1
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Gibney A, Kellett A. Gene Editing with Artificial DNA Scissors. Chemistry 2024; 30:e202401621. [PMID: 38984588 DOI: 10.1002/chem.202401621] [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: 04/24/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/11/2024]
Abstract
Artificial metallo-nucleases (AMNs) are small molecule DNA cleavage agents, also known as DNA molecular scissors, and represent an important class of chemotherapeutic with high clinical potential. This review provides a primary level of exploration on the concepts key to this area including an introduction to DNA structure, function, recognition, along with damage and repair mechanisms. Building on this foundation, we describe hybrid molecules where AMNs are covalently attached to directing groups that provide molecular scissors with enhanced or sequence specific DNA damaging capabilities. As this research field continues to evolve, understanding the applications of AMNs along with synthetic conjugation strategies can provide the basis for future innovations, particularly for designing new artificial gene editing systems.
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Affiliation(s)
- Alex Gibney
- SSPC, The Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Andrew Kellett
- SSPC, The Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland
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2
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Liu Q, Yu Y, Wei G. Oncogenic R248W mutation induced conformational perturbation of the p53 core domain and the structural protection by proteomimetic amyloid inhibitor ADH-6. Phys Chem Chem Phys 2024; 26:20068-20086. [PMID: 39007865 DOI: 10.1039/d4cp02046d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The involvement of p53 aggregation in cancer pathogenesis emphasizes the importance of unraveling the mechanisms underlying mutation-induced p53 destabilization. And understanding how small molecule inhibitors prevent the conversion of p53 into aggregation-primed conformations is pivotal for the development of therapeutics targeting p53-aggregation-associated cancers. A recent experimental study highlights the efficacy of the proteomimetic amyloid inhibitor ADH-6 in stabilizing R248W p53 and inhibiting its aggregation in cancer cells by interacting with the p53 core domain (p53C). However, it remains mostly unclear how R248W mutation induces destabilization of p53C and how ADH-6 stabilizes this p53C mutant and inhibits its aggregation. Herein, we conducted all-atom molecular dynamics simulations of R248W p53C in the absence and presence of ADH-6, as well as that of wild-type (WT) p53C. Our simulations reveal that the R248W mutation results in a shift of helix H2 and β-hairpin S2-S2' towards the mutation site, leading to the destruction of their neighboring β-sheet structure. This further facilitates the formation of a cavity in the hydrophobic core, and reduces the stability of the β-sandwich. Importantly, two crucial aggregation-prone regions (APRs) S9 and S10 are disturbed and more exposed to solvent in R248W p53C, which is conducive to p53C aggregation. Intriguingly, ADH-6 dynamically binds to the mutation site and multiple destabilized regions in R248W p53C, partially inhibiting the shift of helix H2 and β-hairpin S2-S2', thus preventing the disruption of the β-sheets and the formation of the cavity. ADH-6 also reduces the solvent exposure of APRs S9 and S10, which disfavors the aggregation of R248W p53C. Moreover, ADH-6 can preserve the WT-like dynamical network of R248W p53C. Our study elucidates the mechanisms underlying the oncogenic R248W mutation induced p53C destabilization and the structural protection of p53C by ADH-6.
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Affiliation(s)
- Qian Liu
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China.
| | - Yawei Yu
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China.
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China.
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3
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Heath SG, Gray SG, Hamzah EM, O'Connor KM, Bozonet SM, Botha AD, de Cordovez P, Magon NJ, Naughton JD, Goldsmith DLW, Schwartfeger AJ, Sunde M, Buell AK, Morris VK, Göbl C. Amyloid formation and depolymerization of tumor suppressor p16 INK4a are regulated by a thiol-dependent redox mechanism. Nat Commun 2024; 15:5535. [PMID: 38951545 PMCID: PMC11217399 DOI: 10.1038/s41467-024-49581-7] [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: 03/16/2023] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
The conversion of a soluble protein into polymeric amyloid structures is a process that is poorly understood. Here, we describe a fully redox-regulated amyloid system in which cysteine oxidation of the tumor suppressor protein p16INK4a leads to rapid amyloid formation. We identify a partially-structured disulfide-bonded dimeric intermediate species that subsequently assembles into fibrils. The stable amyloid structures disassemble when the disulfide bond is reduced. p16INK4a is frequently mutated in cancers and is considered highly vulnerable to single-point mutations. We find that multiple cancer-related mutations show increased amyloid formation propensity whereas mutations stabilizing the fold prevent transition into amyloid. The complex transition into amyloids and their structural stability is therefore strictly governed by redox reactions and a single regulatory disulfide bond.
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Affiliation(s)
- Sarah G Heath
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Shelby G Gray
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Emilie M Hamzah
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Karina M O'Connor
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Stephanie M Bozonet
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Alex D Botha
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Pierre de Cordovez
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Nicholas J Magon
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Jennifer D Naughton
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Dylan L W Goldsmith
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, Sydney, Australia
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Vanessa K Morris
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
| | - Christoph Göbl
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
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4
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Dai Z, Yang X. The regulation of liquid-liquid phase separated condensates containing nucleic acids. FEBS J 2024; 291:2320-2331. [PMID: 37735903 DOI: 10.1111/febs.16959] [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: 05/19/2023] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023]
Abstract
Liquid-liquid phase separation (LLPS) has been recognized as a universal biological phenomenon. It plays an important role in life activities. LLPS is induced by weak interactions between intrinsically disordered regions or low complex domains. Nucleic acids are widely present in cells, and shown to be closely related to LLPS. Their structure and electronegativity provide the excellent platforms for the formation of phase-separated condensates. In this review, we summarize the interconnected regulation between nucleic acids and LLPS demonstrated in in vivo and in vitro studies. Beside homogeneous and single-phase condensates, complicated and multicompartment LLPS induced by nucleic acids is discussed as well. Recent advances about nucleic-acid-induced LLPS as a new pathogenic mechanism and drug design direction are highlighted, especially virus-mediated disease treatment and prevention.
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Affiliation(s)
- Zhuojun Dai
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaorong Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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5
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Chitluri KK, Emerson IA. The importance of protein domain mutations in cancer therapy. Heliyon 2024; 10:e27655. [PMID: 38509890 PMCID: PMC10950675 DOI: 10.1016/j.heliyon.2024.e27655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Cancer is a complex disease that is caused by multiple genetic factors. Researchers have been studying protein domain mutations to understand how they affect the progression and treatment of cancer. These mutations can significantly impact the development and spread of cancer by changing the protein structure, function, and signalling pathways. As a result, there is a growing interest in how these mutations can be used as prognostic indicators for cancer prognosis. Recent studies have shown that protein domain mutations can provide valuable information about the severity of the disease and the patient's response to treatment. They may also be used to predict the response and resistance to targeted therapy in cancer treatment. The clinical implications of protein domain mutations in cancer are significant, and they are regarded as essential biomarkers in oncology. However, additional techniques and approaches are required to characterize changes in protein domains and predict their functional effects. Machine learning and other computational tools offer promising solutions to this challenge, enabling the prediction of the impact of mutations on protein structure and function. Such predictions can aid in the clinical interpretation of genetic information. Furthermore, the development of genome editing tools like CRISPR/Cas9 has made it possible to validate the functional significance of mutants more efficiently and accurately. In conclusion, protein domain mutations hold great promise as prognostic and predictive biomarkers in cancer. Overall, considerable research is still needed to better define genetic and molecular heterogeneity and to resolve the challenges that remain, so that their full potential can be realized.
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Affiliation(s)
- Kiran Kumar Chitluri
- Bioinformatics Programming Lab, Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - Isaac Arnold Emerson
- Bioinformatics Programming Lab, Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
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6
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Naeimzadeh Y, Tajbakhsh A, Fallahi J. Understanding the prion-like behavior of mutant p53 proteins in triple-negative breast cancer pathogenesis: The current therapeutic strategies and future directions. Heliyon 2024; 10:e26260. [PMID: 38390040 PMCID: PMC10881377 DOI: 10.1016/j.heliyon.2024.e26260] [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: 10/23/2023] [Revised: 01/20/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Breast cancer (BC) is viewed as a significant public health issue and is the primary cause of cancer-related deaths among women worldwide. Triple-negative breast cancer (TNBC) is a particularly aggressive subtype that predominantly affects young premenopausal women. The tumor suppressor p53 playsa vital role in the cellular response to DNA damage, and its loss or mutations are commonly present in many cancers, including BC. Recent evidence suggests that mutant p53 proteins can aggregate and form prion-like structures, which may contribute to the pathogenesis of different types of malignancies, such as BC. This review provides an overview of BC molecular subtypes, the epidemiology of TNBC, and the role of p53 in BC development. We also discuss the potential implications of prion-like aggregation in BC and highlight future research directions. Moreover, a comprehensive analysis of the current therapeutic approaches targeting p53 aggregates in BC treatment is presented. Strategies including small molecules, chaperone inhibitors, immunotherapy, CRISPR-Cas9, and siRNA are discussed, along with their potential benefits and drawbacks. The use of these approaches to inhibit p53 aggregation and degradation represents a promising target for cancer therapy. Future investigations into the efficacy of these approaches against various p53 mutations or binding to non-p53 proteins should be conducted to develop more effective and personalized therapies for BC treatment.
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Affiliation(s)
- Yasaman Naeimzadeh
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran
| | - Amir Tajbakhsh
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jafar Fallahi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran
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7
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Kwan K, Castro-Sandoval O, Ma B, Martelino D, Saffari A, Liu XL, Orvain C, Mellitzer G, Gaiddon C, Storr T. Altering relative metal-binding affinities in multifunctional Metallochaperones for mutant p53 reactivation. J Inorg Biochem 2024; 251:112433. [PMID: 38043136 DOI: 10.1016/j.jinorgbio.2023.112433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 12/05/2023]
Abstract
The p53 protein plays a major role in cancer prevention, and over 50% of cancer diagnoses can be attributed to p53 malfunction. p53 incorporates a structural Zn site that is required for proper protein folding and function, and in many cases point mutations can result in loss of the Zn2+ ion, destabilization of the tertiary structure, and eventual amyloid aggregation. Herein, we report a series of compounds designed to act as small molecule stabilizers of mutant p53, and feature Zn-binding fragments to chaperone Zn2+ to the metal depleted site and restore wild-type (WT) function. Many Zn metallochaperones (ZMCs) have been shown to generate intracellular reactive oxygen species (ROS), likely by chelating redox-active metals such as Fe2+/3+ and Cu+/2+ and undergoing associated Fenton chemistry. High levels of ROS can result in off-target effects and general toxicity, and thus, careful tuning of ligand Zn2+ affinity, in comparison to the affinity for other endogenous metals, is important for selective mutant p53 targeting. In this work we show that by using carboxylate donors in place of pyridine we can change the relative Zn2+/Cu2+ binding ability in a series of ligands, and we investigate the impact of donor group changes on metallochaperone activity and overall cytotoxicity in two mutant p53 cancer cell lines (NUGC3 and SKGT2).
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Affiliation(s)
- Kalvin Kwan
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Omar Castro-Sandoval
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Benjamin Ma
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Diego Martelino
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Ashkan Saffari
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Xi Lan Liu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Christophe Orvain
- Inserm UMR_S 1113, Université de Strasbourg, Molecular Mechanisms of Stress Response and Pathologies, Strasbourg, France
| | - Georg Mellitzer
- Inserm UMR_S 1113, Université de Strasbourg, Molecular Mechanisms of Stress Response and Pathologies, Strasbourg, France
| | - Christian Gaiddon
- Inserm UMR_S 1113, Université de Strasbourg, Molecular Mechanisms of Stress Response and Pathologies, Strasbourg, France.
| | - Tim Storr
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
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8
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Kaur G, Khanna B, Yusuf M, Sharma A, Khajuria A, Alajangi HK, Jaiswal PK, Sachdeva M, Barnwal RP, Singh G. A Path of Novelty from Nanoparticles to Nanobots: Theragnostic Approach for Targeting Cancer Therapy. Crit Rev Ther Drug Carrier Syst 2024; 41:1-38. [PMID: 38305340 DOI: 10.1615/critrevtherdrugcarriersyst.2023046674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Pharmaceutical development of cancer therapeutics is a dynamic area of research. Even after decades of intensive work, cancer continues to be a dreadful disease with an ever-increasing global incidence. The progress of nanotechnology in cancer research has overcome inherent limitations in conventional cancer chemotherapy and fulfilled the need for target-specific drug carriers. Nanotechnology uses the altered patho-physiological microenvironment of malignant cells and offers various advantages like improved solubility, reduced toxicity, prolonged drug circulation with controlled release, circumventing multidrug resistance, and enhanced biodistribution. Early cancer detection has a crucial role in selecting the best drug regime, thus, diagnosis and therapeutics go hand in hand. Furthermore, nanobots are an amazing possibility and promising innovation with numerous significant applications, particularly in fighting cancer and cleaning out blood vessels. Nanobots are tiny robots, ranging in size from 1 to 100 nm. Moreover, the nanobots would work similarly to white blood cells, watching the bloodstream and searching for indications of distress. This review articulates the evolution of various organic and inorganic nanoparticles and nanobots used as therapeutics, along with their pros and cons. It also highlights the shift in diagnostics from conventional methods to more advanced techniques. This rapidly growing domain is providing more space for engineering desired nanoparticles that can show miraculous results in therapeutic and diagnostic trials.
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Affiliation(s)
- Gursharanpreet Kaur
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - Bhawna Khanna
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - Mohammed Yusuf
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - Akanksha Sharma
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India; Department of Biophysics, Panjab University, Chandigarh, 160014, India
| | - Akhil Khajuria
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - Hema K Alajangi
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India; Department of Biophysics, Panjab University, Chandigarh, 160014, India
| | - Pradeep K Jaiswal
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, TX 77843, USA
| | - Mandip Sachdeva
- College of Pharmacy and Pharmaceutical Science, Florida A & M University, Tallahassee, FL, USA
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9
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Shen J, Wang Q, Mao Y, Gao W, Duan S. Targeting the p53 signaling pathway in cancers: Molecular mechanisms and clinical studies. MedComm (Beijing) 2023; 4:e288. [PMID: 37256211 PMCID: PMC10225743 DOI: 10.1002/mco2.288] [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: 10/18/2022] [Revised: 04/25/2023] [Accepted: 05/08/2023] [Indexed: 06/01/2023] Open
Abstract
Tumor suppressor p53 can transcriptionally activate downstream genes in response to stress, and then regulate the cell cycle, DNA repair, metabolism, angiogenesis, apoptosis, and other biological responses. p53 has seven functional domains and 12 splice isoforms, and different domains and subtypes play different roles. The activation and inactivation of p53 are finely regulated and are associated with phosphorylation/acetylation modification and ubiquitination modification, respectively. Abnormal activation of p53 is closely related to the occurrence and development of cancer. While targeted therapy of the p53 signaling pathway is still in its early stages and only a few drugs or treatments have entered clinical trials, the development of new drugs and ongoing clinical trials are expected to lead to the widespread use of p53 signaling-targeted therapy in cancer treatment in the future. TRIAP1 is a novel p53 downstream inhibitor of apoptosis. TRIAP1 is the homolog of yeast mitochondrial intermembrane protein MDM35, which can play a tumor-promoting role by blocking the mitochondria-dependent apoptosis pathway. This work provides a systematic overview of recent basic research and clinical progress in the p53 signaling pathway and proposes that TRIAP1 is an important therapeutic target downstream of p53 signaling.
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Affiliation(s)
- Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang ProvinceSchool of MedicineHangzhou City UniversityHangzhouZhejiangChina
| | - Qurui Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang ProvinceSchool of MedicineHangzhou City UniversityHangzhouZhejiangChina
| | - Yunan Mao
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang ProvinceSchool of MedicineHangzhou City UniversityHangzhouZhejiangChina
| | - Wei Gao
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang ProvinceSchool of MedicineHangzhou City UniversityHangzhouZhejiangChina
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang ProvinceSchool of MedicineHangzhou City UniversityHangzhouZhejiangChina
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10
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Miller JJ, Kwan K, Blanchet A, Orvain C, Mellitzer G, Smith J, Lento C, Nouchikian L, Omoregbee-Leichnitz S, Sabatou M, Wilson D, Gaiddon C, Storr T. Multifunctional metallochaperone modifications for targeting subsite cavities in mutant p53-Y220C. J Inorg Biochem 2023; 242:112164. [PMID: 36871418 DOI: 10.1016/j.jinorgbio.2023.112164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 02/23/2023]
Abstract
The p53 protein, known as the 'guardian of the genome', plays an important role in cancer prevention. Unfortunately, p53 mutations result in compromised activity with over 50% of cancers resulting from point mutations to p53. There is considerable interest in mutant p53 reactivation, with the development of small-molecule reactivators showing promise. We have focused our efforts on the common p53 mutation Y220C, which causes protein unfolding, aggregation, and can result in the loss of a structural Zn from the DNA-binding domain. In addition, the Y220C mutant creates a surface pocket that can be stabilized using small molecules. We previously reported the bifunctional ligand L5 as a Zn metallochaperone and reactivator of the p53-Y220C mutant. Herein we report two new ligands L5-P and L5-O that are designed to act as Zn metallochaperones and non-covalent binders in the Y220C mutant pocket. For L5-P the distance between the Zn-binding di-(2-picolyl)amine function and the pocket-binding diiodophenol was extended in comparison to L5, while for L5-O we extended the pocket-binding moiety via attachment of an alkyne function. While both new ligands displayed similar Zn-binding affinity to L5, neither acted as efficient Zn-metallochaperones. However, the new ligands exhibited significant cytotoxicity in the NCI-60 cell line screen as well as in the NUGC3 Y220C mutant cell line. We identified that the primary mode of cytotoxicity is likely reactive oxygen species (ROS) generation for L5-P and L5-O, in comparison to mutant p53 reactivation for L5, demonstrating that subtle changes to the ligand scaffold can change the toxicity pathway.
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Affiliation(s)
- Jessica J Miller
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, Canada
| | - Kalvin Kwan
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, Canada
| | - Anaïs Blanchet
- Laboratory Streinth, Université de Strasbourg; Inserm, UMR_S 1113 IRFAC, 67200 Strasbourg, France
| | - Christophe Orvain
- Laboratory Streinth, Université de Strasbourg; Inserm, UMR_S 1113 IRFAC, 67200 Strasbourg, France
| | - Georg Mellitzer
- Laboratory Streinth, Université de Strasbourg; Inserm, UMR_S 1113 IRFAC, 67200 Strasbourg, France
| | - Jason Smith
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, Canada
| | - Cristina Lento
- York University, Chemistry Department, 6 Thompson Road, Toronto, Ontario, M3J 1L3, Canada
| | - Lucienne Nouchikian
- York University, Chemistry Department, 6 Thompson Road, Toronto, Ontario, M3J 1L3, Canada
| | | | - Marie Sabatou
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, Canada
| | - Derek Wilson
- York University, Chemistry Department, 6 Thompson Road, Toronto, Ontario, M3J 1L3, Canada
| | - Christian Gaiddon
- Laboratory Streinth, Université de Strasbourg; Inserm, UMR_S 1113 IRFAC, 67200 Strasbourg, France.
| | - Tim Storr
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, Canada.
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11
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Papaleo E, Tiberti M, Arnaudi M, Pecorari C, Faienza F, Cantwell L, Degn K, Pacello F, Battistoni A, Lambrughi M, Filomeni G. TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins. Cell Death Dis 2023; 14:284. [PMID: 37085483 PMCID: PMC10121659 DOI: 10.1038/s41419-023-05780-6] [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: 12/11/2022] [Revised: 03/13/2023] [Accepted: 03/27/2023] [Indexed: 04/23/2023]
Abstract
S-nitrosylation is a post-translational modification in which nitric oxide (NO) binds to the thiol group of cysteine, generating an S-nitrosothiol (SNO) adduct. S-nitrosylation has different physiological roles, and its alteration has also been linked to a growing list of pathologies, including cancer. SNO can affect the function and stability of different proteins, such as the mitochondrial chaperone TRAP1. Interestingly, the SNO site (C501) of TRAP1 is in the proximity of another cysteine (C527). This feature suggests that the S-nitrosylated C501 could engage in a disulfide bridge with C527 in TRAP1, resembling the well-known ability of S-nitrosylated cysteines to resolve in disulfide bridge with vicinal cysteines. We used enhanced sampling simulations and in-vitro biochemical assays to address the structural mechanisms induced by TRAP1 S-nitrosylation. We showed that the SNO site induces conformational changes in the proximal cysteine and favors conformations suitable for disulfide bridge formation. We explored 4172 known S-nitrosylated proteins using high-throughput structural analyses. Furthermore, we used a coarse-grained model for 44 protein targets to account for protein flexibility. This resulted in the identification of up to 1248 proximal cysteines, which could sense the redox state of the SNO site, opening new perspectives on the biological effects of redox switches. In addition, we devised two bioinformatic workflows ( https://github.com/ELELAB/SNO_investigation_pipelines ) to identify proximal or vicinal cysteines for a SNO site with accompanying structural annotations. Finally, we analyzed mutations in tumor suppressors or oncogenes in connection with the conformational switch induced by S-nitrosylation. We classified the variants as neutral, stabilizing, or destabilizing for the propensity to be S-nitrosylated and undergo the population-shift mechanism. The methods applied here provide a comprehensive toolkit for future high-throughput studies of new protein candidates, variant classification, and a rich data source for the research community in the NO field.
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Affiliation(s)
- Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark.
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark.
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Matteo Arnaudi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Chiara Pecorari
- Redox Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Fiorella Faienza
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Lisa Cantwell
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Degn
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Francesca Pacello
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Andrea Battistoni
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Giuseppe Filomeni
- Redox Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
- Center for Healthy Aging, Copenhagen University, 2200, Copenhagen, Denmark
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12
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Ghaderi A, Okhovat MA, Lehto J, De Petris L, Manouchehri Doulabi E, Kokhaei P, Zhong W, Rassidakis GZ, Drakos E, Moshfegh A, Schultz J, Olin T, Österborg A, Mellstedt H, Hojjat-Farsangi M. A Small Molecule Targeting the Intracellular Tyrosine Kinase Domain of ROR1 (KAN0441571C) Induced Significant Apoptosis of Non-Small Cell Lung Cancer (NSCLC) Cells. Pharmaceutics 2023; 15:pharmaceutics15041148. [PMID: 37111634 PMCID: PMC10145660 DOI: 10.3390/pharmaceutics15041148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/09/2023] Open
Abstract
The ROR1 receptor tyrosine kinase is expressed in embryonic tissues but is absent in normal adult tissues. ROR1 is of importance in oncogenesis and is overexpressed in several cancers, such as NSCLC. In this study, we evaluated ROR1 expression in NSCLC patients (N = 287) and the cytotoxic effects of a small molecule ROR1 inhibitor (KAN0441571C) in NSCLC cell lines. ROR1 expression in tumor cells was more frequent in non-squamous (87%) than in squamous (57%) carcinomas patients, while 21% of neuroendocrine tumors expressed ROR1 (p = 0.0001). A significantly higher proportion of p53 negative patients in the ROR1+ group than in the p53 positive non-squamous NSCLC patients (p = 0.03) was noted. KAN0441571C dephosphorylated ROR1 and induced apoptosis (Annexin V/PI) in a time- and dose-dependent manner in five ROR1+ NSCLC cell lines and was superior compared to erlotinib (EGFR inhibitor). Apoptosis was confirmed by the downregulation of MCL-1 and BCL-2, as well as PARP and caspase 3 cleavage. The non-canonical Wnt pathway was involved. The combination of KAN0441571C and erlotinib showed a synergistic apoptotic effect. KAN0441571C also inhibited proliferative (cell cycle analyses, colony formation assay) and migratory (scratch wound healing assay) functions. Targeting NSCLC cells by a combination of ROR1 and EGFR inhibitors may represent a novel promising approach for the treatment of NSCLC patients.
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Affiliation(s)
- Amineh Ghaderi
- Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Mohammad-Ali Okhovat
- Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Jemina Lehto
- Kancera AB, Nanna Svartz Väg 4, 171 65 Solna, Sweden
| | - Luigi De Petris
- Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna, Karolinska Institutet, 171 64 Stockholm, Sweden
- Thoracic Oncology Center, Karolinska Comprehensive Cancer Center, 171 76 Solna, Sweden
| | - Ehsan Manouchehri Doulabi
- Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Parviz Kokhaei
- Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna, Karolinska Institutet, 171 64 Stockholm, Sweden
- Department of Immunology, Arak University of Medical Sciences, Arak 3848170001, Iran
| | - Wen Zhong
- Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Georgios Z. Rassidakis
- Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Elias Drakos
- Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna, Karolinska Institutet, 171 64 Stockholm, Sweden
- Department of Pathology, Medical School, University of Crete, 700 13 Heraklion, Greece
| | - Ali Moshfegh
- Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna, Karolinska Institutet, 171 64 Stockholm, Sweden
- Kancera AB, Nanna Svartz Väg 4, 171 65 Solna, Sweden
| | - Johan Schultz
- Kancera AB, Nanna Svartz Väg 4, 171 65 Solna, Sweden
| | - Thomas Olin
- Kancera AB, Nanna Svartz Väg 4, 171 65 Solna, Sweden
| | - Anders Österborg
- Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna, Karolinska Institutet, 171 64 Stockholm, Sweden
- Department of Hematology, Karolinska University Hospital Solna, 171 64 Solna, Sweden
| | - Håkan Mellstedt
- Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Mohammad Hojjat-Farsangi
- Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna, Karolinska Institutet, 171 64 Stockholm, Sweden
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13
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Li C, Tang Y, Li Q, Liu H, Ma X, He L, Shi H. The prognostic and immune significance of C15orf48 in pan-cancer and its relationship with proliferation and apoptosis of thyroid carcinoma. Front Immunol 2023; 14:1131870. [PMID: 36969231 PMCID: PMC10033576 DOI: 10.3389/fimmu.2023.1131870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023] Open
Abstract
BackgroundC15orf48 was recently identified as an inflammatory response-related gene; however there is limited information on its function in tumors. In this study, we aimed to elucidate the function and potential mechanism of action of C15orf48 in cancer.MethodsWe evaluated the pan-cancer expression, methylation, and mutation data of C15orf48 to analyze its clinical prognostic value. In addition, we explored the pan-cancer immunological characteristics of C15orf48, especially in thyroid cancer (THCA), by correlation analysis. Additionally, we conducted a THCA subtype analysis of C15orf48 to determine its subtype-specific expression and immunological characteristics. Lastly, we evaluated the effects of C15orf48 knockdown on the THCA cell line, BHT101, by in vitro experimentation.ResultsThe results of our study revealed that C15orf48 is differentially expressed in different cancer types and that it can serve as an independent prognostic factor for glioma. Additionally, we found that the epigenetic alterations of C15orf48 are highly heterogeneous in several cancers and that its aberrant methylation and copy number variation are associated with poor prognosis in multiple cancers. Immunoassays elucidated that C15orf48 was significantly associated with macrophage immune infiltration and multiple immune checkpoints in THCA, and was a potential biomarker for PTC. In addition, cell experiments showed that the knockdown of C15orf48 could reduce the proliferation, migration, and apoptosis abilities of THCA cells.ConclusionsThe results of this study indicate that C15orf48 is a potential tumor prognostic biomarker and immunotherapy target, and plays an essential role in the proliferation, migration, and apoptosis of THCA cells.
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Affiliation(s)
- Chaolin Li
- Department of Obstetrics, Jinniu District Maternal and Child Health Hospital, Chengdu, China
| | - Yan Tang
- Department of Medical Laboratory, Jinniu District Maternal and Child Health Hospital, Chengdu, China
| | - Qin Li
- Department of Obstetrics, Jinniu District Maternal and Child Health Hospital, Chengdu, China
| | - Haiyan Liu
- Department of Obstetrics, Jinniu District Maternal and Child Health Hospital, Chengdu, China
| | - Xiaoying Ma
- Department of Obstetrics, Jinniu District Maternal and Child Health Hospital, Chengdu, China
| | - Liu He
- Department of Pediatrics, Jinniu District Maternal and Child Health Hospital, Chengdu, China
| | - Hao Shi
- Department of Pediatrics, Jinniu District Maternal and Child Health Hospital, Chengdu, China
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