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Bronte J, Zhou C, Vempati A, Tam C, Khong J, Hazany S, Hazany S. A Comprehensive Review of Non-Surgical Treatments for Hypertrophic and Keloid Scars in Skin of Color. Clin Cosmet Investig Dermatol 2024; 17:1459-1469. [PMID: 38911337 PMCID: PMC11193462 DOI: 10.2147/ccid.s470997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/02/2024] [Indexed: 06/25/2024]
Abstract
Hypertrophic and keloid scars are fibroproliferative growths resulting from aberrant wound healing. Individuals with Fitzpatrick skin types (FSTs) IV-VI are particularly predisposed to hypertrophic and keloid scarring, yet specific guidelines for these populations are still lacking within the literature. Therefore, this comprehensive review provides a list of various treatments and considerations for hypertrophic and keloid scarring in patients with skin of color. We constructed a comprehensive PubMed search term and performed quadruple-blinded screening on all resulting studies to achieve this objective. Our findings demonstrate 1) the lack of efficacious treatments for raised scars within this population and 2) the need to empirically investigate individualized and multimodal therapeutic options for those with skin of color.
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Affiliation(s)
- Joshua Bronte
- Department of Research, Scar Healing Institute, Los Angeles, CA, USA
| | - Crystal Zhou
- Department of Research, Scar Healing Institute, Los Angeles, CA, USA
| | - Abhinav Vempati
- Department of Research, Scar Healing Institute, Los Angeles, CA, USA
| | - Curtis Tam
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Khong
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sanam Hazany
- Department of Research, Scar Healing Institute, Los Angeles, CA, USA
| | - Salar Hazany
- Department of Research, Scar Healing Institute, Los Angeles, CA, USA
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Salamini-Montemurri M, Vizoso-Vázquez Á, Barreiro-Alonso A, Lorenzo-Catoira L, Rodríguez-Belmonte E, Cerdán ME, Lamas-Maceiras M. The Effect of HMGB1 and HMGB2 on Transcriptional Regulation Differs in Neuroendocrine and Adenocarcinoma Models of Prostate Cancer. Int J Mol Sci 2024; 25:3106. [PMID: 38542079 PMCID: PMC10969884 DOI: 10.3390/ijms25063106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/25/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Human high-mobility group-B (HMGB) proteins regulate gene expression in prostate cancer (PCa), a leading cause of oncological death in men. Their role in aggressive PCa cancers, which do not respond to hormonal treatment, was analyzed. The effects of HMGB1 and HMGB2 silencing upon the expression of genes previously related to PCa were studied in the PCa cell line PC-3 (selected as a small cell neuroendocrine carcinoma, SCNC, PCa model not responding to hormonal treatment). A total of 72% of genes analyzed, using pre-designed primer panels, were affected. HMGB1 behaved mostly as a repressor, but HMGB2 as an activator. Changes in SERPINE1, CDK1, ZWINT, and FN1 expression were validated using qRT-PCR after HMGB1 silencing or overexpression in PC-3 and LNCaP (selected as an adenocarcinoma model of PCa responding to hormonal treatment) cell lines. Similarly, the regulatory role of HMGB2 upon SERPINE1, ZWINT, FN1, IGFPB3, and TYMS expression was validated, finding differences between cell lines. The correlation between the expression of HMGB1, HMGB2, and their targets was analyzed in PCa patient samples and also in PCa subgroups, classified as neuroendocrine positive or negative, in public databases. These results allow a better understanding of the role of HMGB proteins in PCa and contribute to find specific biomarkers for aggressive PCa.
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Affiliation(s)
- Martín Salamini-Montemurri
- Centro Interdisciplinar de Química e Bioloxía (CICA), Campus de Elviña, Universidade da Coruña, As Carballeiras, s/n, 15071 A Coruña, Spain; (M.S.-M.); (Á.V.-V.); (A.B.-A.); (L.L.-C.); (E.R.-B.)
- Facultade de Ciencias, Campus de A Zapateira, Universidade da Coruña, A Fraga, s/n, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Ángel Vizoso-Vázquez
- Centro Interdisciplinar de Química e Bioloxía (CICA), Campus de Elviña, Universidade da Coruña, As Carballeiras, s/n, 15071 A Coruña, Spain; (M.S.-M.); (Á.V.-V.); (A.B.-A.); (L.L.-C.); (E.R.-B.)
- Facultade de Ciencias, Campus de A Zapateira, Universidade da Coruña, A Fraga, s/n, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Aida Barreiro-Alonso
- Centro Interdisciplinar de Química e Bioloxía (CICA), Campus de Elviña, Universidade da Coruña, As Carballeiras, s/n, 15071 A Coruña, Spain; (M.S.-M.); (Á.V.-V.); (A.B.-A.); (L.L.-C.); (E.R.-B.)
- Facultade de Ciencias, Campus de A Zapateira, Universidade da Coruña, A Fraga, s/n, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Lidia Lorenzo-Catoira
- Centro Interdisciplinar de Química e Bioloxía (CICA), Campus de Elviña, Universidade da Coruña, As Carballeiras, s/n, 15071 A Coruña, Spain; (M.S.-M.); (Á.V.-V.); (A.B.-A.); (L.L.-C.); (E.R.-B.)
- Facultade de Ciencias, Campus de A Zapateira, Universidade da Coruña, A Fraga, s/n, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Esther Rodríguez-Belmonte
- Centro Interdisciplinar de Química e Bioloxía (CICA), Campus de Elviña, Universidade da Coruña, As Carballeiras, s/n, 15071 A Coruña, Spain; (M.S.-M.); (Á.V.-V.); (A.B.-A.); (L.L.-C.); (E.R.-B.)
- Facultade de Ciencias, Campus de A Zapateira, Universidade da Coruña, A Fraga, s/n, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - María-Esperanza Cerdán
- Centro Interdisciplinar de Química e Bioloxía (CICA), Campus de Elviña, Universidade da Coruña, As Carballeiras, s/n, 15071 A Coruña, Spain; (M.S.-M.); (Á.V.-V.); (A.B.-A.); (L.L.-C.); (E.R.-B.)
- Facultade de Ciencias, Campus de A Zapateira, Universidade da Coruña, A Fraga, s/n, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Mónica Lamas-Maceiras
- Centro Interdisciplinar de Química e Bioloxía (CICA), Campus de Elviña, Universidade da Coruña, As Carballeiras, s/n, 15071 A Coruña, Spain; (M.S.-M.); (Á.V.-V.); (A.B.-A.); (L.L.-C.); (E.R.-B.)
- Facultade de Ciencias, Campus de A Zapateira, Universidade da Coruña, A Fraga, s/n, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
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Sen A, Karati D. An insight into thymidylate synthase inhibitor as anticancer agents: an explicative review. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03020-y. [PMID: 38446215 DOI: 10.1007/s00210-024-03020-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
Cancer, a widespread challenge to global health, remains a puzzle of intricate molecular dynamics. This review article delves into the mystery of cancer, with a keen focus on understanding the contributory role of thymidylate synthase (TS) in cancer. TS, a vital enzyme in DNA synthesis and repair, emerges as a significant player in the narrative of cancer development. The conversion of deoxyuridine monophosphate (dUMP) to deoxythymidine monophosphate (dTMP) is a major step in producing DNA. Numerous malignancies, including those of the breast, colon, lung, and ovary, have been linked to dysregulation of TS activity. Overexpression or mutations of TS lead to uncontrolled cell proliferation and tumorigenesis molecular interactions and signalling pathways involving TS come under scrutiny, revealing the nuanced connections that propel its involvement in cancer progression. Beyond overexpression and mutations, there emerges a subtle layer of regulation that involves microRNAs (miRNAs). These tiny particles attach to the TS messenger RNA, causing translational repression or its degradation, which in turn affects TS activity. Moving towards the therapeutic realm, thymidylate synthase inhibition acts as a promising anti-cancer strategy. Targeting TS with small-molecule inhibitors could provide a novel approach to treat various cancers. By reducing the number of available nucleotides, TS inhibition would slow down or halt cancer cell division, thus depriving the tumor of the building blocks required for its proliferation and growth. The aim is to assess the viability and effectiveness of targeting TS to halt or slow down cancer progression. There is growing evidence that, in comparison to traditional TS inhibitors, few novel antifolate TS inhibitors are effective against a wider variety of neoplasms, such as lung carcinomas. It has been discovered that TS inhibitors increase cancer tissues' sensitivity to chemotherapy and radiation, increasing their vulnerability to these treatments. This article aims to provide a comprehensive insight into TS, examining its cellular details, detailing the heterocyclic moieties and molecular foundations, and providing a promising future outlook.
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Affiliation(s)
- Aratrika Sen
- Department of Pharmaceutical Technology, School of Pharmacy, Techno India University, Kolkata, 700091, West Bengal, India
| | - Dipanjan Karati
- Department of Pharmaceutical Technology, School of Pharmacy, Techno India University, Kolkata, 700091, West Bengal, India.
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Liu Y, Zhu C, Liang Y, McMinn A, Zheng K, Wang Z, Wang H, Ren L, Shao H, Sung YY, Mok WJ, Wong LL, Wang M. Genome analysis of vB_SupP_AX, a novel N4-like phage infecting Sulfitobacter. Int Microbiol 2024:10.1007/s10123-023-00476-5. [PMID: 38190086 DOI: 10.1007/s10123-023-00476-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/09/2024]
Abstract
Sulfitobacter is a bacterium recognized for its production of AMP-independent sulfite oxidase, which is instrumental in the creation of sulfite biosensors. This capability underscores its ecological and economic relevance. In this study, we present a newly discovered phage, Sulfitobacter phage vB_SupP_AX, which was isolated from Maidao of Qingdao, China. The vB_SupP_AX genome is linear and double-stranded and measures 75,445 bp with a GC content of 49%. It encompasses four transfer RNA (tRNA) sequences and 79 open reading frames (ORFs), one of which is an auxiliary metabolic gene encoding thioredoxin. Consistent with other N4-like phages, vB_SupP_AX possesses three distinct RNA polymerases and is characterized by the presence of four tRNA molecules. Comparative genomic and phylogenetic analyses position vB_SupP_AX and three other viral genomes from the Integrated Microbial Genomes/Virus v4 database within the Rhodovirinae virus subfamily. The identification of vB_SupP_AX enhances our understanding of virus-host interactions within marine ecosystems.
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Affiliation(s)
- Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China.
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China.
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ziyue Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongmin Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Linyi Ren
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Nerus, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Nerus, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Nerus, Malaysia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China.
- Haide College, Ocean University of China, Qingdao, China.
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China.
- The Affiliated Hospital of Qingdao University, Qingdao, China.
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Yu JF, Xu JT, Feng A, Qi BL, Gu J, Deng JY, Zhang XE. Competition between H 4PteGlu and H 2PtePAS Confers para-Aminosalicylic Acid Resistance in Mycobacterium tuberculosis. Antibiotics (Basel) 2023; 13:13. [PMID: 38275323 PMCID: PMC10812664 DOI: 10.3390/antibiotics13010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024] Open
Abstract
Tuberculosis remains a serious challenge to human health worldwide. para-Aminosalicylic acid (PAS) is an important anti-tuberculosis drug, which requires sequential activation by Mycobacterium tuberculosis (M. tuberculosis) dihydropteroate synthase and dihydrofolate synthase (DHFS, FolC). Previous studies showed that loss of function mutations of a thymidylate synthase coding gene thyA caused PAS resistance in M. tuberculosis, but the mechanism is unclear. Here we showed that deleting thyA in M. tuberculosis resulted in increased content of tetrahydrofolate (H4PteGlu) in bacterial cells as they rely on the other thymidylate synthase ThyX to synthesize thymidylate, which produces H4PteGlu during the process. Subsequently, data of in vitro enzymatic activity experiments showed that H4PteGlu hinders PAS activation by competing with hydroxy dihydropteroate (H2PtePAS) for FolC catalysis. Meanwhile, over-expressing folC in ΔthyA strain and a PAS resistant clinical isolate with known thyA mutation partially restored PAS sensitivity, which relieved the competition between H4PteGlu and H2PtePAS. Thus, loss of function mutations in thyA led to increased H4PteGlu content in bacterial cells, which competed with H2PtePAS for catalysis by FolC and hence hindered the activation of PAS, leading to decreased production of hydroxyl dihydrofolate (H2PtePAS-Glu) and finally caused PAS resistance. On the other hand, functional deficiency of thyA in M. tuberculosis pushes the bacterium switch to an unidentified dihydrofolate reductase for H4PteGlu biosynthesis, which might also contribute to the PAS resistance phenotype. Our study revealed how thyA mutations confer PAS resistance in M. tuberculosis and provided new insights into studies on the folate metabolism of the bacterium.
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Affiliation(s)
- Ji-Fang Yu
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jin-Tian Xu
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ao Feng
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bao-Ling Qi
- Shanghai Metabolome Institute-Wuhan (SMI), Wuhan 430000, China
| | - Jing Gu
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jiao-Yu Deng
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Amrofell MB, Rengarajan S, Vo ST, Ramirez Tovar ES, LoBello L, Dantas G, Moon TS. Engineering E. coli strains using antibiotic-resistance-gene-free plasmids. CELL REPORTS METHODS 2023; 3:100669. [PMID: 38086386 PMCID: PMC10753387 DOI: 10.1016/j.crmeth.2023.100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/29/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
We created a generalizable pipeline for antibiotic-resistance-gene-free plasmid (ARGFP)-based cloning using a dual auxotrophic- and essential-gene-based selection strategy. We use auxotrophic selection to construct plasmids in engineered E. coli DH10B cloning strains and both auxotrophic- and essential-gene-based selection to (1) select for recombinant strains and (2) maintain a plasmid in E. coli Nissle 1917, a common chassis for engineered probiotic applications, and E. coli MG1655, the laboratory "wild-type" E. coli strain. We show that our approach has comparable efficiency to that of antibiotic-resistance-gene-based cloning. We also show that the double-knockout Nissle and MG1655 strains are simple to transform with plasmids of interest. Notably, we show that the engineered Nissle strains are amenable to long-term plasmid maintenance in repeated culturing as well as in the mouse gut, demonstrating the potential for broad applications while minimizing the risk of antibiotic resistance spread via horizontal gene transfer.
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Affiliation(s)
- Matthew B Amrofell
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Sunaina Rengarajan
- Department of Medicine, Division of Dermatology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven T Vo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Erick S Ramirez Tovar
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Larissa LoBello
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA.
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Bommisetti P, Bandarian V. Insights into the Mechanism of Installation of 5-Carboxymethylaminomethyl Uridine Hypermodification by tRNA-Modifying Enzymes MnmE and MnmG. J Am Chem Soc 2023; 145:26947-26961. [PMID: 38050996 PMCID: PMC10723064 DOI: 10.1021/jacs.3c10182] [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: 09/15/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023]
Abstract
The evolutionarily conserved bacterial proteins MnmE and MnmG (and their homologues in Eukarya) install a 5-carboxymethylaminomethyl (cmnm5) or a 5-taurinomethyl (τm5) group onto wobble uridines of several tRNA species. The Escherichia coli MnmE binds guanosine-5'-triphosphate (GTP) and methylenetetrahydrofolate (CH2THF), while MnmG binds flavin adenine dinucleotide (FAD) and a reduced nicotinamide adenine dinucleotide (NADH). Together with glycine, MnmEG catalyzes the installation of cmnm5 in a reaction that also requires hydrolysis of GTP. In this letter, we investigated key steps of the MnmEG reaction using a combination of biochemical techniques. We show multiple lines of evidence supporting flavin-iminium FADH[N5═CH2]+ as a central intermediate in the MnmEG reaction. Using a synthetic FADH[N5═CD2]+ analogue, the intermediacy of the FAD in the transfer of the methylene group from CH2THF to the C5 position of U34 was unambiguously demonstrated. Further, MnmEG reactions containing the deuterated flavin-iminium intermediate and alternate nucleophiles such as taurine and ammonia also led to the formation of the anticipated U34-modified tRNAs, showing FAD[N5═CH2]+ as the universal intermediate for all MnmEG homologues. Additionally, an RNA-protein complex stable to urea-denaturing polyacrylamide gel electrophoresis was identified. Studies involving a series of nuclease (RNase T1) and protease (trypsin) digestions along with reverse transcription experiments suggest that the complex may be noncovalent. While the conserved MnmG cysteine C47 and C277 mutant variants were shown to reduce FAD, they were unable to promote the modified tRNA formation. Overall, this study provides critical insights into the biochemical mechanism underlying tRNA modification by the MnmEG.
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Affiliation(s)
- Praneeth Bommisetti
- Department of Chemistry, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake
City, Utah 84112, United States
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8
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Nicastro GG, Burroughs AM, Iyer L, Aravind L. Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems. Nucleic Acids Res 2023; 51:11479-11503. [PMID: 37889040 PMCID: PMC10681802 DOI: 10.1093/nar/gkad879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
While nucleic acid-targeting effectors are known to be central to biological conflicts and anti-selfish element immunity, recent findings have revealed immune effectors that target their building blocks and the cellular energy currency-free nucleotides. Through comparative genomics and sequence-structure analysis, we identified several distinct effector domains, which we named Calcineurin-CE, HD-CE, and PRTase-CE. These domains, along with specific versions of the ParB and MazG domains, are widely present in diverse prokaryotic immune systems and are predicted to degrade nucleotides by targeting phosphate or glycosidic linkages. Our findings unveil multiple potential immune systems associated with at least 17 different functional themes featuring these effectors. Some of these systems sense modified DNA/nucleotides from phages or operate downstream of novel enzymes generating signaling nucleotides. We also uncovered a class of systems utilizing HSP90- and HSP70-related modules as analogs of STAND and GTPase domains that are coupled to these nucleotide-targeting- or proteolysis-induced complex-forming effectors. While widespread in bacteria, only a limited subset of nucleotide-targeting effectors was integrated into eukaryotic immune systems, suggesting barriers to interoperability across subcellular contexts. This work establishes nucleotide-degrading effectors as an emerging immune paradigm and traces their origins back to homologous domains in housekeeping systems.
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Affiliation(s)
- Gianlucca G Nicastro
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - A Maxwell Burroughs
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - Lakshminarayan M Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - L Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
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Benny S, Rajappan Krishnendu P, Kumar S, Bhaskar V, Manisha DS, Abdelgawad MA, Ghoneim MM, Naguib IA, Pappachen LK, Mary Zachariah S, Mathew B, Tp A. A computational investigation of thymidylate synthase inhibitors through a combined approach of 3D-QSAR and pharmacophore modelling. J Biomol Struct Dyn 2023:1-20. [PMID: 37870113 DOI: 10.1080/07391102.2023.2270752] [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: 05/04/2023] [Accepted: 08/03/2023] [Indexed: 10/24/2023]
Abstract
Thymidylate synthase (TS) is a crucial target of cancer drug discovery and is mainly involved in the De novo synthesis of the DNA precursor thymine. In the present study, to generate reliable models and identify a few promising molecules, we combined QSAR modelling with the pharmacophore hypothesis-generating technique. Input molecules were clustered on their similarity, and a cluster of 74 molecules with a pyrimidine moiety was chosen as the set for 3D-QSAR and pharmacophore modelling. Atom-based and field-based 3D-QSAR models were generated and statistically validated with R2 > 0.90 and Q2 > 0.75. The common pharmacophore hypothesis(CPH) generation identified the best six-point model ADHRRR. Using these best models, a library of FDA-approved drugs was screened for activity and filtered via molecular docking, ADME profiling, and molecular dynamics simulations. The top ten promising TS-inhibiting candidates were identified, and their chemical features profitable for TS inhibitors were explored.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonu Benny
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Prayaga Rajappan Krishnendu
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Sunil Kumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Vaishnav Bhaskar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Deepthi S Manisha
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Mohamed A Abdelgawad
- Department of pharmaceutical chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Mohammed M Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Saudi Arabia
| | - Ibrahim A Naguib
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Leena K Pappachen
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Subin Mary Zachariah
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Aneesh Tp
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
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10
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Ding Z, Wu Y, Fang G, Lin Z, Lin K, Fu J, Huang Q, Tang Y, You W, Liu J, Zeng Y. Development and validation a radiomics nomogram for predicting thymidylate synthase status in hepatocellular carcinoma based on Gd-DTPA contrast enhanced MRI. BMC Cancer 2023; 23:991. [PMID: 37848807 PMCID: PMC10580573 DOI: 10.1186/s12885-023-11096-7] [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: 07/05/2022] [Accepted: 06/21/2023] [Indexed: 10/19/2023] Open
Abstract
OBJECTIVES The purpose of this study was to develop and validate a radiomics nomogram for predicting thymidylate synthase (TYMS) status in hepatocellular carcinoma (HCC) by using Gd-DTPA contrast enhanced MRI. METHODS We retrospectively enrolled 147 consecutive patients with surgically confirmed HCC and randomly allocated to training and validation set (7:3). The TYMS status was immunohistochemical determined and classified into low TYMS (positive cells ≤ 25%) and high TYMS (positive cells > 25%) groups. Radiomics features were extracted from the arterial phases and portal venous phase of Gd-DTPA contrast enhanced MRI. Least absolute shrinkage and selection operator (LASSO) were applied for generating the Rad score. Clinical data and MRI findings were assessed to build a clinical model. Rad score combined with clinical features was used to construct radiomics nomogram. RESULTS A total of 2260 features were extracted and reduced to 7 features as the most important discriminators to build the Rad score. InAFP was identified as the only independent clinical factors for TYMS status. The radiomics nomogram showed good discrimination in training (AUC, 0.759; 95% CI 0.665-0.838) and validation set (AUC, 0.739; 95% CI 0.585-0.860), and showed better discrimination capability (P < 0.05) compared with clinical model in training (AUC, 0.656; 95% CI 0.555-0.746) and validation set (AUC, 0.622; 95% CI 0.463-0.764). CONCLUSIONS The radiomics nomogram shows favorable predictive efficacy for TYMS status in HCC, which might be helpful for the personalized treatment of HCC.
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Affiliation(s)
- Zongren Ding
- Department of Hepatopancreatobiliary Surgery, Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou, 350025 China
| | - Yijun Wu
- Department of Hepatopancreatobiliary Surgery, Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou, 350025 China
| | - Guoxu Fang
- Department of Hepatopancreatobiliary Surgery, Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou, 350025 China
| | - Zhaowang Lin
- Department of Radiology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025 China
| | - Kongying Lin
- Department of Hepatopancreatobiliary Surgery, Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou, 350025 China
| | - Jun Fu
- Department of Hepatopancreatobiliary Surgery, Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou, 350025 China
| | - Qizhen Huang
- Department of Radiotherapy, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025 China
| | - Yanyan Tang
- Department of Radiology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025 China
| | - Wuyi You
- Department of Radiology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025 China
| | - Jingfeng Liu
- Fujian Provincial Cancer Hospital, Fuzhou, 350025 China
| | - Yongyi Zeng
- Department of Hepatopancreatobiliary Surgery, Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou, 350025 China
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11
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Tembrock LR, Zink FA, Gilligan TM. Viral Prevalence and Genomic Xenology in the Coevolution of HzNV-2 (Nudiviridae) with Host Helicoverpa zea (Lepidoptera: Noctuidae). INSECTS 2023; 14:797. [PMID: 37887809 PMCID: PMC10607169 DOI: 10.3390/insects14100797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/16/2023] [Accepted: 09/24/2023] [Indexed: 10/28/2023]
Abstract
Insect viruses have been described from numerous lineages, yet patterns of genetic exchange and viral prevalence, which are essential to understanding host-virus coevolution, are rarely studied. In Helicoverpa zea, the virus HzNV-2 can cause deformity of male and female genitalia, resulting in sterility. Using ddPCR, we found that male H. zea with malformed genitalia (agonadal) contained high levels of HzNV-2 DNA, confirming previous work. HzNV-2 was found to be prevalent throughout the United States, at more than twice the rate of the baculovirus HaSNPV, and that it contained several host-acquired DNA sequences. HzNV-2 possesses four recently endogenized lepidopteran genes and several more distantly related genes, including one gene with a bacteria-like sequence found in both host and virus. Among the recently acquired genes is cytosolic serine hydroxymethyltransferase (cSHMT). In nearly all tested H. zea, cSHMT contained a 200 bp transposable element (TE) that was not found in cSHMT of the sister species H. armigera. No other virus has been found with host cSHMT, and the study of this shared copy, including possible interactions, may yield new insights into the function of this gene with possible applications to insect biological control, and gene editing.
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Affiliation(s)
- Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Frida A. Zink
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Todd M. Gilligan
- USDA-APHIS-PPQ-Science & Technology, Identification Technology Program, Fort Collins, CO 80526, USA
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12
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Abstract
Covering: from 2000 up to the very early part of 2023S-Adenosyl-L-methionine (SAM) is a naturally occurring trialkyl sulfonium molecule that is typically associated with biological methyltransfer reactions. However, SAM is also known to donate methylene, aminocarboxypropyl, adenosyl and amino moieties during natural product biosynthetic reactions. The reaction scope is further expanded as SAM itself can be modified prior to the group transfer such that a SAM-derived carboxymethyl or aminopropyl moiety can also be transferred. Moreover, the sulfonium cation in SAM has itself been found to be critical for several other enzymatic transformations. Thus, while many SAM-dependent enzymes are characterized by a methyltransferase fold, not all of them are necessarily methyltransferases. Furthermore, other SAM-dependent enzymes do not possess such a structural feature suggesting diversification along different evolutionary lineages. Despite the biological versatility of SAM, it nevertheless parallels the chemistry of sulfonium compounds used in organic synthesis. The question thus becomes how enzymes catalyze distinct transformations via subtle differences in their active sites. This review summarizes recent advances in the discovery of novel SAM utilizing enzymes that rely on Lewis acid/base chemistry as opposed to radical mechanisms of catalysis. The examples are categorized based on the presence of a methyltransferase fold and the role played by SAM within the context of known sulfonium chemistry.
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Affiliation(s)
- Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Daan Ren
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Byungsun Jeon
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
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13
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Quanrud GM, Lyu Z, Balamurugan SV, Canizal C, Wu HT, Genereux JC. Cellular Exposure to Chloroacetanilide Herbicides Induces Distinct Protein Destabilization Profiles. ACS Chem Biol 2023; 18:1661-1676. [PMID: 37427419 PMCID: PMC10367052 DOI: 10.1021/acschembio.3c00338] [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: 06/08/2023] [Accepted: 06/23/2023] [Indexed: 07/11/2023]
Abstract
Herbicides in the widely used chloroacetanilide class harbor a potent electrophilic moiety, which can damage proteins through nucleophilic substitution. In general, damaged proteins are subject to misfolding. Accumulation of misfolded proteins compromises cellular integrity by disrupting cellular proteostasis networks, which can further destabilize the cellular proteome. While direct conjugation targets can be discovered through affinity-based protein profiling, there are few approaches to probe how cellular exposure to toxicants impacts the stability of the proteome. We apply a quantitative proteomics methodology to identify chloroacetanilide-destabilized proteins in HEK293T cells based on their binding to the H31Q mutant of the human Hsp40 chaperone DNAJB8. We find that a brief cellular exposure to the chloroacetanilides acetochlor, alachlor, and propachlor induces misfolding of dozens of cellular proteins. These herbicides feature distinct but overlapping profiles of protein destabilization, highly concentrated in proteins with reactive cysteine residues. Consistent with the recent literature from the pharmacology field, reactivity is driven by neither inherent nucleophilic nor electrophilic reactivity but is idiosyncratic. We discover that propachlor induces a general increase in protein aggregation and selectively targets GAPDH and PARK7, leading to a decrease in their cellular activities. Hsp40 affinity profiling identifies a majority of propachlor targets identified by competitive activity-based protein profiling (ABPP), but ABPP can only identify about 10% of protein targets identified by Hsp40 affinity profiling. GAPDH is primarily modified by the direct conjugation of propachlor at a catalytic cysteine residue, leading to global destabilization of the protein. The Hsp40 affinity strategy is an effective technique to profile cellular proteins that are destabilized by cellular toxin exposure. Raw proteomics data is available through the PRIDE Archive at PXD030635.
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Affiliation(s)
- Guy M. Quanrud
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ziqi Lyu
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Sunil V. Balamurugan
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Carolina Canizal
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Hoi-Ting Wu
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Joseph C. Genereux
- Department of Chemistry, University of California, Riverside, California 92521, United States
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14
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Zwart NRK, Franken MD, Tissing WJE, Lubberman FJE, McKay JA, Kampman E, Kok DE. Folate, folic acid, and chemotherapy-induced toxicities: a systematic literature review. Crit Rev Oncol Hematol 2023:104061. [PMID: 37353179 DOI: 10.1016/j.critrevonc.2023.104061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023] Open
Abstract
Folate metabolism is a target for various chemotherapeutic drugs. Folate and its synthetic variant folic acid are B-vitamins. To what extent these vitamins impact treatment tolerance in patients with cancer remains unclear. A systematic literature review was conducted on intake and status of folate and folic acid in relation to chemotherapy-induced toxicities in children and adults with cancer. A total of 6,231 publications were identified, of which 40 publications met the inclusion criteria. In 12 out of 22 studies focusing on antifolates, a deficient folate status and lower folate and folic acid intake were associated with a higher risk of toxicities. In 8 out of 14 studies focusing on fluoropyrimidine treatments, a higher folate status and intake were associated with a higher risk of toxicities. These findings might explain interindividual differences in treatment tolerance and highlight the importance of evaluating nutritional status in oncology care.
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Affiliation(s)
- Nienke R K Zwart
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | - Mira D Franken
- Department of Medical Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Wim J E Tissing
- Prinses Máxima Centre for Pediatric Oncology, Utrecht, the Netherlands
| | - Floor J E Lubberman
- Department of Clinical Pharmacy, Hospital Gelderse Vallei, Ede, the Netherlands
| | - Jill A McKay
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Ellen Kampman
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | - Dieuwertje E Kok
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands.
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15
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Liu H, Liu H, Zhou Z, Chung J, Zhang G, Chang J, Parise RA, Chu E, Schmitz JC. Scutellaria baicalensis enhances 5-fluorouracil-based chemotherapy via inhibition of proliferative signaling pathways. Cell Commun Signal 2023; 21:147. [PMID: 37337282 DOI: 10.1186/s12964-023-01156-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/29/2023] [Indexed: 06/21/2023] Open
Abstract
Fluoropyridine-based chemotherapy remains the most widely used treatment for colorectal cancer (CRC). In this study, we investigated the mechanism by which the natural product Scutellaria baicalensis (Huang Qin; HQ) and one of its main components baicalin enhanced 5-fluorouracil (5-FU) antitumor activity against CRC. Cell proliferation assays, cell cycle analysis, reverse-phase protein array (RPPA) analysis, immunoblot analysis, and qRT-PCR were performed to investigate the mechanism(s) of action of HQ and its active components on growth of CRC cells. HQ exhibited in vitro antiproliferative activity against drug resistant human CRC cells, against human and mouse CRC cells with different genetic backgrounds and normal human colon epithelial cells. In vivo animal models were used to document the antitumor activity of HQ and baicalin. The mechanism of growth inhibitory activity of HQ is due to inhibition of proliferative signaling pathways including the CDK-RB pathway. In addition, HQ enhanced the antitumor effects of 5-FU and capecitabine in vivo. Furthermore, we identified baicalin as an active component of HQ. The combination of baicalin and 5-FU demonstrated synergistic activity against 5-FU-resistant RKO-R10 cells. The combination significantly inhibited in vivo tumor growth greater than each treatment alone. RPPA results showed that the signaling pathway alterations in CRC cells were similar following HQ and baicalin treatment. Together, these results indicate that HQ and its component baicalin enhance the effect of 5-fluorouracil-based chemotherapy via inhibition of CDK-RB pathway. These findings may provide the rational basis for developing agents that can overcome the development of cellular drug resistance. Video Abstract.
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Affiliation(s)
- Haizhou Liu
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Ave, Pittsburgh, PA, 15213, USA
| | - Hui Liu
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Ave, Pittsburgh, PA, 15213, USA
- Department of Oncology, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhiyi Zhou
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Ave, Pittsburgh, PA, 15213, USA
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jessica Chung
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Obstetrics and Gynecology, Abington-Jefferson Health, Abington, PA, USA
| | - Guojing Zhang
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Ave, Pittsburgh, PA, 15213, USA
| | - Jin Chang
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Ave, Pittsburgh, PA, 15213, USA
- Department of Radiotherapy, Second Affiliated Hospital, Shandong First Medical University, Tai'an City, China
| | - Robert A Parise
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Ave, Pittsburgh, PA, 15213, USA
| | - Edward Chu
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Ave, Pittsburgh, PA, 15213, USA
- Albert Einstein Cancer Center, Cancer Therapeutics Program, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John C Schmitz
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Ave, Pittsburgh, PA, 15213, USA.
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16
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Dasari M, Pelly SC, Geng J, Gold HB, Pribut N, Sharma SK, D’Erasmo MP, Bartsch PW, Sun C, Toti K, Arnold RS, Petros JA, Xu L, Jiang Y, Miller EJ, Liotta DC. Discovery of 5'-Substituted 5-Fluoro-2'-deoxyuridine Monophosphate Analogs: A Novel Class of Thymidylate Synthase Inhibitors. ACS Pharmacol Transl Sci 2023; 6:702-709. [PMID: 37200809 PMCID: PMC10186355 DOI: 10.1021/acsptsci.2c00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Indexed: 02/25/2023]
Abstract
5-Fluorouracil and 5-fluorouracil-based prodrugs have been used clinically for decades to treat cancer. Their anticancer effects are most prominently ascribed to inhibition of thymidylate synthase (TS) by metabolite 5-fluoro-2'-deoxyuridine 5'-monophosphate (FdUMP). However, 5-fluorouracil and FdUMP are subject to numerous unfavorable metabolic events that can drive undesired systemic toxicity. Our previous research on antiviral nucleotides suggested that substitution at the nucleoside 5'-carbon imposes conformational restrictions on the corresponding nucleoside monophosphates, rendering them poor substrates for productive intracellular conversion to viral polymerase-inhibiting triphosphate metabolites. Accordingly, we hypothesized that 5'-substituted analogs of FdUMP, which is uniquely active at the monophosphate stage, would inhibit TS while preventing undesirable metabolism. Free energy perturbation-derived relative binding energy calculations suggested that 5'(R)-CH3 and 5'(S)-CF3 FdUMP analogs would maintain TS potency. Herein, we report our computational design strategy, synthesis of 5'-substituted FdUMP analogs, and pharmacological assessment of TS inhibitory activity.
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Affiliation(s)
- Madhuri Dasari
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Stephen C. Pelly
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Jiafeng Geng
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Hannah B. Gold
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Nicole Pribut
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Savita K. Sharma
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Michael P. D’Erasmo
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Perry W. Bartsch
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Carrie Sun
- Department
of Urology, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Kiran Toti
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Rebecca S. Arnold
- Department
of Urology, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Winship
Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| | - John A. Petros
- Department
of Urology, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Winship
Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| | - Lingjie Xu
- Junrui
Biotechnology, Hangzhou, Zhejiang 310000, China
| | - Yi Jiang
- Junrui
Biotechnology, Hangzhou, Zhejiang 310000, China
| | - Eric J. Miller
- Winship
Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
- Department
of Pharmacology and Chemical Biology, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
| | - Dennis C. Liotta
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
- Winship
Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
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17
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Krishnan K, Katneni VK, Prabhudas SK, Kaikkolante N, Jangam AK, Katneni UK, Hauton C, Peruzza L, Mudagandur SS, Koyadan VK, Poochirian JK, Jena J. MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus. Virol J 2023; 20:72. [PMID: 37072853 PMCID: PMC10111743 DOI: 10.1186/s12985-023-02035-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/09/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND The genome of the largest known animal virus, the white spot syndrome virus (WSSV) responsible for huge economic losses and loss of employment in aquaculture, suffers from inconsistent annotation nomenclature. Novel genome sequence, circular genome and variable genome length led to nomenclature inconsistencies. Since vast knowledge has already accumulated in the past two decades with inconsistent nomenclature, the insights gained on a genome could not be easily extendable to other genomes. Therefore, the present study aims to perform comparative genomics studies in WSSV on uniform nomenclature. METHODS We have combined the standard mummer tool with custom scripts to develop missing regions finder (MRF) that documents the missing genome regions and coding sequences in virus genomes in comparison to a reference genome and in its annotation nomenclature. The procedure was implemented as web tool and in command-line interface. Using MRF, we have documented the missing coding sequences in WSSV and explored their role in virulence through application of phylogenomics, machine learning models and homologous genes. RESULTS We have tabulated and depicted the missing genome regions, missing coding sequences and deletion hotspots in WSSV on a common annotation nomenclature and attempted to link them to virus virulence. It was observed that the ubiquitination, transcription regulation and nucleotide metabolism might be essentially required for WSSV pathogenesis; and the structural proteins, VP19, VP26 and VP28 are essential for virus assembly. Few minor structural proteins in WSSV would act as envelope glycoproteins. We have also demonstrated the advantage of MRF in providing detailed graphic/tabular output in less time and also in handling of low-complexity, repeat-rich and highly similar regions of the genomes using other virus cases. CONCLUSIONS Pathogenic virus research benefits from tools that could directly indicate the missing genomic regions and coding sequences between isolates/strains. In virus research, the analyses performed in this study provides an advancement to find the differences between genomes and to quickly identify the important coding sequences/genomes that require early attention from researchers. To conclude, the approach implemented in MRF complements similarity-based tools in comparative genomics involving large, highly-similar, length-varying and/or inconsistently annotated viral genomes.
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Affiliation(s)
- Karthic Krishnan
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Vinaya Kumar Katneni
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India.
| | - Sudheesh K Prabhudas
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Nimisha Kaikkolante
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Ashok Kumar Jangam
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Upendra Kumar Katneni
- The Center for Blood Oxygen Transport and Hemostasis, Department of Pediatrics, University of Maryland School of Medicine, Maryland, USA
| | - Chris Hauton
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton Waterfront Campus, Southampton, UK
| | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padua, Italy
| | - Shashi Shekhar Mudagandur
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Vijayan K Koyadan
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Jithendran Karingalakkandy Poochirian
- Aquatic Animal Health and Environment Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
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18
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Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya. Nat Commun 2023; 14:838. [PMID: 36792581 PMCID: PMC9931769 DOI: 10.1038/s41467-023-36487-z] [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: 06/21/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.
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19
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Mafi A, Rezaee M, Hedayati N, Hogan SD, Reiter RJ, Aarabi MH, Asemi Z. Melatonin and 5-fluorouracil combination chemotherapy: opportunities and efficacy in cancer therapy. Cell Commun Signal 2023; 21:33. [PMID: 36759799 PMCID: PMC9912526 DOI: 10.1186/s12964-023-01047-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/14/2023] [Indexed: 02/11/2023] Open
Abstract
Combined chemotherapy is a treatment method based on the simultaneous use of two or more therapeutic agents; it is frequently necessary to produce a more effective treatment for cancer patients. Such combined treatments often improve the outcomes over that of the monotherapy approach, as the drugs synergistically target critical cell signaling pathways or work independently at different oncostatic sites. A better prognosis has been reported in patients treated with combination therapy than in patients treated with single drug chemotherapy. In recent decades, 5-fluorouracil (5-FU) has become one of the most widely used chemotherapy agents in cancer treatment. This medication, which is soluble in water, is used as the first line of anti-neoplastic agent in the treatment of several cancer types including breast, head and neck, stomach and colon cancer. Within the last three decades, many studies have investigated melatonin as an anti-cancer agent; this molecule exhibits various functions in controlling the behavior of cancer cells, such as inhibiting cell growth, inducing apoptosis, and inhibiting invasion. The aim of this review is to comprehensively evaluate the role of melatonin as a complementary agent with 5-FU-based chemotherapy for cancers. Additionally, we identify the potential common signaling pathways by which melatonin and 5-FU interact to enhance the efficacy of the combined therapy. Video abstract.
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Affiliation(s)
- Alireza Mafi
- grid.411036.10000 0001 1498 685XDepartment of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Malihe Rezaee
- grid.411600.2School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran ,grid.411705.60000 0001 0166 0922Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Islamic Republic of Iran
| | - Neda Hedayati
- grid.411746.10000 0004 4911 7066School of Medicine, Iran University of Medical Science, Tehran, Islamic Republic of Iran
| | - Sara Diana Hogan
- grid.8993.b0000 0004 1936 9457Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Russel J. Reiter
- grid.43582.380000 0000 9852 649XDepartment of Cell Systems and Anatomy, UT Health. Long School of Medicine, San Antonio, TX USA
| | - Mohammad-Hossein Aarabi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran.
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
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20
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Finger V, Kufa M, Soukup O, Castagnolo D, Roh J, Korabecny J. Pyrimidine derivatives with antitubercular activity. Eur J Med Chem 2023; 246:114946. [PMID: 36459759 DOI: 10.1016/j.ejmech.2022.114946] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022]
Abstract
Small molecules with antitubercular activity containing the pyrimidine motif in their structure have gained more attention after three drugs, namely GSK 2556286 (GSK-286), TBA-7371 and SPR720, have entered clinical trials. This review provides an overview of recent advances in the hit-to-lead drug discovery studies of antitubercular pyrimidine-containing compounds with the aim to highlight their structural diversity. In the first part, the review discusses the pyrimidine compounds according to their targets, pinpointing the structure-activity relationships of each pyrimidine family. The second part of this review is concentrated on antitubercular pyrimidine derivatives with a yet unexplored or speculative target, dividing the compounds according to their structural types.
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Affiliation(s)
- Vladimir Finger
- Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic; Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec, Kralove, Czech Republic
| | - Martin Kufa
- Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic; Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec, Kralove, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec, Kralove, Czech Republic
| | - Daniele Castagnolo
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, London, United Kingdom
| | - Jaroslav Roh
- Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic.
| | - Jan Korabecny
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec, Kralove, Czech Republic.
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21
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Mteremko D, Chilongola J, Paluch AS, Chacha M. Targeting human thymidylate synthase: Ensemble-based virtual screening for drug repositioning and the role of water. J Mol Graph Model 2023; 118:108348. [PMID: 36257147 DOI: 10.1016/j.jmgm.2022.108348] [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: 06/07/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/29/2022]
Abstract
A drug repositioning computational approach was carried to search inhibitors for human thymidylate synthase. An ensemble-based virtual screening of FDA-approved drugs showed the drugs Imatinib, Lumacaftor and Naldemedine to be likely candidates for repurposing. The role of water in the drug-receptor interactions was revealed by the application of an extended AutoDock scoring function that included the water forcefield. The binding affinity scores when hydrated ligands were docked were improved in the drugs considered. Further binding free energy calculations based on the Molecular Mechanics Poisson-Boltzmann Surface Area method revealed that Imatinib, Lumacaftor and Naldemedine scored -130.7 ± 28.1, -210.6 ± 29.9 and -238.0 ± 25.4 kJ/mol, respectively, showing good binding affinity for the candidates considered. Overall, the analysis of the molecular dynamics trajectory of the receptor-drug complexes revealed stable structures for Imatinib, Lumacaftor and Naldemedine, for the entire simulation time.
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Affiliation(s)
- Denis Mteremko
- The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
| | - Jaffu Chilongola
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Andrew S Paluch
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA
| | - Musa Chacha
- The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania; Arusha Technical College, Arusha, Tanzania
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22
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Walsh CT. Covalent Catalytic Strategies for Enzymes That Modify RNA Molecules on their Tripartite Building Blocks. ACS Chem Biol 2022; 17:2686-2703. [PMID: 36103129 DOI: 10.1021/acschembio.2c00584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The tripartite structures of the four 5'-nucleotide monophosphate (NMP) building blocks in all RNAs enable enzyme-catalyzed chemical modifications to three types of sites: the heterocyclic bases via N- and C-methylations and other alkylations, conversion of the N-glycoside linkages of the uridine moiety to the C-C glycoside link in pseudouridines, and the phosphodiester-mediated processes of 5'-capping, splicing, and 3'-tailing of premRNAs. We examine known cases for enzymatic covalent catalytic strategies that entail transient formation and breakdown of covalent enzyme-RNA adducts in each catalytic cycle. One case involves generation of the required carbon nucleophile during C5 methylation of cytosine residues in RNAs. A second examines the mechanism proposed for pseudouridine synthases and for replacement of a guanine residue in tRNAs by queuosine. The third category involves phosphoric anhydride and phosphodiester chemistry by which viral RNAs encode enzymes for making their own mRNA 5'-caps. This strategy includes the recent finding that the SARS-CoV2 proteins assemble a canonical 5',5'-GTP cap on their 28 900 nucleotide genomic RNA to enable its translation as an mRNA by host translational machinery by way of a covalent RNA-viral enzyme intermediate.
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Affiliation(s)
- Christopher T Walsh
- ChEM-H Institute, Stanford University, Palo Alto, California 94305, United States
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23
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Arlt J, Vlaic S, Feuer R, Thomas M, Settmacher U, Dahmen U, Dirsch O. Selective gene expression profiling contributes to a better understanding of the molecular pathways underlying the histological changes observed after RHMVL. BMC Med Genomics 2022; 15:211. [PMID: 36207717 PMCID: PMC9547442 DOI: 10.1186/s12920-022-01364-z] [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: 01/14/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Background In previous studies, five vasoactive drugs were investigated for their effect on the recovery process after extended liver resection without observing relevant improvements. We hypothesized that an analysis of gene expression could help to identify potentially druggable pathways and could support the selection of promising drug candidates. Methods Liver samples obtained from rats after combined 70% partial hepatectomy and right median hepatic vein ligation (n = 6/group) sacrificed at 0 h, 24 h, 48 h, and 7days were selected for this study. Liver samples were collected from differentially perfused regions of the median lobe (obstruction-zone, border-zone, normal-zone). Gene expression profiling of marker genes regulating hepatic hemodynamics, vascular remodeling, and liver regeneration was performed with microfluidic chips. We used 3 technical replicates from each sample. Raw data were normalized using LEMming and differentially expressed genes were identified using LIMMA. Results The strongest differences were found in obstruction-zone at 24 h and 48 h postoperatively compared to all other groups. mRNA expression of marker genes from hepatic hemodynamics pathways (iNOS,Ptgs2,Edn1) was most upregulated. Conclusion These upregulated genes suggest a strong vasoconstrictive effect promoting arterial hypoperfusion in the obstruction-zone. Reducing iNOS expression using selective iNOS inhibitors seems to be a promising approach to promote vasodilation and liver regeneration. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01364-z.
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Affiliation(s)
- Janine Arlt
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Jena University Hospital, Drackendorfer Str. 1, 07747, Jena, Germany
| | - Sebastian Vlaic
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Ronny Feuer
- Institute for System Dynamics, University of Stuttgart, Pfaffenwaldring 9, 70569, Stuttgart, Germany
| | - Maria Thomas
- Dr. Magarete Fischer-Bosch Institute for Clinical Pharmacology, Auerbachstr. 112, 70376, Stuttgart, Germany
| | - Utz Settmacher
- Department of General, Visceral and Vascular Surgery, Jena University Hospital, Erlanger Allee 101, 07747, Jena, Germany
| | - Uta Dahmen
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Jena University Hospital, Drackendorfer Str. 1, 07747, Jena, Germany.
| | - Olaf Dirsch
- Institute of Pathology, Jena University Hospital, Ziegelmühlenweg 1, 07743, Jena, Germany
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24
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Synthesis and Structure-Activity Relationship Studies of Pyrido [1,2- e]Purine-2,4( 1H,3H)-Dione Derivatives Targeting Flavin-Dependent Thymidylate Synthase in Mycobacterium tuberculosis. Molecules 2022; 27:molecules27196216. [PMID: 36234754 PMCID: PMC9571937 DOI: 10.3390/molecules27196216] [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: 09/06/2022] [Revised: 09/13/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
In 2002, a new class of thymidylate synthase (TS) involved in the de novo synthesis of dTMP named Flavin-Dependent Thymidylate Synthase (FDTS) encoded by the thyX gene was discovered; FDTS is present only in 30% of prokaryote pathogens and not in human pathogens, which makes it an attractive target for the development of new antibacterial agents, especially against multi-resistant pathogens. We report herein the synthesis and structure-activity relationship of a novel series of hitherto unknown pyrido[1,2-e]purine-2,4(1H,3H)-dione analogues. Several synthetics efforts were done to optimize regioselective N1-alkylation through organopalladium cross-coupling. Modelling of potential hits were performed to generate a model of interaction into the active pocket of FDTS to understand and guide further synthetic modification. All those compounds were evaluated on an in-house in vitro NADPH oxidase assays screening as well as against Mycobacterium tuberculosis ThyX. The highest inhibition was obtained for compound 23a with 84.3% at 200 µM without significant cytotoxicity (CC50 > 100 μM) on PBM cells.
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25
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Li YH, Hou HF, Geng Z, Zhang H, She Z, Dong YH. Structural basis of a multi-functional deaminase in chlorovirus PBCV-1. Arch Biochem Biophys 2022; 727:109339. [DOI: 10.1016/j.abb.2022.109339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 11/02/2022]
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Highlighting the Unique Roles of Radical S-Adenosylmethionine Enzymes in Methanogenic Archaea. J Bacteriol 2022; 204:e0019722. [PMID: 35880875 PMCID: PMC9380564 DOI: 10.1128/jb.00197-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Radical S-adenosylmethionine (SAM) enzymes catalyze an impressive variety of difficult biochemical reactions in various pathways across all domains of life. These metalloenzymes employ a reduced [4Fe-4S] cluster and SAM to generate a highly reactive 5'-deoxyadenosyl radical that is capable of initiating catalysis on otherwise unreactive substrates. Interestingly, the genomes of methanogenic archaea encode many unique radical SAM enzymes with underexplored or completely unknown functions. These organisms are responsible for the yearly production of nearly 1 billion tons of methane, a potent greenhouse gas as well as a valuable energy source. Thus, understanding the details of methanogenic metabolism and elucidating the functions of essential enzymes in these organisms can provide insights into strategies to decrease greenhouse gas emissions as well as inform advances in bioenergy production processes. This minireview provides an overview of the current state of the field regarding the functions of radical SAM enzymes in methanogens and discusses gaps in knowledge that should be addressed.
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27
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Alexandrova LA, Khandazhinskaya AL, Matyugina ES, Makarov DA, Kochetkov SN. Analogues of Pyrimidine Nucleosides as Mycobacteria Growth Inhibitors. Microorganisms 2022; 10:microorganisms10071299. [PMID: 35889017 PMCID: PMC9322969 DOI: 10.3390/microorganisms10071299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 01/25/2023] Open
Abstract
Tuberculosis (TB) is the oldest human infection disease. Mortality from TB significantly decreased in the 20th century, because of vaccination and the widespread use of antibiotics. However, about a third of the world’s population is currently infected with Mycobacterium tuberculosis (Mtb) and the death rate from TB is about 1.4–2 million people per year. In the second half of the 20th century, new extensively multidrug-resistant strains of Mtb were identified, which are steadily increasing among TB patients. Therefore, there is an urgent need to develop new anti-TB drugs, which remains one of the priorities of pharmacology and medicinal chemistry. The antimycobacterial activity of nucleoside derivatives and analogues was revealed not so long ago, and a lot of studies on their antibacterial properties have been published. Despite the fact that there are no clinically used drugs based on nucleoside analogues, some progress has been made in this area. This review summarizes current research in the field of the design and study of inhibitors of mycobacteria, primarily Mtb.
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28
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Early Life Stage Folic Acid Deficiency Delays the Neurobehavioral Development and Cognitive Function of Rat Offspring by Hindering De Novo Telomere Synthesis. Int J Mol Sci 2022; 23:ijms23136948. [PMID: 35805953 PMCID: PMC9266327 DOI: 10.3390/ijms23136948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/19/2022] [Accepted: 06/20/2022] [Indexed: 11/20/2022] Open
Abstract
Early life stage folate status may influence neurodevelopment in offspring. The developmental origin of health and disease highlights the importance of the period of the first 1000 days (from conception to 2 years) of life. This study aimed to evaluate the effect of early life stage folic acid deficiency on de novo telomere synthesis, neurobehavioral development, and the cognitive function of offspring rats. The rats were divided into three diet treatment groups: folate-deficient, folate-normal, and folate-supplemented. They were fed the corresponding diet from 5 weeks of age to the end of the lactation period. After weaning, the offspring rats were still fed with the corresponding diet for up to 100 days. Neurobehavioral tests, folic acid and homocysteine (Hcy) levels, relative telomere length in brain tissue, and uracil incorporation in telomere in offspring were measured at different time points. The results showed that folic acid deficiency decreased the level of folic acid, increased the level of Hcy of brain tissue in offspring, increased the wrong incorporation of uracil into telomeres, and hindered de novo telomere synthesis. However, folic acid supplementation increased the level of folic acid, reduced the level of Hcy of brain tissue in offspring, reduced the wrong incorporation of uracil into telomeres, and protected de novo telomere synthesis of offspring, which was beneficial to the development of early sensory-motor function, spatial learning, and memory in adolescence and adulthood. In conclusion, early life stage folic acid deficiency had long-term inhibiting effects on neurodevelopment and cognitive function in offspring.
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Cinobufagin restrains the growth and triggers DNA damage of human hepatocellular carcinoma cells via proteasome-dependent degradation of thymidylate synthase. Chem Biol Interact 2022; 360:109938. [DOI: 10.1016/j.cbi.2022.109938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/22/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022]
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Design, Cytotoxicity and Antiproliferative Activity of 4-Amino-5-methyl-thieno[2,3-d]pyrimidine-6-carboxylates against MFC-7 and MDA-MB-231 Breast Cancer Cell Lines. Molecules 2022; 27:molecules27103314. [PMID: 35630793 PMCID: PMC9148072 DOI: 10.3390/molecules27103314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Novel 4-amino-thieno[2,3-d]pyrimidine-6-carboxylates substituted at the second position were prepared by cyclocondensation of 2-amino-3-cyano-thiophene and aryl nitriles in an acidic medium. The design of the target compounds was based on structural optimization. The derivatives thus obtained were tested in vitro against human and mouse cell lines. The examination of the compound effects on BLAB 3T3 and MFC-10A cells showed that they are safe, making them suitable for subsequent experiments to establish their antitumor activity. The photoirritancy factor of the compounds was calculated. Using the MTT test, the antiproliferative activity to MCF-10A, MCF-7 and MDA-MB-231 cell lines was estimated. The best antiproliferative effect in respect to the MCF-7 cell line revealed compound 2 with IC50 4.3 ± 0.11 µg/mL (0.013 µM). The highest selective index with respect to MCF-7 cells was shown by compound 3 (SI = 19.3), and to MDA-MB-231 cells by compound 2 (SI = 3.7). Based on energy analysis, the most stable conformers were selected and optimized by means of density functional theory (DFT). Ligand efficiency, ligand lipophilicity efficiency and the physicochemical parameters of the target 4-amino-thienopyrimidines were determined. The data obtained indicated that the lead compound among the tested substances is compound 2.
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Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
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Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
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32
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Zhao LN, Kaldis P. Pairing structural reconstruction with catalytic competence to evaluate the mechanisms of key enzymes in the folate-mediated one-carbon pathway. FEBS J 2022; 290:2279-2291. [PMID: 35303396 DOI: 10.1111/febs.16439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/05/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023]
Abstract
Mammalian metabolism comprises a series of interlinking pathways that include two major cycles: the folate and methionine cycles. The folate-mediated metabolic cycle uses several oxidation states of tetrahydrofolate to carry activated one-carbon units to be readily used and interconverted within the cell. They are required for nucleotide synthesis, methylation and metabolism, and particularly for proliferation of cancer cells. Based on the latest progress in genome-wide CRISPR loss-of-function viability screening of 789 cell lines, we focus on the most cancer-dependent enzymes in this pathway, especially those that are hyperactivated in cancer, to provide new insight into the chemical basis for cancer drug development. Since the complete 3D structure of several of these enzymes of the one-carbon pathway in their active form are not available, we used homology modelling integrated with the interpretation of the reaction mechanism. In addition, have reconstructed the most likely scenario for the reactions taking place paired with their catalytic competence that provides a testable framework for this pathway.
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Affiliation(s)
- Li Na Zhao
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Philipp Kaldis
- Department of Clinical Sciences, Lund University, Malmö, Sweden
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33
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Kalman TI. Rational Design of an Orally Active Anticancer Fluoropyrimidine, Pencitabine, a Hybrid of Capecitabine and Gemcitabine. ACS Med Chem Lett 2022; 13:409-416. [PMID: 35300092 PMCID: PMC8919275 DOI: 10.1021/acsmedchemlett.1c00565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/11/2022] [Indexed: 11/30/2022] Open
Abstract
The structure of the anticancer drug capecitabine was redesigned to prevent metabolic conversion to 5-fluorouracil and its associated potentially fatal toxicities. The resulting cytidine analogue, pencitabine, is a hybrid of capecitabine and gemcitabine, another anticancer drug in clinical use. Preliminary biological evaluation revealed that pencitabine is cytotoxic in vitro in cell culture and orally active in vivo in a human xenograft test system. Pencitabine may mimic the known therapeutically advantageous combination of its parent drugs. Pencitabine is postulated to interfere with DNA synthesis and function by inhibiting multiple nucleotide-metabolizing enzymes and by misincorporation into DNA. Based on detailed mechanistic analyses and literature precedents, the hypothesis is put forward that the significant DNA damage caused by pencitabine may be accounted for by two additional effects not shown by the parent drugs: inhibition of DNA glycosylases involved in base excision repair and of DNA (cytosine-5)-methyltransferase involved in epigenetic regulation of cellular metabolism.
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Affiliation(s)
- Thomas I Kalman
- Departments of Chemistry, Pharmacology and Toxicology, and School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, the State University of New York, Natural Sciences Complex, Buffalo, New York 14260, United States
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34
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Bonagas N, Gustafsson NMS, Henriksson M, Marttila P, Gustafsson R, Wiita E, Borhade S, Green AC, Vallin KSA, Sarno A, Svensson R, Göktürk C, Pham T, Jemth AS, Loseva O, Cookson V, Kiweler N, Sandberg L, Rasti A, Unterlass JE, Haraldsson M, Andersson Y, Scaletti ER, Bengtsson C, Paulin CBJ, Sanjiv K, Abdurakhmanov E, Pudelko L, Kunz B, Desroses M, Iliev P, Färnegårdh K, Krämer A, Garg N, Michel M, Häggblad S, Jarvius M, Kalderén C, Jensen AB, Almlöf I, Karsten S, Zhang SM, Häggblad M, Eriksson A, Liu J, Glinghammar B, Nekhotiaeva N, Klingegård F, Koolmeister T, Martens U, Llona-Minguez S, Moulson R, Nordström H, Parrow V, Dahllund L, Sjöberg B, Vargas IL, Vo DD, Wannberg J, Knapp S, Krokan HE, Arvidsson PI, Scobie M, Meiser J, Stenmark P, Berglund UW, Homan EJ, Helleday T. Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress. NATURE CANCER 2022; 3:156-172. [PMID: 35228749 PMCID: PMC8885417 DOI: 10.1038/s43018-022-00331-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/10/2022] [Indexed: 11/09/2022]
Abstract
The folate metabolism enzyme MTHFD2 (methylenetetrahydrofolate dehydrogenase/cyclohydrolase) is consistently overexpressed in cancer but its roles are not fully characterized, and current candidate inhibitors have limited potency for clinical development. In the present study, we demonstrate a role for MTHFD2 in DNA replication and genomic stability in cancer cells, and perform a drug screen to identify potent and selective nanomolar MTHFD2 inhibitors; protein cocrystal structures demonstrated binding to the active site of MTHFD2 and target engagement. MTHFD2 inhibitors reduced replication fork speed and induced replication stress followed by S-phase arrest and apoptosis of acute myeloid leukemia cells in vitro and in vivo, with a therapeutic window spanning four orders of magnitude compared with nontumorigenic cells. Mechanistically, MTHFD2 inhibitors prevented thymidine production leading to misincorporation of uracil into DNA and replication stress. Overall, these results demonstrate a functional link between MTHFD2-dependent cancer metabolism and replication stress that can be exploited therapeutically with this new class of inhibitors.
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Affiliation(s)
- Nadilly Bonagas
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Nina M S Gustafsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Martin Henriksson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Petra Marttila
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Robert Gustafsson
- Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden
| | - Elisée Wiita
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Sanjay Borhade
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Alanna C Green
- Weston Park Cancer Centre, Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, UK
| | - Karl S A Vallin
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Antonio Sarno
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Richard Svensson
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Camilla Göktürk
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Therese Pham
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Olga Loseva
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Victoria Cookson
- Weston Park Cancer Centre, Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, UK
| | - Nicole Kiweler
- Cancer Metabolism Group, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Lars Sandberg
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Organic Chemistry, Stockholm University, Solna, Sweden
| | - Azita Rasti
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Judith E Unterlass
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Martin Haraldsson
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Yasmin Andersson
- Drug Discovery and Development Platform, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Solna, Sweden
| | - Emma R Scaletti
- Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden.,Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Christoffer Bengtsson
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Organic Chemistry, Stockholm University, Solna, Sweden
| | - Cynthia B J Paulin
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Kumar Sanjiv
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Eldar Abdurakhmanov
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Linda Pudelko
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Ben Kunz
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Matthieu Desroses
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Petar Iliev
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Katarina Färnegårdh
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Organic Chemistry, Stockholm University, Solna, Sweden
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
| | - Neeraj Garg
- Department of Medicinal Chemistry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maurice Michel
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Sara Häggblad
- Biochemical and Cellular Screening Facility, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Malin Jarvius
- Department of Medical Sciences, Division of Cancer Pharmacology and Computational Medicine, Uppsala University, Uppsala, Sweden
| | - Christina Kalderén
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Amanda Bögedahl Jensen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Ingrid Almlöf
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Stella Karsten
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Si Min Zhang
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Maria Häggblad
- Biochemical and Cellular Screening Facility, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Anders Eriksson
- Karolinska High Throughput Centre, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jianping Liu
- Karolinska High Throughput Centre, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Björn Glinghammar
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Natalia Nekhotiaeva
- Karolinska High Throughput Centre, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Fredrik Klingegård
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Organic Chemistry, Stockholm University, Solna, Sweden
| | - Tobias Koolmeister
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Ulf Martens
- Biochemical and Cellular Screening Facility, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Sabin Llona-Minguez
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Ruth Moulson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Helena Nordström
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Vendela Parrow
- Department of Medical Sciences, Division of Cancer Pharmacology and Computational Medicine, Uppsala University, Uppsala, Sweden
| | - Leif Dahllund
- Drug Discovery and Development Platform, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Solna, Sweden
| | - Birger Sjöberg
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Irene L Vargas
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Duy Duc Vo
- Department of Medicinal Chemistry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Wannberg
- Department of Medicinal Chemistry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
| | - Hans E Krokan
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per I Arvidsson
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Martin Scobie
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Johannes Meiser
- Cancer Metabolism Group, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Pål Stenmark
- Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden.,Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Evert J Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden. .,Weston Park Cancer Centre, Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, UK.
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35
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Costantino L, Ferrari S, Santucci M, Salo-Ahen OMH, Carosati E, Franchini S, Lauriola A, Pozzi C, Trande M, Gozzi G, Saxena P, Cannazza G, Losi L, Cardinale D, Venturelli A, Quotadamo A, Linciano P, Tagliazucchi L, Moschella MG, Guerrini R, Pacifico S, Luciani R, Genovese F, Henrich S, Alboni S, Santarem N, da Silva Cordeiro A, Giovannetti E, Peters GJ, Pinton P, Rimessi A, Cruciani G, Stroud RM, Wade RC, Mangani S, Marverti G, D'Arca D, Ponterini G, Costi MP. Destabilizers of the thymidylate synthase homodimer accelerate its proteasomal degradation and inhibit cancer growth. eLife 2022; 11:73862. [PMID: 36475542 PMCID: PMC9831607 DOI: 10.7554/elife.73862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Drugs that target human thymidylate synthase (hTS), a dimeric enzyme, are widely used in anticancer therapy. However, treatment with classical substrate-site-directed TS inhibitors induces over-expression of this protein and development of drug resistance. We thus pursued an alternative strategy that led us to the discovery of TS-dimer destabilizers. These compounds bind at the monomer-monomer interface and shift the dimerization equilibrium of both the recombinant and the intracellular protein toward the inactive monomers. A structural, spectroscopic, and kinetic investigation has provided evidence and quantitative information on the effects of the interaction of these small molecules with hTS. Focusing on the best among them, E7, we have shown that it inhibits hTS in cancer cells and accelerates its proteasomal degradation, thus causing a decrease in the enzyme intracellular level. E7 also showed a superior anticancer profile to fluorouracil in a mouse model of human pancreatic and ovarian cancer. Thus, over sixty years after the discovery of the first TS prodrug inhibitor, fluorouracil, E7 breaks the link between TS inhibition and enhanced expression in response, providing a strategy to fight drug-resistant cancers.
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Affiliation(s)
- Luca Costantino
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Stefania Ferrari
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Matteo Santucci
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Outi MH Salo-Ahen
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical StudiesHeidelbergGermany
| | - Emanuele Carosati
- Department of Chemistry, Biology and Biotechnology, University of PerugiaPerugiaItaly
| | - Silvia Franchini
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Angela Lauriola
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of SienaSienaItaly
| | - Matteo Trande
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Gaia Gozzi
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Puneet Saxena
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Giuseppe Cannazza
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Lorena Losi
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Daniela Cardinale
- Respiratory, Critical Care & Anesthesia UCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Alberto Venturelli
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Antonio Quotadamo
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | | | - Maria Gaetana Moschella
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly,Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena, ItalyModenaItaly
| | - Remo Guerrini
- Department of Chemical and Pharmaceutical Science, University of FerraraFerraraItaly
| | - Salvatore Pacifico
- Department of Chemical and Pharmaceutical Science, University of FerraraFerraraItaly
| | - Rosaria Luciani
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Filippo Genovese
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Stefan Henrich
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical StudiesHeidelbergGermany
| | - Silvia Alboni
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | | | - Anabela da Silva Cordeiro
- IBMC I3SPortoPortugal,Department of Biological Sciences, Faculty of Pharmacy, University of PortoPortoPortugal
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081HV, Vrije Universiteit AmsterdamAmsterdamNetherlands,CancerPharmacology Lab, Fondazione Pisana per la ScienzaPisaItaly
| | - Godefridus J Peters
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081HV, Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - Paolo Pinton
- Dept. of Medical Sciences and Laboratory for Technologies of Advanced Therapies (LTTA), University of FerraraFerraraItaly
| | - Alessandro Rimessi
- Dept. of Medical Sciences and Laboratory for Technologies of Advanced Therapies (LTTA), University of FerraraFerraraItaly
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of PerugiaPerugiaItaly
| | - Robert M Stroud
- Biochemistry and Biophysics Department, University of California San FranciscoSan FranciscoUnited States
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical StudiesHeidelbergGermany,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg UniversityHeidelbergGermany,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg UniversityHeidelbergGermany
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of SienaSienaItaly
| | - Gaetano Marverti
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Domenico D'Arca
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Glauco Ponterini
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
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36
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Choi SH, Jeon B, Kim N, Wu HH, Ko TP, Ruszczycky MW, Isiorho EA, Liu YN, Keatinge-Clay AT, Tsai MD, Liu HW. Evidence for an Enzyme-Catalyzed Rauhut-Currier Reaction during the Biosynthesis of Spinosyn A. J Am Chem Soc 2021; 143:20291-20295. [PMID: 34813308 DOI: 10.1021/jacs.1c09482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The catalog of enzymes known to catalyze the nucleophile-assisted formation of C-C bonds is extremely small, and there is presently no definitive example of a biological Rauhut-Currier reaction. Biosynthesis of the polyketide insecticide spinosyn A in Saccharopolyspora spinosa involves a [4 + 2]-cycloaddition and a subsequent intramolecular C-C bond formation catalyzed by SpnF and SpnL, respectively. Isotope tracer experiments and kinetic isotope effects, however, imply that the SpnL-catalyzed reaction proceeds without initial deprotonation of the substrate. The crystal structure of SpnL exhibits high similarity to SAM-dependent methyltransferases as well as SpnF. The residue Cys60 is also shown to reside in the SpnL active site, and the Cys60Ala SpnL mutant is found to be devoid of activity. Moreover, SpnL is covalently modified at Cys60 and irreversibly inactivated when it is coincubated with a fluorinated substrate analogue designed as a suicide inactivator of nucleophile-assisted C-C bond formation. These results suggest that SpnL catalyzes a biological Rauhut-Currier reaction.
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Affiliation(s)
- Sei-Hyun Choi
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Byungsun Jeon
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Namho Kim
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hsin-Hui Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Mark W Ruszczycky
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Eta A Isiorho
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yung-Nan Liu
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.,Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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37
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Li S, Zhao J, Lv L, Dong D. Identification and Validation of TYMS as a Potential Biomarker for Risk of Metastasis Development in Hepatocellular Carcinoma. Front Oncol 2021; 11:762821. [PMID: 34858842 PMCID: PMC8630669 DOI: 10.3389/fonc.2021.762821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/21/2021] [Indexed: 12/21/2022] Open
Abstract
Metastasis is the major cause of hepatocellular carcinoma (HCC) mortality. Unfortunately, there are few reports on effective biomarkers for HCC metastasis. This study aimed to discover potential key genes of HCC, which could provide new insights for HCC metastasis. GEO (Gene Expression Omnibus) microarray and TCGA (The Cancer Genome Atlas) datasets were integrated to screen for candidate genes involved in HCC metastasis. Differentially expressed genes (DEGs) were screened, and then we performed enrichment analysis of Gene Ontology (GO), together with Kyoto Encyclopedia of Genes and Genomes (KEGG). A protein-protein interaction network was then built and analyzed utilizing STRING and Cytoscape, followed by the identification of 10 hub genes by cytoHubba. Four genes were associated with survival, their prognostic value was verified by prognostic signature analysis. Thymidylate synthase (TYMS) gene was identified as significant HCC metastasis-associated genes after mRNA expression validation and IHC analysis. TYMS silencing in HCC cells remarkedly inhibited growth and invasion. Finally, we found TYMS silencing dramatically decrease DNA synthesis and extracellular matrix (ECM) degradation, resulting in the inhibition of HCC metastasis, indicating TYMS had close associations with HCC development. These findings provided new insights into HCC metastasis and identified candidate gene prognosis signatures for HCC metastasis.
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Affiliation(s)
- Shuai Li
- Department of Pharmacy, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jingyuan Zhao
- Regenerative Medicine Center, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Linlin Lv
- Department of Pharmacy, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Deshi Dong
- Department of Pharmacy, The First Affiliated Hospital of Dalian Medical University, Dalian, China
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38
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Karimi L, Jaberi M, Asadi M, Zarredar H, Zafari V, Bornehdeli S, Niknam S, Kermani TA. Significance of microRNA-330-5p/TYMS Expression Axis in the Pathogenesis of Colorectal Tumorigenesis. J Gastrointest Cancer 2021; 53:965-970. [PMID: 34651293 DOI: 10.1007/s12029-021-00695-x] [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] [Accepted: 08/18/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common types of cancer worldwide. A number of dysregulated microRNAs (miRNAs) have been linked to CRC progression and treatment response and are thought to be promising prognostic biomarkers for this cancer. microRNA-330 (miR-330-5p) has been reported to inhibit cell proliferation through suppressing thymidylate synthase (TYMS). In the current study, miR-330-5p, TYMS, and their interactions were investigated to evaluate their therapeutic and diagnostic value for CRC treatment. METHODS The expression levels of miR-330-5p and TYMS were evaluated in silico using TCGA datasets for CRC. Data validation was performed on a set of internal samples (100 pairs of CRC tumor specimens and adjacent non-cancerous samples) utilizing real-time PCR assay. The linkage between clinicopathological parameters and expression levels was also investigated. RESULTS TCGA results indicated that miR-330-5p and TYMS were significantly upregulated and downregulated in the CRC, respectively. Real-time PCR results confirmed that the expression of miR-330-5p was significantly upregulated in tumor tissues relative to marginal tissues (P = 0.0005), whereas TYMS expression was significantly downregulated (P = 0.0001). The transcript level of miR-330-5p was associated with tumor stage and lymph node metastases. CONCLUSION The microRNA-330 inhibited cell proliferation by suppressing thymidylate synthase (TYMS) in colorectal cancer. Therefore, suggesting that they are valuable factors for further studies of alternative treatment and diagnostic methods.
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Affiliation(s)
- Leila Karimi
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Milad Jaberi
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Milad Asadi
- Department of Basic Oncology, Health Institute of Ege University, Izmir, Turkey
| | - Habib Zarredar
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Venus Zafari
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soghra Bornehdeli
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saman Niknam
- Department of General Surgery, Sina Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Touraj Asvadi Kermani
- Department of General Surgery, School of Medicine, Imam Reza Hospital, Tabriz University of Medical Sciences, P.O. Box: 5175971583, Tabriz, Iran.
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39
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Dozova N, Lacombat F, Lombard M, Hamdane D, Plaza P. Ultrafast dynamics of fully reduced flavin in catalytic structures of thymidylate synthase ThyX. Phys Chem Chem Phys 2021; 23:22692-22702. [PMID: 34605505 DOI: 10.1039/d1cp03379d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thymidylate is a vital DNA precursor synthesized by thymidylate synthases. ThyX is a flavin-dependent thymidylate synthase found in several human pathogens and absent in humans, which makes it a potential target for antimicrobial drugs. This enzyme methylates the 2'-deoxyuridine 5'-monophosphate (dUMP) to 2'-deoxythymidine 5'-monophosphate (dTMP) using a reduced flavin adenine dinucleotide (FADH-) as prosthetic group and (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2THF) as a methylene donor. Recently, it was shown that ThyX-catalyzed reaction is a complex process wherein FADH- promotes both methylene transfer and reduction of the transferred methylene into a methyl group. Here, we studied the dynamic and photophysics of FADH- bound to ThyX, in several substrate-binding states (no substrate, in the presence of dUMP or folate or both) by femtosecond transient absorption spectroscopy. This methodology provides valuable information about the ground-state configuration of the isoalloxazine moiety of FADH- and the rigidity of its local environment, through spectra shape and excited-state lifetime parameters. In the absence of substrate, the environment of FADH- in ThyX is only mildly more constrained than that of free FADH- in solution. The addition of dUMP however narrows the distribution of ground-state configurations and increases the constraints on the butterfly bending motion in the excited state. Folate binding results in the selection of new ground-state configurations, presumably located at a greater distance from the conical intersection where excited-state decay occurs. When both substrates are present, the ground-state configuration appears on the contrary rather limited to a geometry close to the conical intersection, which explains the relatively fast excited-state decay (100 ps on the average), even if the environment of the isoalloxazine is densely packed. Hence, although the environment of the flavin is dramatically constrained, FADH- retains a dynamic necessary to shuttle carbon from folate to dUMP. Our study demonstrates the high sensitivity of FADH- photophysics to the constraints exerted by its immediate surroundings.
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Affiliation(s)
- Nadia Dozova
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Fabien Lacombat
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Sorbonne Université, 75005 Paris, France.
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Sorbonne Université, 75005 Paris, France.
| | - Pascal Plaza
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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The LarB carboxylase/hydrolase forms a transient cysteinyl-pyridine intermediate during nickel-pincer nucleotide cofactor biosynthesis. Proc Natl Acad Sci U S A 2021; 118:2106202118. [PMID: 34548397 DOI: 10.1073/pnas.2106202118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
Enzymes possessing the nickel-pincer nucleotide (NPN) cofactor catalyze C2 racemization or epimerization reactions of α-hydroxyacid substrates. LarB initiates synthesis of the NPN cofactor from nicotinic acid adenine dinucleotide (NaAD) by performing dual reactions: pyridinium ring C5 carboxylation and phosphoanhydride hydrolysis. Here, we show that LarB uses carbon dioxide, not bicarbonate, as the substrate for carboxylation and activates water for hydrolytic attack on the AMP-associated phosphate of C5-carboxylated-NaAD. Structural investigations show that LarB has an N-terminal domain of unique fold and a C-terminal domain homologous to aminoimidazole ribonucleotide carboxylase/mutase (PurE). Like PurE, LarB is octameric with four active sites located at subunit interfaces. The complex of LarB with NAD+, an analog of NaAD, reveals the formation of a covalent adduct between the active site Cys221 and C4 of NAD+, resulting in a boat-shaped dearomatized pyridine ring. The formation of such an intermediate with NaAD would enhance the reactivity of C5 to facilitate carboxylation. Glu180 is well positioned to abstract the C5 proton, restoring aromaticity as Cys221 is expelled. The structure of as-isolated LarB and its complexes with NAD+ and the product AMP identify additional residues potentially important for substrate binding and catalysis. In combination with these findings, the results from structure-guided mutagenesis studies lead us to propose enzymatic mechanisms for both the carboxylation and hydrolysis reactions of LarB that are distinct from that of PurE.
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Apigenin enhances apoptosis induction by 5-fluorouracil through regulation of thymidylate synthase in colorectal cancer cells. Redox Biol 2021; 47:102144. [PMID: 34562873 PMCID: PMC8476449 DOI: 10.1016/j.redox.2021.102144] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/05/2021] [Accepted: 09/19/2021] [Indexed: 12/18/2022] Open
Abstract
Although effective drugs have been developed, including 5-fluorouracil (5-FU), advanced colorectal cancer (CRC) shows low therapeutic sensitivity resulting from the development of 5-FU resistance. Thymidylate synthase (TS) is a target protein of 5-FU, and elevated TS lowers the 5-FU sensitivity of CRC cells. Here, we tested the efficacy of several candidate phytochemicals against human CRC-derived HCT116 cells expressing wild-type tumor suppressor protein P53 and HT29 cells expressing mutant P53. Among them, we found that apigenin enhanced the inhibitory effect of 5-FU on cell viability. In addition, apigenin inhibited the upregulation of TS induced by 5-FU. Apigenin also potentiated 5-FU-induced apoptosis of HCT116 cells and enhanced cell cycle disruption. Furthermore, apigenin increased reactive oxygen species production, intracellular and intramitochondrial Ca2+ concentrations, and mitochondrial membrane potential upon cotreatment with 5-FU. Knockdown of forkhead box protein M, a transcription factor modulating 5-FU sensitivity, enhanced the potentiation of apoptosis by apigenin in HCT116 cells. Moreover, apigenin suppressed TS expression and inhibited the viability of 5-FU-resistant HCT116 cells. Therefore, apigenin may improve the therapeutic efficacy of 5-FU against CRC by suppressing TS, but apoptosis induction is mainly dependent on functional P53. Apigenin inhibits the upregulation of TS induced by 5-FU for apoptosis of CRC. FOXM1 silencing enhances the potentiation of apoptosis by apigenin. Suppressing TS and promoting P53 activity by apigenin reduce acquired 5-FU resistance.
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Pyrimidine Biosynthetic Enzyme CAD: Its Function, Regulation, and Diagnostic Potential. Int J Mol Sci 2021; 22:ijms221910253. [PMID: 34638594 PMCID: PMC8508918 DOI: 10.3390/ijms221910253] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/18/2021] [Accepted: 09/19/2021] [Indexed: 01/10/2023] Open
Abstract
CAD (Carbamoyl-phosphate synthetase 2, Aspartate transcarbamoylase, and Dihydroorotase) is a multifunctional protein that participates in the initial three speed-limiting steps of pyrimidine nucleotide synthesis. Over the past two decades, extensive investigations have been conducted to unmask CAD as a central player for the synthesis of nucleic acids, active intermediates, and cell membranes. Meanwhile, the important role of CAD in various physiopathological processes has also been emphasized. Deregulation of CAD-related pathways or CAD mutations cause cancer, neurological disorders, and inherited metabolic diseases. Here, we review the structure, function, and regulation of CAD in mammalian physiology as well as human diseases, and provide insights into the potential to target CAD in future clinical applications.
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Arimura Y, Minato Y, Wada T, Nakayama M, Ryumon A, Hirata N, Nakajima C, Suzuki Y, Ato M, Kobayashi K, Ohara N, Iida S, Ohara N. Attempt of thyX gene silencing and construction of a thyX deleted clone in a Mycobacterium bovis BCG. Microbiol Immunol 2021; 66:10-14. [PMID: 34546594 DOI: 10.1111/1348-0421.12944] [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: 08/26/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/01/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, possess flavin-dependent thymidylate synthase, ThyX. Since thyX is absent in humans and was shown to be essential for M. tuberculosis normal growth, ThyX is thought to be an attractive novel TB drug target. This study assessed thyX essentiality in Mycobacterium bovis BCG strains using CRISPR interference based gene silencing and found that thyX is not essential in an M. bovis BCG Tokyo derivative strain. A thyX deletion mutant strain was successfully constructed from that strain, which reinforces the non-essentiality of thyX under a certain genetic background.
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Affiliation(s)
- Yuki Arimura
- Department of Oral and Maxillofacial Reconstructive Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yusuke Minato
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Takayuki Wada
- Department of Microbiology, Graduate School of Human Life Science, Osaka City University, Osaka, Japan
| | - Masaaki Nakayama
- Department of Oral Microbiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan.,Advanced Research Center for Oral and Craniofacial Sciences, Dental School, Okayama University, Okayama, Japan
| | - Ayako Ryumon
- Department of Oral Microbiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Nao Hirata
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Manabu Ato
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuo Kobayashi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Naoko Ohara
- Department of Operative Dentistry, Okayama University Hospital, Okayama University, Okayama, Japan
| | - Seiji Iida
- Department of Oral and Maxillofacial Reconstructive Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Naoya Ohara
- Department of Oral Microbiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan.,Advanced Research Center for Oral and Craniofacial Sciences, Dental School, Okayama University, Okayama, Japan
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Biteau NG, Roy V, Lambry JC, Becker HF, Myllykallio H, Agrofoglio LA. Synthesis of acyclic nucleoside phosphonates targeting flavin-dependent thymidylate synthase in Mycobacterium tuberculosis. Bioorg Med Chem 2021; 46:116351. [PMID: 34391120 DOI: 10.1016/j.bmc.2021.116351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/16/2021] [Accepted: 07/30/2021] [Indexed: 10/20/2022]
Abstract
Flavin-Dependent Thymidylate Synthase (FDTS) encoded by ThyX gene was discovered as a new class of thymidylate synthase involved in the de novo synthesis of dTMP named only in 30 % of human pathogenic bacteria. This target was pursed for the development of new antibacterial agents against multiresistant pathogens. We have developed a new class of ANPs based on the mimic of two natural's cofactors (dUMP and FAD) as inhibitors against Mycobacterium tuberculosis ThyX. Several synthetic efforts were performed to optimize regioselective N1-alkylation, cross-coupling metathesis and Sonogashira cross-coupling. Compound 19c showed a poor 31.8% inhibitory effect on ThyX at 200 μM.
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Affiliation(s)
| | - Vincent Roy
- ICOA, Univ. Orléans, CNRS UMR 7311, F-45067 Orléans, France.
| | | | - Hubert F Becker
- LOB, INSERM U696-CNRS UMR 7645, Ecole Polytechnique, 91128 Palaiseau, France; Sorbonne Université, Faculté des Sciences et Ingénierie, 75005 Paris, France
| | - Hannu Myllykallio
- LOB, INSERM U696-CNRS UMR 7645, Ecole Polytechnique, 91128 Palaiseau, France
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Lee YJ, Dai N, Müller SI, Guan C, Parker MJ, Fraser ME, Walsh SE, Sridar J, Mulholland A, Nayak K, Sun Z, Lin YC, Comb DG, Marks K, Gonzalez R, Dowling DP, Bandarian V, Saleh L, Corrêa IR, Weigele PR. Pathways of thymidine hypermodification. Nucleic Acids Res 2021; 50:3001-3017. [PMID: 34522950 PMCID: PMC8989533 DOI: 10.1093/nar/gkab781] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/25/2021] [Accepted: 09/12/2021] [Indexed: 11/15/2022] Open
Abstract
The DNAs of bacterial viruses are known to contain diverse, chemically complex modifications to thymidine that protect them from the endonuclease-based defenses of their cellular hosts, but whose biosynthetic origins are enigmatic. Up to half of thymidines in the Pseudomonas phage M6, the Salmonella phage ViI, and others, contain exotic chemical moieties synthesized through the post-replicative modification of 5-hydroxymethyluridine (5-hmdU). We have determined that these thymidine hypermodifications are derived from free amino acids enzymatically installed on 5-hmdU. These appended amino acids are further sculpted by various enzyme classes such as radical SAM isomerases, PLP-dependent decarboxylases, flavin-dependent lyases and acetyltransferases. The combinatorial permutations of thymidine hypermodification genes found in viral metagenomes from geographically widespread sources suggests an untapped reservoir of chemical diversity in DNA hypermodifications.
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Affiliation(s)
- Yan-Jiun Lee
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Nan Dai
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Stephanie I Müller
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Chudi Guan
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Mackenzie J Parker
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Morgan E Fraser
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Shannon E Walsh
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Janani Sridar
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Andrew Mulholland
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Krutika Nayak
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Zhiyi Sun
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Yu-Cheng Lin
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Donald G Comb
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Katherine Marks
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Reyaz Gonzalez
- Chemistry Department, University of Massachusetts Boston, 100 William T. Morrissey Blvd. Boston, MA02125, USA
| | - Daniel P Dowling
- Chemistry Department, University of Massachusetts Boston, 100 William T. Morrissey Blvd. Boston, MA02125, USA
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East Salt Lake City, UT 84112, USA
| | - Lana Saleh
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Ivan R Corrêa
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Peter R Weigele
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
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Benfatto S, Serçin Ö, Dejure FR, Abdollahi A, Zenke FT, Mardin BR. Uncovering cancer vulnerabilities by machine learning prediction of synthetic lethality. Mol Cancer 2021; 20:111. [PMID: 34454516 PMCID: PMC8401190 DOI: 10.1186/s12943-021-01405-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Synthetic lethality describes a genetic interaction between two perturbations, leading to cell death, whereas neither event alone has a significant effect on cell viability. This concept can be exploited to specifically target tumor cells. CRISPR viability screens have been widely employed to identify cancer vulnerabilities. However, an approach to systematically infer genetic interactions from viability screens is missing. METHODS Here we describe PAn-canceR Inferred Synthetic lethalities (PARIS), a machine learning approach to identify cancer vulnerabilities. PARIS predicts synthetic lethal (SL) interactions by combining CRISPR viability screens with genomics and transcriptomics data across hundreds of cancer cell lines profiled within the Cancer Dependency Map. RESULTS Using PARIS, we predicted 15 high confidence SL interactions within 549 DNA damage repair (DDR) genes. We show experimental validation of an SL interaction between the tumor suppressor CDKN2A, thymidine phosphorylase (TYMP) and the thymidylate synthase (TYMS), which may allow stratifying patients for treatment with TYMS inhibitors. Using genome-wide mapping of SL interactions for DDR genes, we unraveled a dependency between the aldehyde dehydrogenase ALDH2 and the BRCA-interacting protein BRIP1. Our results suggest BRIP1 as a potential therapeutic target in ~ 30% of all tumors, which express low levels of ALDH2. CONCLUSIONS PARIS is an unbiased, scalable and easy to adapt platform to identify SL interactions that should aid in improving cancer therapy with increased availability of cancer genomics data.
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Affiliation(s)
- Salvatore Benfatto
- BioMed X Institute (GmbH), Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Özdemirhan Serçin
- BioMed X Institute (GmbH), Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Francesca R Dejure
- BioMed X Institute (GmbH), Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Amir Abdollahi
- Division of Molecular and Translational Radiation Oncology, National Centre for Tumour Diseases (NCT), Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Frank T Zenke
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Balca R Mardin
- BioMed X Institute (GmbH), Im Neuenheimer Feld 583, 69120, Heidelberg, Germany.
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Chen X, Chothia SY, Basran J, Hopkinson RJ. Formaldehyde regulates tetrahydrofolate stability and thymidylate synthase catalysis. Chem Commun (Camb) 2021; 57:5778-5781. [PMID: 33997872 DOI: 10.1039/d1cc01425k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tetrahydrofolic acid and formaldehyde are key human metabolites but their physiologically relevant chemistry is undefined. Our NMR studies confirm formaldehyde as a product of tetrahydrofolic acid degradation but also reveal their reaction regulates the stability of tetrahydrofolic acid. These observations identify a novel non-enzymatic feedback mechanism regulating formaldehyde and folate metabolism that has important implications for folate-targeting chemotherapy in cancer and other diseases.
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Affiliation(s)
- Xiaolei Chen
- Leicester Institute of Structural and Chemical Biology and School of Chemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7RH, UK.
| | - Sara Y Chothia
- Leicester Institute of Structural and Chemical Biology and School of Chemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7RH, UK.
| | - Jaswir Basran
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7RH, UK
| | - Richard J Hopkinson
- Leicester Institute of Structural and Chemical Biology and School of Chemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7RH, UK.
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48
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Zhang H, Wei Y, Lin L, Liu J, Chu R, Cao P, Ang EL, Zhao H, Yuchi Z, Zhang Y. Structural and Biochemical Investigation of UTP Cyclohydrolase. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haibin Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore 138669
| | - Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Jiayi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Ruoxing Chu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Peng Cao
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore 138669
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore 138669
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
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49
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Abuawad A, Bozack AK, Saxena R, Gamble MV. Nutrition, one-carbon metabolism and arsenic methylation. Toxicology 2021; 457:152803. [PMID: 33905762 PMCID: PMC8349595 DOI: 10.1016/j.tox.2021.152803] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 12/16/2022]
Abstract
Exposure to arsenic (As) is a major public health concern globally. Inorganic As (InAs) undergoes hepatic methylation to form monomethyl (MMAs)- and dimethyl (DMAs)-arsenical species, facilitating urinary As elimination. MMAsIII is considerably more toxic than either InAsIII or DMAsV, and a higher proportion of MMAs in urine has been associated with risk for a wide range of adverse health outcomes. Efficiency of As methylation differs substantially between species, between individuals, and across populations. One-carbon metabolism (OCM) is a biochemical pathway that provides methyl groups for the methylation of As, and is influenced by folate and other micronutrients, such as vitamin B12, choline, betaine and creatine. A growing body of evidence has demonstrated that OCM-related micronutrients play a critical role in As methylation. This review will summarize observational epidemiological studies, interventions, and relevant experimental evidence examining the role that OCM-related micronutrients have on As methylation, toxicity of As, and risk for associated adverse health-related outcomes. There is fairly robust evidence supporting the impact of folate on As methylation, and some evidence from case-control studies indicating that folate nutritional status influences risk for As-induced skin lesions and bladder cancer. However, the potential for folate to be protective for other As-related health outcomes, and the potential beneficial effects of other OCM-related micronutrients on As methylation and risk for health outcomes are less well studied and warrant additional research.
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Affiliation(s)
- Ahlam Abuawad
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Anne K Bozack
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA; Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Roheeni Saxena
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Mary V Gamble
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
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50
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Desrosiers V, Barat C, Breton Y, Ouellet M, Tremblay MJ. Thymidylate synthase is essential for efficient HIV-1 replication in macrophages. Virology 2021; 561:47-57. [PMID: 34146963 DOI: 10.1016/j.virol.2021.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/09/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022]
Abstract
Thymidylate synthase (TS) is a key enzyme in nucleotide biosynthesis. A study performed by our group on human monocyte-derived macrophages (MDMs) infected with HIV-1 showed that many enzymes related to the folate cycle pathway, such as TS, are upregulated in productively infected cells. Here, we suggest that TS is essential for an effective HIV-1 infection in MDMs. Indeed, a TS specific small interfering RNA (siRNA) as well as the TS specific inhibitor Raltitrexed (RTX) caused a reduction in productively infected cells. Quantitative PCR analysis showed that this treatment decreased the efficacy of the early steps of the viral cycle. The RTX inhibitory effect was counteracted by dNTP addition. These results suggest that TS is essential for the early stages of HIV-1 infection by providing optimal dNTP concentrations in MDMs. TS and its related pathway may thus be considered as a potential therapeutic target for HIV-1 treatment.
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Affiliation(s)
- Vincent Desrosiers
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada
| | - Corinne Barat
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada
| | - Yann Breton
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada
| | - Michel Ouellet
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada
| | - Michel J Tremblay
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada; Département de Microbiologie-infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC, G1V 0A6, Canada.
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