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Probing the Binding Requirements of Modified Nucleosides with the DNA Nuclease SNM1A. Molecules 2021; 26:molecules26020320. [PMID: 33435514 PMCID: PMC7827217 DOI: 10.3390/molecules26020320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022] Open
Abstract
SNM1A is a nuclease that is implicated in DNA interstrand crosslink repair and, as such, its inhibition is of interest for overcoming resistance to chemotherapeutic crosslinking agents. However, the number and identity of the metal ion(s) in the active site of SNM1A are still unconfirmed, and only a limited number of inhibitors have been reported to date. Herein, we report the synthesis and evaluation of a family of malonate-based modified nucleosides to investigate the optimal positioning of metal-binding groups in nucleoside-derived inhibitors for SNM1A. These compounds include ester, carboxylate and hydroxamic acid malonate derivatives which were installed in the 5'-position or 3'-position of thymidine or as a linkage between two nucleosides. Evaluation as inhibitors of recombinant SNM1A showed that nine of the twelve compounds tested had an inhibitory effect at 1 mM concentration. The most potent compound contains a hydroxamic acid malonate group at the 5'-position. Overall, our studies advance the understanding of requirements for nucleoside-derived inhibitors for SNM1A and indicate that groups containing a negatively charged group in close proximity to a metal chelator, such as hydroxamic acid malonates, are promising structures in the design of inhibitors.
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Olivieri D, Tarroni R, Della Ca' N, Mancuso R, Gabriele B, Spadoni G, Carfagna C. Bis‐Alkoxycarbonylation of Acrylic Esters and Amides for the Synthesis of 2‐Alkoxycarbonyl or 2‐Carbamoyl Succinates. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900918] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Diego Olivieri
- Department of Industrial Chemistry “T. Montanari” University of Bologna Viale Risorgimento 4 40136 Bologna (BO) Italy
| | - Riccardo Tarroni
- Department of Industrial Chemistry “T. Montanari” University of Bologna Viale Risorgimento 4 40136 Bologna (BO) Italy
| | - Nicola Della Ca'
- Department of Chemistry, Life Sciences and Environmental Sustainability (SCVSA) University of Parma Parco Area delle Scienze 17A 43124 Parma Italy
| | - Raffaella Mancuso
- Department of Chemistry and Chemical Technologies University of Calabria Via P. Bucci 12/C 87036 Arcavacata di Rende (CS) Italy
| | - Bartolo Gabriele
- Department of Chemistry and Chemical Technologies University of Calabria Via P. Bucci 12/C 87036 Arcavacata di Rende (CS) Italy
| | - Gilberto Spadoni
- Department of Biomolecular Sciences University of Urbino “Carlo Bo” Piazza Rinascimento 6 61029 Urbino (PU) Italy
| | - Carla Carfagna
- Department of Industrial Chemistry “T. Montanari” University of Bologna Viale Risorgimento 4 40136 Bologna (BO) Italy
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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Vergne-Vaxelaire C, Mariage A, Petit JL, Fossey-Jouenne A, Guérard-Hélaine C, Darii E, Debard A, Nepert S, Pellouin V, Lemaire M, Zaparucha A, Salanoubat M, de Berardinis V. Characterization of a thermotolerant ROK-type mannofructokinase from Streptococcus mitis: application to the synthesis of phosphorylated sugars. Appl Microbiol Biotechnol 2018; 102:5569-5583. [DOI: 10.1007/s00253-018-9018-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/29/2018] [Accepted: 04/10/2018] [Indexed: 01/08/2023]
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Li D, Luong TTM, Dan WJ, Ren Y, Nien HX, Zhang AL, Gao JM. Natural products as sources of new fungicides (IV): Synthesis and biological evaluation of isobutyrophenone analogs as potential inhibitors of class-II fructose-1,6-bisphosphate aldolase. Bioorg Med Chem 2017; 26:386-393. [PMID: 29248352 DOI: 10.1016/j.bmc.2017.10.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/24/2017] [Accepted: 10/30/2017] [Indexed: 11/19/2022]
Abstract
Several recently identified antifungal compounds share the backbone structure of acetophenones. The aim of the present study was to develop new isobutyrophenone analogs as new antifungal agents. A series of new 2,4-dihydroxy-5-methyl isobutyrophenone derivatives were prepared and characterized by 1H, 13C NMR and MS spectroscopic data. These products were evaluated for in vitro antifungal activities against seven plant fungal pathogens by the mycelial growth inhibitory rate assay. Compounds 3, 4a, 5a, 5b, 5e, 5f and 5g showed a broad-spectrum high antifungal activity. On the other hand, for the first time, these compounds were also assayed as potential inhibitors against Class II fructose-1,6-bisphosphate aldolase (Fba) from the rice blast fungus, Magnaporthe grisea. Compounds 5e and 5g were found to exhibit the inhibition constants (Ki) for 15.12 and 14.27 μM, respectively, as the strongest competitive inhibitors against Fba activity. The possible binding-modes of compounds 5e and 5g were further analyzed by molecular docking algorithms. The results strongly suggested that compound 5g could be a promising lead for the discovery of new fungicides via targeting Class II Fba.
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Affiliation(s)
- Ding Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, Shaanxi Engineering Center of Bioresource Chemistry & Sustainable Utilization, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Tuong Thi Mai Luong
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, Shaanxi Engineering Center of Bioresource Chemistry & Sustainable Utilization, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China; Institute of Scientific Research and Technological Development, Thu Dau Mot University, Binh Duong, Viet Nam
| | - Wen-Jia Dan
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, Shaanxi Engineering Center of Bioresource Chemistry & Sustainable Utilization, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Yanliang Ren
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China.
| | - Hoang Xuan Nien
- Institute of Scientific Research and Technological Development, Thu Dau Mot University, Binh Duong, Viet Nam
| | - An-Ling Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, Shaanxi Engineering Center of Bioresource Chemistry & Sustainable Utilization, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, Shaanxi Engineering Center of Bioresource Chemistry & Sustainable Utilization, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
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Han X, Zhu X, Hong Z, Wei L, Ren Y, Wan F, Zhu S, Peng H, Guo L, Rao L, Feng L, Wan J. Structure-Based Rational Design of Novel Inhibitors Against Fructose-1,6-Bisphosphate Aldolase from Candida albicans. J Chem Inf Model 2017; 57:1426-1438. [DOI: 10.1021/acs.jcim.6b00763] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Xinya Han
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xiuyun Zhu
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Zongqin Hong
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Lin Wei
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yanliang Ren
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Fen Wan
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Shuaihua Zhu
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Hao Peng
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Li Guo
- Hubei Environmental
Monitoring Central Station, Wuhan 430072, Hubei China
| | - Li Rao
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Lingling Feng
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Jian Wan
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
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Zhang Y, Borrel A, Ghemtio L, Regad L, Boije af Gennäs G, Camproux AC, Yli-Kauhaluoma J, Xhaard H. Structural Isosteres of Phosphate Groups in the Protein Data Bank. J Chem Inf Model 2017; 57:499-516. [DOI: 10.1021/acs.jcim.6b00519] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Alexandre Borrel
- Laboratoire
Molécules Thérapeutiques in silico (MTi), UMRS-973, Université Paris Diderot, Sorbonne Paris Cité, INSERM, F-75013 Paris, France
| | | | - Leslie Regad
- Laboratoire
Molécules Thérapeutiques in silico (MTi), UMRS-973, Université Paris Diderot, Sorbonne Paris Cité, INSERM, F-75013 Paris, France
| | | | - Anne-Claude Camproux
- Laboratoire
Molécules Thérapeutiques in silico (MTi), UMRS-973, Université Paris Diderot, Sorbonne Paris Cité, INSERM, F-75013 Paris, France
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Li T, Gao X, Yang L, Shi Y, Gao Q. Methyl 6-Amino-6-deoxy-d-pyranoside-Conjugated Platinum(II) Complexes for Glucose Transporter (GLUT)-Mediated Tumor Targeting: Synthesis, Cytotoxicity, and Cellular Uptake Mechanism. ChemMedChem 2016; 11:1069-77. [DOI: 10.1002/cmdc.201600079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Taoli Li
- 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; 92 Weijin Road, Nankai District Tianjin 300072 P.R. China
| | - Xiangqian Gao
- 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; 92 Weijin Road, Nankai District Tianjin 300072 P.R. China
| | - Liu Yang
- Department of Biochemistry; Gudui BioPharma Technology Inc.; 5 Lanyuan Road, Huayuan Industrial Park Tianjin 300384 P.R. China
| | - Yunli Shi
- 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; 92 Weijin Road, Nankai District Tianjin 300072 P.R. China
| | - Qingzhi Gao
- 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; 92 Weijin Road, Nankai District Tianjin 300072 P.R. China
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Amiable C, Pochet S. Unprecedented formation of 8(R),5′-O-cycloribonucleosides through a triflation reaction of purine ribonucleosides. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.03.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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