, The University of Sydney, Sydney, NSW 2006, Australia
| | - Michael T Bowen
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Faculty of Science, School of Psychology, The University of Sydney, Sydney, NSW 2006, Australia
| | - Lyndsey L Anderson
- Brain and Mind Centre, The Lambert Initiative for Cannabinoid Therapeutics, The University of Sydney, Sydney, NSW 2006, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Faculty of Medicine and Health, Discipline of Pharmacology, The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
4
|
Patel SM, Dash RC, Hadden MK. Translesion synthesis inhibitors as a new class of cancer chemotherapeutics. Expert Opin Investig Drugs 2021; 30:13-24. [PMID: 33179552 PMCID: PMC7832080 DOI: 10.1080/13543784.2021.1850692] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/10/2020] [Indexed: 10/23/2022]
Abstract
Introduction: Translesion synthesis (TLS) is a DNA damage tolerance mechanism that replaces the replicative DNA polymerase with a specialized, low-fidelity TLS DNA polymerase that can copy past DNA lesions during active replication. Recent studies have demonstrated a primary role for TLS in replicating past DNA lesions induced by first-line genotoxic agents, resulting in decreased efficacy and acquired chemoresistance. With this in mind, targeting TLS as a combination strategy with first-line genotoxic agents has emerged as a promising approach to develop a new class of anti-cancer adjuvant agents. Areas covered: In this review, we provide a brief background on TLS and its role in cancer. We also discuss the identification and development of inhibitors that target various TLS DNA polymerases or key protein-protein interactions (PPIs) in the TLS machinery. Expert opinion: TLS inhibitors have demonstrated initial promise; however, their continued study is essential to more fully understand the clinical potential of this emerging class of anti-cancer chemotherapeutics. It will be important to determine whether a specific protein involved in TLS is an optimal target. In addition, an expanded understanding of what current genotoxic chemotherapies synergize with TLS inhibitors will guide the clinical strategies for devising combination therapies.
Collapse
Affiliation(s)
- Seema M Patel
- Department of Pharmaceutical Sciences, University of Connecticut , Storrs, CT, United States
| | - Radha Charan Dash
- Department of Pharmaceutical Sciences, University of Connecticut , Storrs, CT, United States
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut , Storrs, CT, United States
| |
Collapse
|
5
|
Mammalian DNA Polymerase Kappa Activity and Specificity. Molecules 2019; 24:molecules24152805. [PMID: 31374881 PMCID: PMC6695781 DOI: 10.3390/molecules24152805] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/27/2019] [Accepted: 07/30/2019] [Indexed: 12/31/2022] Open
Abstract
DNA polymerase (pol) kappa is a Y-family translesion DNA polymerase conserved throughout all domains of life. Pol kappa is special6 ized for the ability to copy DNA containing minor groove DNA adducts, especially N2-dG adducts, as well as to extend primer termini containing DNA damage or mismatched base pairs. Pol kappa generally cannot copy DNA containing major groove modifications or UV-induced photoproducts. Pol kappa can also copy structured or non-B-form DNA, such as microsatellite DNA, common fragile sites, and DNA containing G quadruplexes. Thus, pol kappa has roles both in maintaining and compromising genomic integrity. The expression of pol kappa is altered in several different cancer types, which can lead to genome instability. In addition, many cancer-associated single-nucleotide polymorphisms have been reported in the POLK gene, some of which are associated with poor survival and altered chemotherapy response. Because of this, identifying inhibitors of pol kappa is an active area of research. This review will address these activities of pol kappa, with a focus on lesion bypass and cellular mutagenesis.
Collapse
|
6
|
Ketkar A, Maddukuri L, Penthala NR, Reed MR, Zafar MK, Crooks PA, Eoff RL. Inhibition of Human DNA Polymerases Eta and Kappa by Indole-Derived Molecules Occurs through Distinct Mechanisms. ACS Chem Biol 2019; 14:1337-1351. [PMID: 31082191 DOI: 10.1021/acschembio.9b00304] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Overexpression of human DNA polymerase kappa (hpol κ) in glioblastoma is associated with shorter survival time and resistance to the alkylating agent temozolomide (TMZ), making it an attractive target for the development of small-molecule inhibitors. We previously reported on the development and characterization of indole barbituric acid-derived (IBA) inhibitors of translesion DNA synthesis polymerases (TLS pols). We have now identified a potent and selective inhibitor of hpol κ based on the indole-aminoguanidine (IAG) chemical scaffold. The most promising IAG analogue, IAG-10, exhibited greater inhibitory action against hpol κ than any other human Y-family member, as well as pols from the A-, B-, and X-families. Inhibition of hpol κ by IAG analogues appears to proceed through a mechanism that is distinct from inhibition of hpol η based on changes in DNA binding affinity and nucleotide insertion kinetics. By way of comparison, both IAG and IBA analogues inhibited binary complex formation by hpol κ and ternary complex formation by hpol η. Decreasing the concentration of enzyme and DNA in the reaction mixture lowered the IC50 value of IAG-10 to submicromolar values, consistent with inhibition of binary complex formation for hpol κ. Chemical footprinting experiments revealed that IAG-10 binds to a cleft between the finger, little finger, and N-clasp domains on hpol κ and that this likely disrupts the interaction between the N-clasp and the TLS pol core. In cell culture, IAG-10 potentiated the antiproliferative activity and DNA damaging effects of TMZ in hpol κ-proficient cells but not in hpol κ-deficient cells, indicative of a target-dependent effect. Mutagenic replication across alkylation damage increased in hpol κ-proficient cells treated with IAG-10, while no change in mutation frequency was observed for hpol κ-deficient cells. In summary, we developed a potent and selective small-molecule inhibitor of hpol κ that takes advantage of structural features unique to this TLS enzyme to potentiate TMZ, a standard-of-care drug used in the treatment of malignant brain tumors. Furthermore, the IAG scaffold represents a new chemical space for the exploration of TLS pol inhibitors, which could prove useful as a strategy for improving patient response to genotoxic drugs.
Collapse
Affiliation(s)
- Amit Ketkar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
| | - Leena Maddukuri
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
| | - Narsimha R. Penthala
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
| | - Megan R. Reed
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
| | - Maroof K. Zafar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
| | - Peter A. Crooks
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
| | - Robert L. Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
| |
Collapse
|
7
|
Gallo D, Brown GW. Post-replication repair: Rad5/HLTF regulation, activity on undamaged templates, and relationship to cancer. Crit Rev Biochem Mol Biol 2019; 54:301-332. [PMID: 31429594 DOI: 10.1080/10409238.2019.1651817] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/12/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022]
Abstract
The eukaryotic post-replication repair (PRR) pathway allows completion of DNA replication when replication forks encounter lesions on the DNA template and are mediated by post-translational ubiquitination of the DNA sliding clamp proliferating cell nuclear antigen (PCNA). Monoubiquitinated PCNA recruits translesion synthesis (TLS) polymerases to replicate past DNA lesions in an error-prone manner while addition of K63-linked polyubiquitin chains signals for error-free template switching to the sister chromatid. Central to both branches is the E3 ubiquitin ligase and DNA helicase Rad5/helicase-like transcription factor (HLTF). Mutations in PRR pathway components lead to genomic rearrangements, cancer predisposition, and cancer progression. Recent studies have challenged the notion that the PRR pathway is involved only in DNA lesion tolerance and have shed new light on its roles in cancer progression. Molecular details of Rad5/HLTF recruitment and function at replication forks have emerged. Mounting evidence indicates that PRR is required during lesion-less replication stress, leading to TLS polymerase activity on undamaged templates. Analysis of PRR mutation status in human cancers and PRR function in cancer models indicates that down regulation of PRR activity is a viable strategy to inhibit cancer cell growth and reduce chemoresistance. Here, we review these findings, discuss how they change our views of current PRR models, and look forward to targeting the PRR pathway in the clinic.
Collapse
Affiliation(s)
- David Gallo
- Department of Biochemistry and Donnelly Centre, University of Toronto , Toronto , Canada
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto , Toronto , Canada
| |
Collapse
|
8
|
Zhan Y, He Z, Liu X, Miao N, Lin F, Xu W, Mu S, Mu H, Yuan M, Cao X, Jin H, Liu Z, Li Y, Zhang B. Aspirin-induced attenuation of adipogenic differentiation of bone marrow mesenchymal stem cells is accompanied by the disturbed epigenetic modification. Int J Biochem Cell Biol 2018; 98:29-42. [DOI: 10.1016/j.biocel.2018.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/05/2018] [Accepted: 02/13/2018] [Indexed: 12/15/2022]
|
9
|
Zafar MK, Maddukuri L, Ketkar A, Penthala NR, Reed MR, Eddy S, Crooks PA, Eoff RL. A Small-Molecule Inhibitor of Human DNA Polymerase η Potentiates the Effects of Cisplatin in Tumor Cells. Biochemistry 2018; 57:1262-1273. [PMID: 29345908 DOI: 10.1021/acs.biochem.7b01176] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Translesion DNA synthesis (TLS) performed by human DNA polymerase eta (hpol η) allows tolerance of damage from cis-diamminedichloroplatinum(II) (CDDP or cisplatin). We have developed hpol η inhibitors derived from N-aryl-substituted indole barbituric acid (IBA), indole thiobarbituric acid (ITBA), and indole quinuclidine scaffolds and identified 5-((5-chloro-1-(naphthalen-2-ylmethyl)-1H-indol-3-yl)methylene)-2-thioxodihydropyrimidine-4,6(1H,5H)-dione (PNR-7-02), an ITBA derivative that inhibited hpol η activity with an IC50 value of 8 μM and exhibited 5-10-fold specificity for hpol η over replicative pols. We conclude from kinetic analyses, chemical footprinting assays, and molecular docking that PNR-7-02 binds to a site on the little finger domain and interferes with the proper orientation of template DNA to inhibit hpol η. A synergistic increase in CDDP toxicity was observed in hpol η-proficient cells co-treated with PNR-7-02 (combination index values = 0.4-0.6). Increased γH2AX formation accompanied treatment of hpol η-proficient cells with CDDP and PNR-7-02. Importantly, PNR-7-02 did not impact the effect of CDDP on cell viability or γH2AX in hpol η-deficient cells. In summary, we observed hpol η-dependent effects on DNA damage/replication stress and sensitivity to CDDP in cells treated with PNR-7-02. The ability to employ a small-molecule inhibitor of hpol η to improve the cytotoxic effect of CDDP may aid in the development of more effective chemotherapeutic strategies.
Collapse
Affiliation(s)
- Maroof K Zafar
- Department of Biochemistry and Molecular Biology, ‡Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Leena Maddukuri
- Department of Biochemistry and Molecular Biology, ‡Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Amit Ketkar
- Department of Biochemistry and Molecular Biology, ‡Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Narsimha R Penthala
- Department of Biochemistry and Molecular Biology, ‡Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Megan R Reed
- Department of Biochemistry and Molecular Biology, ‡Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Sarah Eddy
- Department of Biochemistry and Molecular Biology, ‡Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Peter A Crooks
- Department of Biochemistry and Molecular Biology, ‡Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Robert L Eoff
- Department of Biochemistry and Molecular Biology, ‡Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| |
Collapse
|
10
|
Zafar MK, Eoff RL. Translesion DNA Synthesis in Cancer: Molecular Mechanisms and Therapeutic Opportunities. Chem Res Toxicol 2017; 30:1942-1955. [PMID: 28841374 DOI: 10.1021/acs.chemrestox.7b00157] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The genomic landscape of cancer is one marred by instability, but the mechanisms that underlie these alterations are multifaceted and remain a topic of intense research. Cellular responses to DNA damage and/or replication stress can affect genome stability in tumors and influence the response of patients to therapy. In addition to direct repair, DNA damage tolerance (DDT) is an element of genomic maintenance programs that contributes to the etiology of several types of cancer. DDT mechanisms primarily act to resolve replication stress, and this can influence the effectiveness of genotoxic drugs. Translesion DNA synthesis (TLS) is an important component of DDT that facilitates direct bypass of DNA adducts and other barriers to replication. The central role of TLS in the bypass of drug-induced DNA lesions, the promotion of tumor heterogeneity, and the involvement of these enzymes in the maintenance of the cancer stem cell niche presents an opportunity to leverage inhibition of TLS as a way of improving existing therapies. In the review that follows, we summarize mechanisms of DDT, misregulation of TLS in cancer, and discuss the potential for targeting these pathways as a means of improving cancer therapies.
Collapse
Affiliation(s)
- Maroof K Zafar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Robert L Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| |
Collapse
|
11
|
Korzhnev DM, Hadden MK. Targeting the Translesion Synthesis Pathway for the Development of Anti-Cancer Chemotherapeutics. J Med Chem 2016; 59:9321-9336. [PMID: 27362876 DOI: 10.1021/acs.jmedchem.6b00596] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human cells possess tightly controlled mechanisms to rescue DNA replication following DNA damage caused by environmental and endogenous carcinogens using a set of low-fidelity translesion synthesis (TLS) DNA polymerases. These polymerases can copy over replication blocking DNA lesions while temporarily leaving them unrepaired, preventing cell death at the expense of increasing mutation rates and contributing to the onset and progression of cancer. In addition, TLS has been implicated as a major cellular mechanism promoting acquired resistance to genotoxic chemotherapy. Owing to its central role in mutagenesis and cell survival after DNA damage, inhibition of the TLS pathway has emerged as a potential target for the development of anticancer agents. This review will recap our current understanding of the structure and regulation of DNA polymerase complexes that mediate TLS and describe how this knowledge is beginning to translate into the development of small molecule TLS inhibitors.
Collapse
Affiliation(s)
- Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center , Farmington, Connecticut 06030, United States
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269, United States
| |
Collapse
|
12
|
Madadi NR, Zong H, Ketkar A, Zheng C, Penthala NR, Janganati V, Bommagani S, Eoff RL, Guzman ML, Crooks PA. Synthesis and evaluation of a series of resveratrol analogues as potent anti-cancer agents that target tubulin. MEDCHEMCOMM 2015; 6:788-794. [PMID: 26257861 PMCID: PMC4527554 DOI: 10.1039/c4md00478g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A series of novel diarylacrylonitrile and trans-stilbene analogues of resveratrol has been synthesized and evaluated for their anticancer activities against a panel of 60 human cancer cell lines. The diarylacrylonitrile analogues 3b and 4a exhibited the most potent anticancer activity of all the analogues synthesized in this study, with GI50 values of < 10 nM against almost all the cell lines in the human cancer cell panel. Compounds 3b and 4a were also screened against the acute myeloid leukemia (AML) cell line, MV4-11, and were found to have potent cytotoxic properties that are likely mediated through inhibition of tubulin polymerization. Results from molecular docking studies indicate a common binding site for 4a and 3b on the 3,3-tubulin heterodimer, with a slightly more favorable binding for 3b compared to 4a; this is consistent with the results from the microtubule assays, which demonstrate that 4a is more potent than 3b in inhibiting tubulin polymerization in MV4-11 cells. Taken together, these data suggest that diarylacrylonitriles 3b and 4a may have potential as antitubulin therapeutics for treatment of both solid and hematological tumors.
Collapse
Affiliation(s)
- Nikhil R. Madadi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Hongliang Zong
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Medical College of Cornell University, New York, NY
| | - Amit Ketkar
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Chen Zheng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Narsimha R. Penthala
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Venumadhav Janganati
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Shobanbabu Bommagani
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Robert L. Eoff
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Monica L. Guzman
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Medical College of Cornell University, New York, NY
| | - Peter A. Crooks
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| |
Collapse
|
13
|
Zhao L, Pence MG, Eoff RL, Yuan S, Fercu CA, Guengerich FP. Elucidation of kinetic mechanisms of human translesion DNA polymerase κ using tryptophan mutants. FEBS J 2014; 281:4394-410. [PMID: 25065501 PMCID: PMC4182141 DOI: 10.1111/febs.12947] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/18/2014] [Accepted: 07/23/2014] [Indexed: 02/05/2023]
Abstract
To investigate the conformational dynamics of human DNA polymerase κ (hpol κ), we generated two mutants, Y50W (N-clasp region) and Y408W (linker between the thumb and little finger domains), using a Trp-null mutant (W214Y/W392H) of the hpol κ catalytic core enzyme. These mutants retained catalytic activity and similar patterns of selectivity for bypassing the DNA adduct 7,8-dihydro-8-oxo-2'-deoxyguanosine, as indicated by the results of steady-state and pre-steady-state kinetic experiments. Stopped-flow kinetic assays with hpol κ Y50W and T408W revealed a decrease in Trp fluorescence with the template G:dCTP pair but not for any mispairs. This decrease in fluorescence was not rate-limiting and is considered to be related to a conformational change necessary for correct nucleotidyl transfer. When a free 3'-hydroxyl was present on the primer, the Trp fluorescence returned to the baseline level at a rate similar to the observed kcat , suggesting that this change occurs during or after nucleotidyl transfer. However, polymerization rates (kpol ) of extended-product formation were fast, indicating that the slow fluorescence step follows phosphodiester bond formation and is rate-limiting. Pyrophosphate formation and release were fast and are likely to precede the slower relaxation step. The available kinetic data were used to fit a simplified minimal model. The extracted rate constants confirmed that the conformational change after phosphodiester bond formation was rate-limiting for hpol κ catalysis with the template G:dCTP pair.
Collapse
Affiliation(s)
- Linlin Zhao
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN, 37232 USA
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48859 USA
| | - Matthew G. Pence
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN, 37232 USA
| | - Robert L. Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205 USA
| | - Shuai Yuan
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN, 37232 USA
| | - Catinca A. Fercu
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN, 37232 USA
| | - F. Peter Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN, 37232 USA
| |
Collapse
|
14
|
Kim J, Song I, Jo A, Shin JH, Cho H, Eoff RL, Guengerich FP, Choi JY. Biochemical analysis of six genetic variants of error-prone human DNA polymerase ι involved in translesion DNA synthesis. Chem Res Toxicol 2014; 27:1837-52. [PMID: 25162224 PMCID: PMC4203391 DOI: 10.1021/tx5002755] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
DNA
polymerase (pol) ι is the most error-prone among the
Y-family polymerases that participate in translesion synthesis (TLS).
Pol ι can bypass various DNA lesions, e.g., N2-ethyl(Et)G, O6-methyl(Me)G,
8-oxo-7,8-dihydroguanine (8-oxoG), and an abasic site, though frequently
with low fidelity. We assessed the biochemical effects of six reported
genetic variations of human pol ι on its TLS properties, using
the recombinant pol ι (residues 1–445) proteins and DNA
templates containing a G, N2-EtG, O6-MeG, 8-oxoG, or abasic site. The Δ1–25
variant, which is the N-terminal truncation of 25
residues resulting from an initiation codon variant (c.3G > A)
and
also is the formerly misassigned wild-type, exhibited considerably
higher polymerase activity than wild-type with Mg2+ (but
not with Mn2+), coinciding with its steady-state kinetic
data showing a ∼10-fold increase in kcat/Km for nucleotide incorporation
opposite templates (only with Mg2+). The R96G variant,
which lacks a R96 residue known to interact with the incoming nucleotide,
lost much of its polymerase activity, consistent with the kinetic
data displaying 5- to 72-fold decreases in kcat/Km for nucleotide incorporation
opposite templates either with Mg2+ or Mn2+,
except for that opposite N2-EtG with Mn2+ (showing a 9-fold increase for dCTP incorporation). The
Δ1–25 variant bound DNA 20- to 29-fold more tightly than
wild-type (with Mg2+), but the R96G variant bound DNA 2-fold
less tightly than wild-type. The DNA-binding affinity of wild-type,
but not of the Δ1–25 variant, was ∼7-fold stronger
with 0.15 mM Mn2+ than with Mg2+. The results
indicate that the R96G variation severely impairs most of the Mg2+- and Mn2+-dependent TLS abilities of pol ι,
whereas the Δ1–25 variation selectively and substantially
enhances the Mg2+-dependent TLS capability of pol ι,
emphasizing the potential translational importance of these pol ι
genetic variations, e.g., individual differences in TLS, mutation,
and cancer susceptibility to genotoxic carcinogens.
Collapse
Affiliation(s)
- Jinsook Kim
- Division of Pharmacology, Department of Molecular Cell Biology, and ‡Department of Physiology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 440-746, Republic of Korea
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Song I, Kim EJ, Kim IH, Park EM, Lee KE, Shin JH, Guengerich FP, Choi JY. Biochemical characterization of eight genetic variants of human DNA polymerase κ involved in error-free bypass across bulky N(2)-guanyl DNA adducts. Chem Res Toxicol 2014; 27:919-30. [PMID: 24725253 DOI: 10.1021/tx500072m] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA polymerase (pol) κ, one of the Y-family polymerases, has been shown to function in error-free translesion DNA synthesis (TLS) opposite the bulky N(2)-guanyl DNA lesions induced by many carcinogens such as polycyclic aromatic hydrocarbons. We analyzed the biochemical properties of eight reported human pol κ variants positioned in the polymerase core domain, using the recombinant pol κ (residues 1-526) protein and the DNA template containing an N(2)-CH2(9-anthracenyl)G (N(2)-AnthG). The truncation R219X was devoid of polymerase activity, and the E419G and Y432S variants showed much lower polymerase activity than wild-type pol κ. In steady-state kinetic analyses, E419G and Y432S displayed 20- to 34-fold decreases in kcat/Km for dCTP insertion opposite G and N(2)-AnthG compared to that of wild-type pol κ. The L21F, I39T, and D189G variants, as well as E419G and Y432S, displayed 6- to 22-fold decreases in kcat/Km for next-base extension from C paired with N(2)-AnthG, compared to that of wild-type pol κ. The defective Y432S variant had 4- to 5-fold lower DNA-binding affinity than wild-type, while a slightly more efficient S423R variant possessed 2- to 3-fold higher DNA-binding affinity. These results suggest that R219X abolishes and the E419G, Y432S, L21F, I39T, and D189G variations substantially impair the TLS ability of pol κ opposite bulky N(2)-G lesions in the insertion step opposite the lesion and/or the subsequent extension step, raising the possibility that certain nonsynonymous pol κ genetic variations translate into individual differences in susceptibility to genotoxic carcinogens.
Collapse
Affiliation(s)
- Insil Song
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 440-746, Republic of Korea
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Coggins GE, Maddukuri L, Penthala NR, Hartman JH, Eddy S, Ketkar A, Crooks PA, Eoff RL. N-Aroyl indole thiobarbituric acids as inhibitors of DNA repair and replication stress response polymerases. ACS Chem Biol 2013; 8:1722-9. [PMID: 23679919 DOI: 10.1021/cb400305r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Using a robust and quantitative assay, we have identified a novel class of DNA polymerase inhibitors that exhibits some specificity against an enzyme involved in resistance to anti-cancer drugs, namely, human DNA polymerase eta (hpol η). In our initial screen, we identified the indole thiobarbituric acid (ITBA) derivative 5-((1-(2-bromobenzoyl)-5-chloro-1H-indol-3-yl)methylene)-2-thioxodihydropyrimidine-4,6(1H,5H)-dione (ITBA-12) as an inhibitor of the Y-family DNA member hpol η, an enzyme that has been associated with increased resistance to cisplatin and doxorubicin treatments. An additional seven DNA polymerases from different subfamilies were tested for inhibition by ITBA-12. Hpol η was the most potently inhibited enzyme (30 ± 3 μM), with hpol β, hpol γ, and hpol κ exhibiting comparable but higher IC50 values of 41 ± 24, 49 ± 6, and 59 ± 11 μM, respectively. The other polymerases tested had IC50 values closer to 80 μM. Steady-state kinetic analysis was used to investigate the mechanism of polymerase inhibition by ITBA-12. Based on changes in the Michaelis constant, it was determined that ITBA-12 acts as an allosteric (or partial) competitive inhibitor of dNTP binding. The parent ITBA scaffold was modified to produce 20 derivatives and establish structure-activity relationships by testing for inhibition of hpol η. Two compounds with N-naphthoyl Ar-substituents, ITBA-16 and ITBA-19, were both found to have improved potency against hpol η with IC50 values of 16 ± 3 μM and 17 ± 3 μM, respectively. Moreover, the specificity of ITBA-16 was improved relative to that of ITBA-12. The presence of a chloro substituent at position 5 on the indole ring appears to be crucial for effective inhibition of hpol η, with the indole N-1-naphthoyl and N-2-naphthoyl analogues being the most potent inhibitors of hpol η. These results provide a framework from which second-generation ITBA derivatives may be developed against specialized polymerases that are involved in mechanisms of radio- and chemo-resistance.
Collapse
Affiliation(s)
- Grace E. Coggins
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232-0146,
United States
| | | | | | | | | | | | | | | |
Collapse
|