1
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Mori M, Cocorullo M, Tresoldi A, Cazzaniga G, Gelain A, Stelitano G, Chiarelli LR, Tomaiuolo M, Delre P, Mangiatordi GF, Garofalo M, Cassetta A, Covaceuszach S, Villa S, Meneghetti F. Structural basis for specific inhibition of salicylate synthase from Mycobacterium abscessus. Eur J Med Chem 2024; 265:116073. [PMID: 38169270 DOI: 10.1016/j.ejmech.2023.116073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024]
Abstract
Blocking iron uptake and metabolism has been emerging as a promising therapeutic strategy for the development of novel antimicrobial compounds. Like all mycobacteria, M. abscessus (Mab) has evolved several countermeasures to scavenge iron from host carrier proteins, including the production of siderophores, which play a crucial role in these processes. In this study, we solved, for the first time, the crystal structure of Mab-SaS, the first enzyme involved in the biosynthesis of siderophores. Moreover, we screened a small, focused library and identified a compound exhibiting a potent inhibitory effect against Mab-SaS (IC50 ≈ 2 μM). Its binding mode was investigated by means of Induced Fit Docking simulations, performed on the crystal structure presented herein. Furthermore, cytotoxicity data and pharmacokinetic predictions revealed the safety and drug-likeness of this class of compounds. Finally, the crystallographic data were used to optimize the model for future virtual screening campaigns. Taken together, the findings of our study pave the way for the identification of potent Mab-SaS inhibitors, based on both established and unexplored chemotypes.
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Affiliation(s)
- Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Mario Cocorullo
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A. Ferrata 9, 27100, Pavia, Italy
| | - Andrea Tresoldi
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giulia Cazzaniga
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Arianna Gelain
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giovanni Stelitano
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A. Ferrata 9, 27100, Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A. Ferrata 9, 27100, Pavia, Italy
| | - Martina Tomaiuolo
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, 34149, Trieste, Italy
| | - Pietro Delre
- Institute of Crystallography, National Research Council, Via G. Amendola 122/o, 70126, Bari, Italy
| | - Giuseppe F Mangiatordi
- Institute of Crystallography, National Research Council, Via G. Amendola 122/o, 70126, Bari, Italy
| | - Mariangela Garofalo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via F. Marzolo 5, 35131, Padova, Italy
| | - Alberto Cassetta
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, 34149, Trieste, Italy
| | - Sonia Covaceuszach
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, 34149, Trieste, Italy.
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy.
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
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2
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Wu X, Wang W, Stelitano G, Riabova O, Wang B, Niu W, Cocorullo M, Shi R, Chiarelli LR, Makarov V, Lu Y, Li C, Qiao C. Benzothiozinone derivatives with anti-tubercular Activity-Further side chain investigation. Eur J Med Chem 2024; 264:115976. [PMID: 38039794 DOI: 10.1016/j.ejmech.2023.115976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
A series of novel benzothiozinone (BTZ) derivatives were designed, prepared and evaluated for antituberculosis activity. Specifically, the BTZ pharmacophore is retained and the previous heterocyclic ring linker is replaced by alkynyl or vinyl linker, the resulting compounds displayed about 5-fold improved antimycobacterial activity. We further revealed that the linker attached tail group affects the compound metabolic stability, potency and other drug like properties. This work led to the discovery of two compounds (A1 and A11) with acceptable low MICs and improved metabolic stability. The representative compound A11 demonstrated bactericidal efficacy in an acute TB infection mouse model.
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Affiliation(s)
- Xiaomei Wu
- College of Pharmaceutical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Wenxin Wang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu Province, China
| | - Giovanni Stelitano
- Department of Biology and Biotechnology, University of Pavia, Pavia, 27100, Italy
| | - Olga Riabova
- Research Center of Biotechnology, The Russian Academy of Sciences, Moscow, 119071, Russia
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Wei Niu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Mario Cocorullo
- Department of Biology and Biotechnology, University of Pavia, Pavia, 27100, Italy
| | - Rui Shi
- College of Pharmaceutical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, 27100, Italy
| | - Vadim Makarov
- Research Center of Biotechnology, The Russian Academy of Sciences, Moscow, 119071, Russia
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.
| | - Chuan Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Zhongshan Institute for Drug Discovery, Zhongshan, 528400, Guangdong Province, China.
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China.
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3
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Mori M, Villa S, Chiarelli LR, Meneghetti F, Bellinzoni M. Structural Study of a New MbtI-Inhibitor Complex: Towards an Optimized Model for Structure-Based Drug Discovery. Pharmaceuticals (Basel) 2023; 16:1559. [PMID: 38004425 PMCID: PMC10675255 DOI: 10.3390/ph16111559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
MbtI from Mycobacterium tuberculosis (Mtb) is a Mg2+-dependent salicylate synthase, belonging to the chorismate-utilizing enzyme (CUE) family. As a fundamental player in iron acquisition, MbtI promotes the survival and pathogenicity of Mtb in the infected host. Hence, it has emerged in the last decade as an innovative, potential target for the anti-virulence therapy of tuberculosis. In this context, 5-phenylfuran-2-carboxylic acids have been identified as potent MbtI inhibitors. The first co-crystal structure of MbtI in complex with a member of this class was described in 2020, showing the enzyme adopting an open configuration. Due to the high mobility of the loop adjacent to the binding pocket, large portions of the amino acid chain were not defined in the electron density map, hindering computational efforts aimed at structure-driven ligand optimization. Herein, we report a new, high-resolution co-crystal structure of MbtI with a furan-based derivative, in which the closed configuration of the enzyme allowed tracing the entirety of the active site pocket in the presence of the bound inhibitor. Moreover, we describe a new crystal structure of MbtI in open conformation and in complex with the known inhibitor methyl-AMT, suggesting that in vitro potency is not related to the observed enzyme conformation. These findings will prove fundamental to enhance the potency of this series via rational structure-based drug-design approaches.
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Affiliation(s)
- Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (S.V.); (F.M.)
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (S.V.); (F.M.)
| | - Laurent R. Chiarelli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via A. Ferrata 9, 27100 Pavia, Italy;
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (S.V.); (F.M.)
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015 Paris, France
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4
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Fan D, Wang B, Stelitano G, Savková K, Riabova O, Shi R, Wu X, Chiarelli LR, Mikušová K, Makarov V, Lu Y, Hong Y, Qiao C. Side Chain-Modified Benzothiazinone Derivatives with Anti-Mycobacterial Activity. Biomedicines 2023; 11:1975. [PMID: 37509615 PMCID: PMC10377601 DOI: 10.3390/biomedicines11071975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Tuberculosis (TB) is a leading infectious disease with serious antibiotic resistance. The benzothiazinone (BTZ) scaffold PBTZ169 kills Mycobacterium tuberculosis (Mtb) through the inhibition of the essential cell wall enzyme decaprenylphosphoryl-β-D-ribose 2'-oxidase (DprE1). PBTZ169 shows anti-TB potential in animal models and pilot clinical tests. Although highly potent, the BTZ type DprE1 inhibitors in general show extremely low aqueous solubility, which adversely affects the drug-like properties. To improve the compounds physicochemical properties, we generated a series of BTZ analogues. Several optimized compounds had MIC values against Mtb lower than 0.01 µM. The representative compound 37 displays improved solubility and bioavailability compared to the lead compound. Additionally, compound 37 shows Mtb-killing ability in an acute infection mouse model.
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Affiliation(s)
- Dongguang Fan
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research, Beijing Chest Hospital, Beijing 101149, China
| | - Giovanni Stelitano
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Karin Savková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | - Olga Riabova
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Rui Shi
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Xiaomei Wu
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | - Vadim Makarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research, Beijing Chest Hospital, Beijing 101149, China
| | - Yuzhi Hong
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, China
- Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, Suzhou Medical College, Soochow University, Suzhou 215123, China
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
- Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, Suzhou Medical College, Soochow University, Suzhou 215123, China
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5
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Cocorullo M, Chiarelli LR, Stelitano G. Improving Protection to Prevent Bacterial Infections: Preliminary Applications of Reverse Vaccinology against the Main Cystic Fibrosis Pathogens. Vaccines (Basel) 2023; 11:1221. [PMID: 37515037 PMCID: PMC10384294 DOI: 10.3390/vaccines11071221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Reverse vaccinology is a powerful tool that was recently used to develop vaccines starting from a pathogen genome. Some bacterial infections have the necessity to be prevented then treated. For example, individuals with chronic pulmonary diseases, such as Cystic Fibrosis, are prone to develop infections and biofilms in the thick mucus that covers their lungs, mainly caused by Burkholderia cepacia complex, Haemophilus influenzae, Mycobacterium abscessus complex, Pseudomonas aeruginosa and Staphylococcus aureus. These infections are complicated to treat and prevention remains the best strategy. Despite the availability of vaccines against some strains of those pathogens, it is necessary to improve the immunization of people with Cystic Fibrosis against all of them. An effective approach is to develop a broad-spectrum vaccine to utilize proteins that are well conserved across different species. In this context, reverse vaccinology, a method based on computational analysis of the genome of various microorganisms, appears as one of the most promising tools for the identification of putative targets for broad-spectrum vaccine development. This review provides an overview of the vaccines that are under development by reverse vaccinology against the aforementioned pathogens, as well as the progress made so far.
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Affiliation(s)
- Mario Cocorullo
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A. Ferrata 9, 27100 Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A. Ferrata 9, 27100 Pavia, Italy
| | - Giovanni Stelitano
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A. Ferrata 9, 27100 Pavia, Italy
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6
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Recchia D, Stelitano G, Stamilla A, Gutierrez DL, Degiacomi G, Chiarelli LR, Pasca MR. Mycobacterium abscessus Infections in Cystic Fibrosis Individuals: A Review on Therapeutic Options. Int J Mol Sci 2023; 24:ijms24054635. [PMID: 36902066 PMCID: PMC10002592 DOI: 10.3390/ijms24054635] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/02/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
Mycobacterium abscessus is an opportunistic pathogen that mainly colonizes and infects cystic fibrosis patients' lungs. M. abscessus is naturally resistant to many antibiotics such as rifamycin, tetracyclines and β-lactams. The current therapeutic regimens are not very effective and are mostly based on repurposed drugs used against Mycobacterium tuberculosis infections. Thus, new approaches and novel strategies are urgently needed. This review aims to provide an overview of the latest ongoing findings to fight M. abscessus infections by analyzing emerging and alternative treatments, novel drug delivery strategies, and innovative molecules.
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7
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Buroni S, Chiarelli LR. Antibiotics' Sustainability: Another Issue in the Fight against Antimicrobial Resistance. Curr Top Med Chem 2022; 22:1979-1981. [PMID: 35578852 DOI: 10.2174/1568026622666220516114647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/28/2022] [Accepted: 04/07/2022] [Indexed: 12/15/2022]
Abstract
The spread of antimicrobial resistance (AMR) is still a major threat to global health that is likely to worsen also as a consequence of the COVID-19 pandemic. For this reason, there is an urgent need to develop new compounds and novel alternative treatments. Furthermore, the new lines of action must consider the issue of antibiotics' sustainability. Within this persrective, we have highlighted the main points on which actions in this perspective are possible.
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Affiliation(s)
- Silvia Buroni
- Department of Biology & Biotechnology 'Lazzaro Spallanzani', University of Pavia, Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology & Biotechnology 'Lazzaro Spallanzani', University of Pavia, Pavia, Italy
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8
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Shi R, Wang B, Stelitano G, Wu X, Shan Y, Wu Y, Wang X, Chiarelli LR, Lu Y, Qiao C. Development of 6-Methanesulfonyl-8-nitrobenzothiazinone Based Antitubercular Agents. ACS Med Chem Lett 2022; 13:593-598. [PMID: 35450361 PMCID: PMC9014434 DOI: 10.1021/acsmedchemlett.1c00652] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/04/2022] [Indexed: 11/28/2022] Open
Abstract
The 6-trifluoro substituted 8-nitrobenzothiazinones (BTZs) represent a novel type of antitubercular agents, and their high antimycobacterial activity is related to the inhibition of decaprenylphosphoryl-β-d-ribose 2'-oxidase (DprE1), an enzyme essential for the biosynthesis of mycobacterial cell wall. While extraordinary whole-cell activity was reported for the clinically advanced compound PBTZ169, its poor aqueous solubility signals the potential low bioavailability. To ameliorate the BTZ physiochemical property, a series of 6-methanesulfonyl substituted compounds were designed and prepared, and their antitubercular activity and DprE1 inhibition ability were evaluated. Among these compounds, MsPBTZ169 and compounds 2 and 8 exhibited minimum inhibitory concentrations (MICs) of less than 40 nM; moreover, these compounds displayed increased aqueous solubility and acceptable metabolic stability. Taken together, this study suggested that the 6-methanesulfonyl substituted 8-nitrobenzothiazinone derivatives, in combination with side chain modification, might provide BTZ type antitubercular agents with improved drug-like properties.
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Affiliation(s)
- Rui Shi
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, P. R. China
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research, Beijing Chest Hospital, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Giovanni Stelitano
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Xiaomei Wu
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, P. R. China
| | - Yuanyuan Shan
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, P. R. China
| | - Yue Wu
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, P. R. China
| | - Xin Wang
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, P. R. China
| | - Laurent R. Chiarelli
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research, Beijing Chest Hospital, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, P. R. China
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9
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Cazzaniga G, Mori M, Meneghetti F, Chiarelli LR, Stelitano G, Caligiuri I, Rizzolio F, Ciceri S, Poli G, Staver D, Ortore G, Tuccinardi T, Villa S. Virtual screening and crystallographic studies reveal an unexpected γ-lactone derivative active against MptpB as a potential antitubercular agent. Eur J Med Chem 2022; 234:114235. [DOI: 10.1016/j.ejmech.2022.114235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/03/2022] [Accepted: 02/23/2022] [Indexed: 11/04/2022]
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10
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Fan D, Wang B, Stelitano G, Savková K, Shi R, Huszár S, Han Q, Mikušová K, Chiarelli LR, Lu Y, Qiao C. Structural and Activity Relationships of 6-Sulfonyl-8-Nitrobenzothiazinones as Antitubercular Agents. J Med Chem 2021; 64:14526-14539. [PMID: 34609861 DOI: 10.1021/acs.jmedchem.1c01049] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The benzothiazinone (BTZ) scaffold compound PBTZ169 kills Mycobacterium tuberculosis by inhibiting the essential flavoenzyme DprE1, consequently blocking the synthesis of the cell wall component arabinans. While extraordinarily potent against M. tuberculosis with a minimum inhibitory concentration (MIC) less than 0.2 ng/mL, its low aqueous solubility and bioavailability issues need to be addressed. Here, we designed and synthesized a series of 6-methanesulfonyl substituted BTZ analogues; further exploration introduced five-member aromatic heterocycles as linkers to attach an aryl group as the side chain. Our work led to the discovery of a number of BTZ derived compounds with potent antitubercular activity. The optimized compounds 6 and 38 exhibited MIC 47 and 30 nM, respectively. Compared to PBTZ169, both compounds displayed increased aqueous solubility and higher stability in human liver microsomes. This study suggested that an alternative side-chain modification strategy could be implemented to improve the druglike properties of the BTZ-based compounds.
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Affiliation(s)
- Dongguang Fan
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, P. R. China
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research, Beijing Chest Hospital, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Giovanni Stelitano
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Karin Savková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Rui Shi
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, P. R. China
| | - Stanislav Huszár
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Quanquan Han
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, P. R. China
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research, Beijing Chest Hospital, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, P. R. China
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11
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Affiliation(s)
- Silvia Buroni
- Department of Biology & Biotechnology 'Lazzaro Spallanzani', University of Pavia, Pavia, 27100, Italy
| | - Laurent R Chiarelli
- Department of Biology & Biotechnology 'Lazzaro Spallanzani', University of Pavia, Pavia, 27100, Italy
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12
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Farjallah A, Chiarelli LR, Forbak M, Degiacomi G, Danel M, Goncalves F, Carayon C, Seguin C, Fumagalli M, Záhorszká M, Vega E, Abid S, Grzegorzewicz A, Jackson M, Peixoto A, Korduláková J, Pasca MR, Lherbet C, Chassaing S. A Coumarin-Based Analogue of Thiacetazone as Dual Covalent Inhibitor and Potential Fluorescent Label of HadA in Mycobacterium tuberculosis. ACS Infect Dis 2021; 7:552-565. [PMID: 33617235 DOI: 10.1021/acsinfecdis.0c00325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A novel coumarin-based molecule, designed as a fluorescent surrogate of a thiacetazone-derived antitubercular agent, was quickly and easily synthesized from readily available starting materials. This small molecule, coined Coum-TAC, exhibited a combination of appropriate physicochemical and biological properties, including resistance toward hydrolysis and excellent antitubercular efficiency similar to that of well-known thiacetazone derivatives, as well as efficient covalent labeling of HadA, a relevant therapeutic target to combat Mycobacterium tuberculosis. More remarkably, Coum-TAC was successfully implemented as an imaging probe that is capable of labeling Mycobacterium tuberculosis in a selective manner, with an enrichment at the level of the poles, thus giving for the first time relevant insights about the polar localization of HadA in the mycobacteria.
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Affiliation(s)
- Asma Farjallah
- ITAV, Université de Toulouse, CNRS USR3505, UPS, 1 place Pierre Potier, 31106 Toulouse Cedex 1, France
- Laboratoire de Chimie Appliquée: Hétérocycles, Corps Gras et Polymères, Faculté des sciences de Sfax, Université de Sfax, Sfax, Tunisie
| | - Laurent R. Chiarelli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Martin Forbak
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Giulia Degiacomi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Mathieu Danel
- ITAV, Université de Toulouse, CNRS USR3505, UPS, 1 place Pierre Potier, 31106 Toulouse Cedex 1, France
| | - Fernanda Goncalves
- ITAV, Université de Toulouse, CNRS USR3505, UPS, 1 place Pierre Potier, 31106 Toulouse Cedex 1, France
- Laboratoire de Synthèse et Physico-Chimie de Molécules d’Intérêt Biologique (SPCMIB), Université Paul Sabatier-Toulouse III/CNRS (UMR5068), 118 route de Narbonne, F-31062 Toulouse, France
| | - Chantal Carayon
- Laboratoire de Synthèse et Physico-Chimie de Molécules d’Intérêt Biologique (SPCMIB), Université Paul Sabatier-Toulouse III/CNRS (UMR5068), 118 route de Narbonne, F-31062 Toulouse, France
| | - Cendrine Seguin
- Laboratoire de Conception et Application de Molécules Bioactives (LCAMB), CNRS-UMR7199, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Marco Fumagalli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Monika Záhorszká
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Elodie Vega
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Souhir Abid
- Chemistry Department, College of Science and Arts, Jouf University, Al Qurayyat, Saudi Arabia
- Laboratoire de Chimie Appliquée: Hétérocycles, Corps Gras et Polymères, Faculté des sciences de Sfax, Université de Sfax, Sfax, Tunisie
| | - Anna Grzegorzewicz
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Antonio Peixoto
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Jana Korduláková
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Christian Lherbet
- ITAV, Université de Toulouse, CNRS USR3505, UPS, 1 place Pierre Potier, 31106 Toulouse Cedex 1, France
- Laboratoire de Synthèse et Physico-Chimie de Molécules d’Intérêt Biologique (SPCMIB), Université Paul Sabatier-Toulouse III/CNRS (UMR5068), 118 route de Narbonne, F-31062 Toulouse, France
| | - Stefan Chassaing
- ITAV, Université de Toulouse, CNRS USR3505, UPS, 1 place Pierre Potier, 31106 Toulouse Cedex 1, France
- Laboratoire de Synthèse, Réactivité Organiques & Catalyse (LASYROC), Institut de Chimie, CNRS-UMR7177, Université de Strasbourg, 4 rue Blaise Pascal, 67070 Strasbourg, France
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13
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Mori M, Stelitano G, Chiarelli LR, Cazzaniga G, Gelain A, Barlocco D, Pini E, Meneghetti F, Villa S. Synthesis, Characterization, and Biological Evaluation of New Derivatives Targeting MbtI as Antitubercular Agents. Pharmaceuticals (Basel) 2021; 14:155. [PMID: 33668554 PMCID: PMC7918538 DOI: 10.3390/ph14020155] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 01/09/2023] Open
Abstract
Tuberculosis (TB) causes millions of deaths every year, ranking as one of the most dangerous infectious diseases worldwide. Because several pathogenic strains of Mycobacterium tuberculosis (Mtb) have developed resistance against most of the established anti-TB drugs, new therapeutic options are urgently needed. An attractive target for the development of new antitubercular agents is the salicylate synthase MbtI, an essential enzyme for the mycobacterial siderophore biochemical machinery, absent in human cells. A set of analogues of I and II, two of the most potent MbtI inhibitors identified to date, was synthesized, characterized, and tested to elucidate the structural requirements for achieving an efficient MbtI inhibition and a potent antitubercular activity with this class of compounds. The structure-activity relationships (SAR) here discussed evidenced the importance of the furan as part of the pharmacophore and led to the preparation of six new compounds (IV-IX), which gave us the opportunity to examine a hitherto unexplored position of the phenyl ring. Among them emerged 5-(3-cyano-5-(trifluoromethyl)phenyl)furan-2-carboxylic acid (IV), endowed with comparable inhibitory properties to the previous leads, but a better antitubercular activity, which is a key issue in MbtI inhibitor research. Therefore, compound IV offers promising prospects for future studies on the development of novel agents against mycobacterial infections.
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Affiliation(s)
- Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (G.C.); (A.G.); (D.B.); (E.P.); (S.V.)
| | - Giovanni Stelitano
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via A. Ferrata 9, 27100 Pavia, Italy; (G.S.); (L.R.C.)
| | - Laurent R. Chiarelli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via A. Ferrata 9, 27100 Pavia, Italy; (G.S.); (L.R.C.)
| | - Giulia Cazzaniga
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (G.C.); (A.G.); (D.B.); (E.P.); (S.V.)
| | - Arianna Gelain
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (G.C.); (A.G.); (D.B.); (E.P.); (S.V.)
| | - Daniela Barlocco
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (G.C.); (A.G.); (D.B.); (E.P.); (S.V.)
| | - Elena Pini
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (G.C.); (A.G.); (D.B.); (E.P.); (S.V.)
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (G.C.); (A.G.); (D.B.); (E.P.); (S.V.)
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (G.C.); (A.G.); (D.B.); (E.P.); (S.V.)
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14
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Chiarelli LR, Degiacomi G, Egorova A, Makarov V, Pasca MR. Nitric oxide-releasing compounds for the treatment of lung infections. Drug Discov Today 2020; 26:542-550. [PMID: 33181094 DOI: 10.1016/j.drudis.2020.10.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/01/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022]
Abstract
The spread of acquired drug resistance and of microorganisms naturally resistant to antibiotics is a major threat to global health, leading to an urgent need for novel antimicrobial compounds. Exogenous nitric oxide (NO) represents an attractive and promising antimicrobial approach, showing both bactericidal and biofilm dispersal activities. Numerous studies have been performed to develop NO donor scaffolds, including small molecules, macromolecular compounds, nanoparticles (NPs), and polymeric materials. This approach has resulted in successful outcomes, with some NO-releasing compounds entering clinical practice. In this review, we highlight the importance of this strategy, with a focus on lung infections.
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Affiliation(s)
- Laurent R Chiarelli
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Giulia Degiacomi
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Anna Egorova
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt 33-2, 119071, Moscow, Russia
| | - Vadim Makarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt 33-2, 119071, Moscow, Russia
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
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15
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Liu L, Kong C, Fumagalli M, Savková K, Xu Y, Huszár S, Sammartino JC, Fan D, Chiarelli LR, Mikušová K, Sun Z, Qiao C. Design, synthesis and evaluation of covalent inhibitors of DprE1 as antitubercular agents. Eur J Med Chem 2020; 208:112773. [PMID: 32898793 DOI: 10.1016/j.ejmech.2020.112773] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/05/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022]
Abstract
Decaprenylphosphoryl-β-d-ribose 2'-oxidoreductase (DprE1) is a promising drug target for the development of novel anti-tubercular agents, and inhibitors of DprE1 are being investigated extensively. Among them, the 1,3-benzothiazinone compounds such as BTZ043, and its closer congener, PBTZ169, are undergoing clinical studies. It has been shown that both BTZ compounds are prodrugs, the nitro group is reduced to nitroso first, to which an adjacent Cys387 in the DprE1 binding pocket is covalently bound and results in suicide enzyme inhibition. We figured that replacement of the nitro with an electrophilic warhead would still achieve covalent interaction with nucleophilic Cys387, while the required reductive activation could be circumvented. To test this hypothesis, a number of covalent inhibitors of DprE1 were designed and prepared. The compounds inhibitory potency against DprE1 and anti-tubercular activity were investigated, their chemical reactivity, formation of covalent adduct between the warhead and the enzyme was demonstrated by mass spectrometry.
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Affiliation(s)
- Lingfeng Liu
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123, PR China
| | - Chengcheng Kong
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing, 101149, PR China
| | - Marco Fumagalli
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Karin Savková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Yiwen Xu
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123, PR China
| | - Stanislav Huszár
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - José C Sammartino
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy; University School for Advanced Studies - IUSS Pavia, Piazza Della Vittoria 15, 27100, Pavia, Italy
| | - Dongguang Fan
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123, PR China
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy.
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - Zhaogang Sun
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing, 101149, PR China.
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123, PR China.
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16
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Mori M, Stelitano G, Gelain A, Pini E, Chiarelli LR, Sammartino JC, Poli G, Tuccinardi T, Beretta G, Porta A, Bellinzoni M, Villa S, Meneghetti F. Shedding X-ray Light on the Role of Magnesium in the Activity of Mycobacterium tuberculosis Salicylate Synthase (MbtI) for Drug Design. J Med Chem 2020; 63:7066-7080. [PMID: 32530281 PMCID: PMC8008425 DOI: 10.1021/acs.jmedchem.0c00373] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
The
Mg2+-dependent Mycobacterium tuberculosis salicylate synthase (MbtI) is a key enzyme involved in the biosynthesis
of siderophores. Because iron is essential for the survival and pathogenicity
of the microorganism, this protein constitutes an attractive target
for antitubercular therapy, also considering the absence of homologous
enzymes in mammals. An extension of the structure–activity
relationships of our furan-based candidates allowed us to disclose
the most potent competitive inhibitor known to date (10, Ki = 4 μM), which also proved
effective on mycobacterial cultures. By structural studies, we characterized
its unexpected Mg2+-independent binding mode. We also investigated
the role of the Mg2+ cofactor in catalysis, analyzing the
first crystal structure of the MbtI–Mg2+–salicylate
ternary complex. Overall, these results pave the way for the development
of novel antituberculars through the rational design of improved MbtI
inhibitors.
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Affiliation(s)
- Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Giovanni Stelitano
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Elena Pini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Laurent R Chiarelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - José C Sammartino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - Giulio Poli
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Giangiacomo Beretta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via G. Celoria 2, 20133 Milano, Italy
| | - Alessio Porta
- Dipartimento di Chimica, Università degli Studi di Pavia, via T. Taramelli 12, 27100 Pavia, Italy
| | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75015 Paris, France
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
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17
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Chiarelli LR, Scoffone VC, Trespidi G, Barbieri G, Riabova O, Monakhova N, Porta A, Manina G, Riccardi G, Makarov V, Buroni S. Chemical, Metabolic, and Cellular Characterization of a FtsZ Inhibitor Effective Against Burkholderia cenocepacia. Front Microbiol 2020; 11:562. [PMID: 32318042 PMCID: PMC7154053 DOI: 10.3389/fmicb.2020.00562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/16/2020] [Indexed: 12/02/2022] Open
Abstract
There is an urgent need for new antimicrobials to treat the opportunistic Gram-negative Burkholderia cenocepacia, which represents a problematic challenge for cystic fibrosis patients. Recently, a benzothiadiazole derivative, C109, was shown to be effective against the infections caused by B. cenocepacia and other Gram-negative and-positive bacteria. C109 has a promising cellular target, the cell division protein FtsZ, and a recently developed PEGylated formulation make it an attractive molecule to counteract Burkholderia infections. However, the ability of efflux pumps to extrude it out of the cell represents a limitation for its use. Here, more than 50 derivatives of C109 were synthesized and tested against Gram-negative species and the Gram-positive Staphylococcus aureus. In addition, their activity was evaluated on the purified FtsZ protein. The chemical, metabolic and cellular stability of C109 has been assayed using different biological systems, including quantitative single-cell imaging. However, no further improvement on C109 was achieved, and the role of efflux in resistance was further confirmed. Also, a novel nitroreductase that can inactivate the compound was characterized, but it does not appear to play a role in natural resistance. All these data allowed a deep characterization of the compound, which will contribute to a further improvement of its properties.
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Affiliation(s)
- Laurent R Chiarelli
- Laboratory of Molecular Microbiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Viola Camilla Scoffone
- Laboratory of Molecular Microbiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Gabriele Trespidi
- Laboratory of Molecular Microbiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Giulia Barbieri
- Laboratory of Molecular Microbiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Olga Riabova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Natalia Monakhova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Alessio Porta
- Organic Chemistry Section, Department of Chemistry, University of Pavia, Pavia, Italy
| | - Giulia Manina
- Microbial Individuality and Infection Group, Cell Biology and Infection Department, Institut Pasteur, Paris, France
| | - Giovanna Riccardi
- Laboratory of Molecular Microbiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Vadim Makarov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Silvia Buroni
- Laboratory of Molecular Microbiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
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18
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Mori G, Orena BS, Chiarelli LR, Degiacomi G, Riabova O, Sammartino JC, Makarov V, Riccardi G, Pasca MR. Rv0579 Is Involved in the Resistance to the TP053 Antitubercular Prodrug. Front Microbiol 2020; 11:292. [PMID: 32158439 PMCID: PMC7052010 DOI: 10.3389/fmicb.2020.00292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/10/2020] [Indexed: 11/25/2022] Open
Abstract
Tuberculosis remains one of the leading causes of death from a single pathogen globally. It is estimated that 1/4 of the world’s population harbors latent tuberculosis, but only a 5–10% of patients will develop active disease. During latent infection, Mycobacterium tuberculosis can persist unaffected by drugs for years in a non-replicating state with low metabolic activity. The rate of the successful tuberculosis treatment is curbed by the presence of these non-replicating bacilli that can resuscitate after decades and also by the spread of M. tuberculosis drug-resistant strains. International agencies, including the World Health Organization, urge the international community to combat this global health emergency. The thienopyrimidine TP053 is a promising new antitubercular lead compound highly active against both replicating and non-replicating M. tuberculosis cells, with an in vitro MIC of 0.125 μg/ml. TP053 is a prodrug activated by the reduced form of the mycothiol-dependent reductase Mrx2, encoded by Rv2466c gene. After its activation, TP053 releases nitric oxide and a highly reactive metabolite, explaining its activity also against M. tuberculosis non-replicating cells. In this work, a new mechanism of TP053 resistance was discovered. M. tuberculosis spontaneous mutants resistant to TP053 were isolated harboring the mutation L240V in Rv0579, a protein with unknown function, but without mutation in Rv2466c gene. Recombineering method demonstrated that this mutation is linked to TP053 resistance. To better characterize Rv0579, the protein was recombinantly produced in Escherichia coli and a direct interaction between the Mrx2 activated TP053 and Rv0579 was shown by an innovative target-fishing experiment based on click chemistry. Thanks to achieved results, a possible contribution of Rv0579 in M. tuberculosis RNA metabolism was hypothesized, linked to toxin anti-toxin system. Overall, these data confirm the role of Rv0579 in TP053 resistance and consequently in the metabolism of this prodrug.
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Affiliation(s)
- Giorgia Mori
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Beatrice Silvia Orena
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Giulia Degiacomi
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Olga Riabova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - José Camilla Sammartino
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Vadim Makarov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Giovanna Riccardi
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
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19
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Chiarelli LR, Salina EG, Mori G, Azhikina T, Riabova O, Lepioshkin A, Grigorov A, Forbak M, Madacki J, Orena BS, Manfredi M, Gosetti F, Buzzi A, Degiacomi G, Sammartino JC, Marengo E, Korduláková J, Riccardi G, Mikušová K, Makarov V, Pasca MR. New Insights into the Mechanism of Action of the Thienopyrimidine Antitubercular Prodrug TP053. ACS Infect Dis 2020; 6:313-323. [PMID: 31729215 DOI: 10.1021/acsinfecdis.9b00388] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The thienopyrimidine TP053 is an antitubercular prodrug active against both replicating and nonreplicating Mycobacterium tuberculosis (M. tuberculosis) cells, which requires activation by the mycothiol-dependent nitroreductase Mrx2. The investigation of the mechanism of action of TP053 revealed that Mrx2 releases nitric oxide from this drug both in the enzyme assays with purified Mrx2 and in mycobacterial cultures, which can explain its activity against nonreplicating bacilli, similar to pretomanid activated by the nitroreductase Ddn. In addition, we identified a highly reactive metabolite, 2-(4-mercapto-6-(methylamino)-2-phenylpyrimidin-5-yl)ethan-1-ol, which can contribute to the antimycobacterial effects on replicating cells as well as on nonreplicating cells. In summary, we explain the mechanism of action of TP053 on both replicating and nonreplicating M. tuberculosis and report a novel activity for Mrx2, which in addition to Ddn, represents another example of nitroreductase releasing nitric oxide from its substrate. These findings are particularly relevant in the context of drugs targeting nonreplicating M. tuberculosis, which is shown to be killed by increased levels of nitric oxide.
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Affiliation(s)
- Laurent R. Chiarelli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Elena G. Salina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospekt 33-2, Moscow 119071, Russia
| | - Giorgia Mori
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Tatyana Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Street, Moscow 117997, Russia
| | - Olga Riabova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospekt 33-2, Moscow 119071, Russia
| | - Alexander Lepioshkin
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospekt 33-2, Moscow 119071, Russia
| | - Artem Grigorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Street, Moscow 117997, Russia
| | - Martin Forbak
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, CH1, Bratislava SK-842 15, Slovakia
| | - Jan Madacki
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, CH1, Bratislava SK-842 15, Slovakia
| | - Beatrice Silvia Orena
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Marcello Manfredi
- Department of Translational Medicine, Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, Corso Trieste 15, Novara 28100, Italy
- ISALIT, Spin-off of Department of Sciences and Technological Innovation, Via A. Canobio 4/6, Novara 28100, Italy
| | - Fabio Gosetti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Teresa Michel 11, Alessandria 15121, Italy
| | - Arianna Buzzi
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Teresa Michel 11, Alessandria 15121, Italy
| | - Giulia Degiacomi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - José Camilla Sammartino
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Teresa Michel 11, Alessandria 15121, Italy
| | - Jana Korduláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, CH1, Bratislava SK-842 15, Slovakia
| | - Giovanna Riccardi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, CH1, Bratislava SK-842 15, Slovakia
| | - Vadim Makarov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospekt 33-2, Moscow 119071, Russia
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
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20
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Buroni S, Makarov V, Scoffone VC, Trespidi G, Riccardi G, Chiarelli LR. The cell division protein FtsZ as a cellular target to hit cystic fibrosis pathogens. Eur J Med Chem 2020; 190:112132. [PMID: 32066012 DOI: 10.1016/j.ejmech.2020.112132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 11/25/2022]
Abstract
Cystic fibrosis is a rare genetic disease characterized by the production of dehydrated mucus in the lung able to trap bacteria and rendering their proliferation particularly dangerous, thus leading to chronic infections. Among these bacteria, Staphylococcus aureus and Pseudomonas aeruginosa play a major role while, within emerging pathogens, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Burkholderia cepacia complex species, as well as non-tuberculous mycobacteria are listed. Since a common feature of these bacteria is the high level of drug resistance, cell division, and in particular FtsZ, has been explored as a novel therapeutic target for the design of new molecules with antibacterial properties. This review summarizes and provides insight into recent advances in the discovery of compounds targeting FtsZ: the majority of them exhibit anti-staphylococcal activity, while a few were directed against the cystic fibrosis Gram negative pathogens.
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Affiliation(s)
- Silvia Buroni
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Vadim Makarov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Viola Camilla Scoffone
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Gabriele Trespidi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Giovanna Riccardi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.
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21
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Costabile G, Provenzano R, Azzalin A, Scoffone VC, Chiarelli LR, Rondelli V, Grillo I, Zinn T, Lepioshkin A, Savina S, Miro A, Quaglia F, Makarov V, Coenye T, Brocca P, Riccardi G, Buroni S, Ungaro F. PEGylated mucus-penetrating nanocrystals for lung delivery of a new FtsZ inhibitor against Burkholderia cenocepacia infection. Nanomedicine 2019; 23:102113. [PMID: 31669084 DOI: 10.1016/j.nano.2019.102113] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/16/2019] [Accepted: 10/05/2019] [Indexed: 01/15/2023]
Abstract
C109 is a potent but poorly soluble FtsZ inhibitor displaying promising activity against Burkholderia cenocepacia, a high-risk pathogen for cystic fibrosis (CF) sufferers. To harness C109 for inhalation, we developed nanocrystal-embedded dry powders for inhalation suspension consisting in C109 nanocrystals stabilized with D-α-tocopheryl polyethylene glycol 1000 succinate (TPGS) embedded in hydroxypropyl-β-cyclodextrin (CD). The powders could be safely re-dispersed in water for in vitro aerosolization. Owing to the presence of a PEG shell, the rod shape and the peculiar aspect ratio, C109 nanocrystals were able to diffuse through artificial CF mucus. The promising technological features were completed by encouraging in vitro/in vivo effects. The formulations displayed no toxicity towards human bronchial epithelial cells and were active against planktonic and sessile B. cenocepacia strains. The efficacy of C109 nanosuspensions in combination with piperacillin was confirmed in a Galleria mellonella infection model, strengthening their potential for combined therapy of B. cenocepacia lung infections.
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Affiliation(s)
| | - Romina Provenzano
- Department of Pharmacy, University of Napoli "Federico II", Napoli, Italy
| | - Alberto Azzalin
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Viola Camilla Scoffone
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Valeria Rondelli
- Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, Segrate, (MI), Italy
| | | | - Thomas Zinn
- ESRF-The European Synchrotron, Grenoble, France
| | - Alexander Lepioshkin
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Svetlana Savina
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Agnese Miro
- Department of Pharmacy, University of Napoli "Federico II", Napoli, Italy
| | - Fabiana Quaglia
- Department of Pharmacy, University of Napoli "Federico II", Napoli, Italy
| | - Vadim Makarov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Paola Brocca
- Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, Segrate, (MI), Italy
| | - Giovanna Riccardi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Silvia Buroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy.
| | - Francesca Ungaro
- Department of Pharmacy, University of Napoli "Federico II", Napoli, Italy.
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22
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Chiarelli LR, Mori M, Beretta G, Gelain A, Pini E, Sammartino JC, Stelitano G, Barlocco D, Costantino L, Lapillo M, Poli G, Caligiuri I, Rizzolio F, Bellinzoni M, Tuccinardi T, Villa S, Meneghetti F. New insight into structure-activity of furan-based salicylate synthase (MbtI) inhibitors as potential antitubercular agents. J Enzyme Inhib Med Chem 2019; 34:823-828. [PMID: 30889995 PMCID: PMC6427685 DOI: 10.1080/14756366.2019.1589462] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Starting from the analysis of the hypothetical binding mode of our previous furan-based hit (I), we successfully achieved our objective to replace the nitro moiety, leading to the disclosure of a new lead exhibiting a strong activity against MbtI. Our best candidate 1 h displayed a Ki of 8.8 µM and its antimycobacterial activity (MIC99 = 250 µM) is conceivably related to mycobactin biosynthesis inhibition. These results support the hypothesis that 5-phenylfuran-2-carboxylic derivatives are a promising class of MbtI inhibitors.
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Affiliation(s)
- Laurent R Chiarelli
- a Department of Biology and Biotechnology "L Spallanzani" , University of Pavia , Pavia , Italy
| | - Matteo Mori
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Giangiacomo Beretta
- c Department of Environmental Science and Policy , University of Milano , Milano , Italy
| | - Arianna Gelain
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Elena Pini
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Josè Camilla Sammartino
- a Department of Biology and Biotechnology "L Spallanzani" , University of Pavia , Pavia , Italy
| | - Giovanni Stelitano
- a Department of Biology and Biotechnology "L Spallanzani" , University of Pavia , Pavia , Italy
| | - Daniela Barlocco
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Luca Costantino
- d Department of Life Sciences , University of Modena e Reggio Emilia , Modena , Italy
| | | | - Giulio Poli
- e Department of Pharmacy , University of Pisa , Pisa , Italy
| | - Isabella Caligiuri
- f Pathology Unit, Department of Molecular Biology and Translational Research , National Cancer Institute and Center for Molecular Biomedicine , Aviano , Italy
| | - Flavio Rizzolio
- f Pathology Unit, Department of Molecular Biology and Translational Research , National Cancer Institute and Center for Molecular Biomedicine , Aviano , Italy.,g Department of Molecular Science and Nanosystems , Ca' Foscari University of Venezia , Venezia-Mestre , Italy
| | | | | | - Stefania Villa
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Fiorella Meneghetti
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
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23
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Buroni S, Scoffone VC, Fumagalli M, Makarov V, Cagnone M, Trespidi G, De Rossi E, Forneris F, Riccardi G, Chiarelli LR. Investigating the Mechanism of Action of Diketopiperazines Inhibitors of the Burkholderia cenocepacia Quorum Sensing Synthase CepI: A Site-Directed Mutagenesis Study. Front Pharmacol 2018; 9:836. [PMID: 30108505 PMCID: PMC6079302 DOI: 10.3389/fphar.2018.00836] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/11/2018] [Indexed: 12/24/2022] Open
Abstract
Quorum sensing (QS) is a bacterial intercellular communication process which controls the production of major virulence factors, such as proteases, siderophores, and toxins, as well as biofilm formation. Since the inhibition of this pathway reduces bacterial virulence, QS is considered a valuable candidate drug target, particularly for the treatment of opportunistic infections, such as those caused by Burkholderia cenocepacia in cystic fibrosis patients. Diketopiperazine inhibitors of the acyl homoserine lactone synthase CepI have been recently described. These compounds are able to impair the ability of B. cenocepacia to produce proteases, siderophores, and to form biofilm, being also active in a Caenorhabditis elegans infection model. However, the precise mechanism of action of the compounds, as well as their effect on the cell metabolism, fundamental for candidate drug optimization, are still not completely defined. Here, we performed a proteomic analysis of B. cenocepacia cells treated with one of these inhibitors, and compared it with a cepI deleted strain. Our results demonstrate that the effects of the compound are similar to the deletion of cepI, clearly confirming that these molecules function as inhibitors of the acyl homoserine lactone synthase. Moreover, to deepen our knowledge about the binding mechanisms of the compound to CepI, we exploited previously published in silico structural insights about this enzyme structure and validated different candidate binding pockets on the enzyme surface using site-directed mutagenesis and biochemical analyses. Our experiments identified a region near the predicted S-adenosylmethionine binding site critically involved in interactions with the inhibitor. These results could be useful for future structure-based optimization of these CepI inhibitors.
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Affiliation(s)
- Silvia Buroni
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Viola C Scoffone
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Vadim Makarov
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | | | - Gabriele Trespidi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Edda De Rossi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Federico Forneris
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Giovanna Riccardi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
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24
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Chiarelli LR, Mori M, Barlocco D, Beretta G, Gelain A, Pini E, Porcino M, Mori G, Stelitano G, Costantino L, Lapillo M, Bonanni D, Poli G, Tuccinardi T, Villa S, Meneghetti F. Discovery and development of novel salicylate synthase (MbtI) furanic inhibitors as antitubercular agents. Eur J Med Chem 2018; 155:754-763. [PMID: 29940465 DOI: 10.1016/j.ejmech.2018.06.033] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/05/2018] [Accepted: 06/13/2018] [Indexed: 01/10/2023]
Abstract
We report on the virtual screening, synthesis, and biological evaluation of new furan derivatives targeting Mycobacterium tuberculosis salicylate synthase (MbtI). A receptor-based virtual screening procedure was applied to screen the Enamine database, identifying two compounds, I and III, endowed with a good enzyme inhibitory activity. Considering the most active compound I as starting point for the development of novel MbtI inhibitors, we obtained new derivatives based on the furan scaffold. Among the SAR performed on this class, compound 1a emerged as the most potent MbtI inhibitor reported to date (Ki = 5.3 μM). Moreover, compound 1a showed a promising antimycobacterial activity (MIC99 = 156 μM), which is conceivably related to mycobactin biosynthesis inhibition.
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Affiliation(s)
- Laurent R Chiarelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Daniela Barlocco
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giangiacomo Beretta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Elena Pini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Marianna Porcino
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giorgia Mori
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Giovanni Stelitano
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Luca Costantino
- Dipartimento Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via Campi 103, 41121, Modena, Italy
| | - Margherita Lapillo
- Dipartimento di Farmacia, Università di Pisa, via Bonanno 6, 56126, Pisa, Italy
| | - Davide Bonanni
- Dipartimento di Farmacia, Università di Pisa, via Bonanno 6, 56126, Pisa, Italy
| | - Giulio Poli
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, 53100, Siena, Italy
| | - Tiziano Tuccinardi
- Dipartimento di Farmacia, Università di Pisa, via Bonanno 6, 56126, Pisa, Italy.
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy.
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
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25
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Scoffone VC, Chiarelli LR, Trespidi G, Mentasti M, Riccardi G, Buroni S. Burkholderia cenocepacia Infections in Cystic Fibrosis Patients: Drug Resistance and Therapeutic Approaches. Front Microbiol 2017; 8:1592. [PMID: 28878751 PMCID: PMC5572248 DOI: 10.3389/fmicb.2017.01592] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/04/2017] [Indexed: 12/29/2022] Open
Abstract
Burkholderia cenocepacia is an opportunistic pathogen particularly dangerous for cystic fibrosis (CF) patients. It can cause a severe decline in CF lung function possibly developing into a life-threatening systemic infection known as cepacia syndrome. Antibiotic resistance and presence of numerous virulence determinants in the genome make B. cenocepacia extremely difficult to treat. Better understanding of its resistance profiles and mechanisms is crucial to improve management of these infections. Here, we present the clinical distribution of B. cenocepacia described in the last 6 years and methods for identification and classification of epidemic strains. We also detail new antibiotics, clinical trials, and alternative approaches reported in the literature in the last 5 years to tackle B. cenocepacia resistance issue. All together these findings point out the urgent need of new and alternative therapies to improve CF patients’ life expectancy.
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Affiliation(s)
- Viola C Scoffone
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
| | | | - Gabriele Trespidi
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
| | - Massimo Mentasti
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health EnglandLondon, United Kingdom.,Department of Microbiology, Royal Cornwall HospitalTruro, United Kingdom
| | - Giovanna Riccardi
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
| | - Silvia Buroni
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
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26
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Esposito M, Szadocka S, Degiacomi G, Orena BS, Mori G, Piano V, Boldrin F, Zemanová J, Huszár S, Barros D, Ekins S, Lelièvre J, Manganelli R, Mattevi A, Pasca MR, Riccardi G, Ballell L, Mikušová K, Chiarelli LR. A Phenotypic Based Target Screening Approach Delivers New Antitubercular CTP Synthetase Inhibitors. ACS Infect Dis 2017; 3:428-437. [PMID: 28475832 DOI: 10.1021/acsinfecdis.7b00006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite its great potential, the target-based approach has been mostly unsuccessful in tuberculosis drug discovery, while whole cell phenotypic screening has delivered several active compounds. However, for many of these hits, the cellular target has not yet been identified, thus preventing further target-based optimization of the compounds. In this context, the newly validated drug target CTP synthetase PyrG was exploited to assess a target-based approach of already known, but untargeted, antimycobacterial compounds. To this purpose the publically available GlaxoSmithKline antimycobacterial compound set was assayed, uncovering a series of 4-(pyridin-2-yl)thiazole derivatives which efficiently inhibit the Mycobacterium tuberculosis PyrG enzyme activity, one of them showing low activity against the human CTP synthetase. The three best compounds were ATP binding site competitive inhibitors, with Ki values ranging from 3 to 20 μM, but did not show any activity against a small panel of different prokaryotic and eukaryotic kinases, thus demonstrating specificity for the CTP synthetases. Metabolic labeling experiments demonstrated that the compounds directly interfere not only with CTP biosynthesis, but also with other CTP dependent biochemical pathways, such as lipid biosynthesis. Moreover, using a M. tuberculosis pyrG conditional knock-down strain, it was shown that the activity of two compounds is dependent on the intracellular concentration of the CTP synthetase. All these results strongly suggest a role of PyrG as a target of these compounds, thus strengthening the value of this kind of approach for the identification of new scaffolds for drug development.
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Affiliation(s)
- Marta Esposito
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Sára Szadocka
- Department
of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina CH1, 84215 Bratislava, Slovakia
| | - Giulia Degiacomi
- Department
of Molecular Medicine, University of Padova, via Gabelli 63, 35121 Padova, Italy
| | - Beatrice S. Orena
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Giorgia Mori
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Valentina Piano
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Francesca Boldrin
- Department
of Molecular Medicine, University of Padova, via Gabelli 63, 35121 Padova, Italy
| | - Júlia Zemanová
- Department
of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina CH1, 84215 Bratislava, Slovakia
| | - Stanislav Huszár
- Department
of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina CH1, 84215 Bratislava, Slovakia
| | - David Barros
- Diseases
of the Developing World, GlaxoSmithKline, Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Sean Ekins
- Collaborative Drug Discovery Inc., 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, United States
| | - Joel Lelièvre
- Diseases
of the Developing World, GlaxoSmithKline, Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Riccardo Manganelli
- Department
of Molecular Medicine, University of Padova, via Gabelli 63, 35121 Padova, Italy
| | - Andrea Mattevi
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Maria Rosalia Pasca
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Giovanna Riccardi
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Lluis Ballell
- Diseases
of the Developing World, GlaxoSmithKline, Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Katarína Mikušová
- Department
of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina CH1, 84215 Bratislava, Slovakia
| | - Laurent R. Chiarelli
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
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27
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Spadaro F, Scoffone VC, Chiarelli LR, Fumagalli M, Buroni S, Riccardi G, Forneris F. The Crystal Structure of Burkholderia cenocepacia DfsA Provides Insights into Substrate Recognition and Quorum Sensing Fatty Acid Biosynthesis. Biochemistry 2016; 55:3241-50. [PMID: 27198181 DOI: 10.1021/acs.biochem.6b00178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Burkholderia cenocepacia is a major concern among respiratory tract infections in cystic fibrosis patients. This pathogen is particularly difficult to treat because of its high level of resistance to the clinically relevant antimicrobial agents. In B. cenocepacia, the quorum sensing cell-cell communication system is involved in different processes that are important for bacterial virulence, such as biofilm formation and protease and siderophore production. Targeting the enzymes involved in this process represents a promising therapeutic approach. With the aim of finding effective quorum sensing inhibitors, we have determined the three-dimensional structure of B. cenocepacia diffusible factor synthase A, DfsA. This bifunctional crotonase (dehydratase/thioesterase) produces the characteristic quorum sensing molecule of B. cenocepacia, cis-2-dodecenoic acid or BDSF, starting from 3-hydroxydodecanoyl-acyl carrier protein. Unexpectedly, the crystal structure revealed the presence of a lipid molecule in the catalytic site of the enzyme, which was identified as dodecanoic acid. Our biochemical characterization shows that DfsA is able to use dodecanoyl-acyl carrier protein as a substrate, demonstrating that dodecanoic acid, the product of this reaction, is released very slowly from the DfsA active site, therefore acting as a DfsA inhibitor. This molecule shows an unprecedented conformational arrangement inside the DfsA active site. In contrast with previous hypotheses, our data illustrate how DfsA and closely related homologous enzymes can recognize long hydrophobic substrates without large conformational changes or assistance by additional regulator molecules. The elucidation of the substrate binding mode in DfsA provides the starting point for structure-based drug discovery studies targeting B. cenocepacia quorum sensing-assisted virulence.
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Affiliation(s)
- Francesca Spadaro
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia , Via Ferrata 9/A, 27100 Pavia, Italy
| | - Viola C Scoffone
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia , Via Ferrata 9/A, 27100 Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia , Via Ferrata 9/A, 27100 Pavia, Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia , Via Ferrata 9/A, 27100 Pavia, Italy
| | - Silvia Buroni
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia , Via Ferrata 9/A, 27100 Pavia, Italy
| | - Giovanna Riccardi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia , Via Ferrata 9/A, 27100 Pavia, Italy
| | - Federico Forneris
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia , Via Ferrata 9/A, 27100 Pavia, Italy
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28
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Tiwari R, Miller PA, Chiarelli LR, Mori G, Šarkan M, Centárová I, Cho S, Mikušová K, Franzblau SG, Oliver AG, Miller MJ. Design, Syntheses, and Anti-TB Activity of 1,3-Benzothiazinone Azide and Click Chemistry Products Inspired by BTZ043. ACS Med Chem Lett 2016; 7:266-70. [PMID: 26985313 DOI: 10.1021/acsmedchemlett.5b00424] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/03/2016] [Indexed: 11/28/2022] Open
Abstract
Electron deficient nitroaromatic compounds such as BTZ043 and its closest congener, PBTZ169, and related agents are a promising new class of anti-TB compounds. Herein we report the design and syntheses of 1,3-benzothiazinone azide (BTZ-N3) and related click chemistry products based on the molecular mode of activation of BTZ043. Our computational docking studies indicate that BTZ-N3 binds in the essentially same pocket as that of BTZ043. Detailed biochemical studies with cell envelope enzyme fractions of Mycobacterium smegmatis combined with our model biochemical reactivity studies with nucleophiles indicated that, in contrast to BTZ043, the azide analogue may have a different mode of activation for anti-TB activity. Subsequent enzymatic studies with recombinant DprE1 from Mtb followed by MIC determination in NTB1 strain of Mtb (harboring Cys387Ser mutation in DprE1 and is BTZ043 resistant) unequivocally indicated that BTZ-N3 is an effective reversible and noncovalent inhibitor of DprE1.
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Affiliation(s)
- Rohit Tiwari
- Department
of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland
Science Hall, Notre Dame, Indiana 46556, United States
| | - Patricia A. Miller
- Department
of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland
Science Hall, Notre Dame, Indiana 46556, United States
| | - Laurent R. Chiarelli
- Department
of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Giorgia Mori
- Department
of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Michal Šarkan
- Department
of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Ivana Centárová
- Department
of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Sanghyun Cho
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Katarína Mikušová
- Department
of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Scott G. Franzblau
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Allen G. Oliver
- Department
of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland
Science Hall, Notre Dame, Indiana 46556, United States
| | - Marvin J. Miller
- Department
of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland
Science Hall, Notre Dame, Indiana 46556, United States
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29
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Albesa-Jové D, Comino N, Tersa M, Mohorko E, Urresti S, Dainese E, Chiarelli LR, Pasca MR, Manganelli R, Makarov V, Riccardi G, Svergun DI, Glockshuber R, Guerin ME. The Redox State Regulates the Conformation of Rv2466c to Activate the Antitubercular Prodrug TP053. J Biol Chem 2015; 290:31077-89. [PMID: 26546681 DOI: 10.1074/jbc.m115.677039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 11/06/2022] Open
Abstract
Rv2466c is a key oxidoreductase that mediates the reductive activation of TP053, a thienopyrimidine derivative that kills replicating and non-replicating Mycobacterium tuberculosis, but whose mode of action remains enigmatic. Rv2466c is a homodimer in which each subunit displays a modular architecture comprising a canonical thioredoxin-fold with a Cys(19)-Pro(20)-Trp(21)-Cys(22) motif, and an insertion consisting of a four α-helical bundle and a short α-helical hairpin. Strong evidence is provided for dramatic conformational changes during the Rv2466c redox cycle, which are essential for TP053 activity. Strikingly, a new crystal structure of the reduced form of Rv2466c revealed the binding of a C-terminal extension in α-helical conformation to a pocket next to the active site cysteine pair at the interface between the thioredoxin domain and the helical insertion domain. The ab initio low-resolution envelopes obtained from small angle x-ray scattering showed that the fully reduced form of Rv2466c adopts a "closed" compact conformation in solution, similar to that observed in the crystal structure. In contrast, the oxidized form of Rv2466c displays an "open" conformation, where tertiary structural changes in the α-helical subdomain suffice to account for the observed conformational transitions. Altogether our structural, biochemical, and biophysical data strongly support a model in which the formation of the catalytic disulfide bond upon TP053 reduction triggers local structural changes that open the substrate binding site of Rv2466c allowing the release of the activated, reduced form of TP053. Our studies suggest that similar structural changes might have a functional role in other members of the thioredoxin-fold superfamily.
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Affiliation(s)
- David Albesa-Jové
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain, the IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Natalia Comino
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Montse Tersa
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Elisabeth Mohorko
- the Institute for Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Saioa Urresti
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | | | - Laurent R Chiarelli
- Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Maria Rosalia Pasca
- Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | | | - Vadim Makarov
- the A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia, and
| | - Giovanna Riccardi
- Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Dmitri I Svergun
- the European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, D-22603 Hamburg, Germany
| | - Rudi Glockshuber
- the Institute for Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Marcelo E Guerin
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain, the IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain,
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30
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Mori G, Chiarelli LR, Esposito M, Makarov V, Bellinzoni M, Hartkoorn RC, Degiacomi G, Boldrin F, Ekins S, de Jesus Lopes Ribeiro AL, Marino LB, Centárová I, Svetlíková Z, Blaško J, Kazakova E, Lepioshkin A, Barilone N, Zanoni G, Porta A, Fondi M, Fani R, Baulard AR, Mikušová K, Alzari PM, Manganelli R, de Carvalho LPS, Riccardi G, Cole ST, Pasca MR. Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG. ACTA ACUST UNITED AC 2015; 22:917-27. [PMID: 26097035 PMCID: PMC4521081 DOI: 10.1016/j.chembiol.2015.05.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/25/2015] [Accepted: 05/30/2015] [Indexed: 11/06/2022]
Abstract
To combat the emergence of drug-resistant strains of Mycobacterium tuberculosis, new antitubercular agents and novel drug targets are needed. Phenotypic screening of a library of 594 hit compounds uncovered two leads that were active against M. tuberculosis in its replicating, non-replicating, and intracellular states: compounds 7947882 (5-methyl-N-(4-nitrophenyl)thiophene-2-carboxamide) and 7904688 (3-phenyl-N-[(4-piperidin-1-ylphenyl)carbamothioyl]propanamide). Mutants resistant to both compounds harbored mutations in ethA (rv3854c), the gene encoding the monooxygenase EthA, and/or in pyrG (rv1699) coding for the CTP synthetase, PyrG. Biochemical investigations demonstrated that EthA is responsible for the activation of the compounds, and by mass spectrometry we identified the active metabolite of 7947882, which directly inhibits PyrG activity. Metabolomic studies revealed that pharmacological inhibition of PyrG strongly perturbs DNA and RNA biosynthesis, and other metabolic processes requiring nucleotides. Finally, the crystal structure of PyrG was solved, paving the way for rational drug design with this newly validated drug target. Two compounds activated by EthA kill M. tuberculosis through PyrG inhibition EthA metabolite is active against PyrG and M. tuberculosis growth Definition of the mechanism of activation and validation of PyrG as a new drug target
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Affiliation(s)
- Giorgia Mori
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Marta Esposito
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Vadim Makarov
- A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Marco Bellinzoni
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Université Paris Diderot, Sorbonne Paris Cité, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Ruben C Hartkoorn
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Giulia Degiacomi
- Department of Molecular Medicine, University of Padova, 35128 Padua, Italy
| | - Francesca Boldrin
- Department of Molecular Medicine, University of Padova, 35128 Padua, Italy
| | - Sean Ekins
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010, USA
| | | | - Leonardo B Marino
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK; Faculty of Pharmaceutical Sciences, UNESP - Univ Estadual Paulista, Araraquara, São Paulo 14801-902, Brazil
| | - Ivana Centárová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Zuzana Svetlíková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Jaroslav Blaško
- Institute of Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovak Republic
| | - Elena Kazakova
- A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Alexander Lepioshkin
- A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Nathalie Barilone
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Université Paris Diderot, Sorbonne Paris Cité, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Giuseppe Zanoni
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Alessio Porta
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, Florence 50019, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Sesto Fiorentino, Florence 50019, Italy
| | - Alain R Baulard
- Institut Pasteur de Lille, Center for Infection and Immunity, 59019 Lille, France
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Pedro M Alzari
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Université Paris Diderot, Sorbonne Paris Cité, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | | | | | - Giovanna Riccardi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland.
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy.
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31
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Neres J, Hartkoorn RC, Chiarelli LR, Gadupudi R, Pasca MR, Mori G, Venturelli A, Savina S, Makarov V, Kolly GS, Molteni E, Binda C, Dhar N, Ferrari S, Brodin P, Delorme V, Landry V, de Jesus Lopes Ribeiro AL, Farina D, Saxena P, Pojer F, Carta A, Luciani R, Porta A, Zanoni G, De Rossi E, Costi MP, Riccardi G, Cole ST. 2-Carboxyquinoxalines kill mycobacterium tuberculosis through noncovalent inhibition of DprE1. ACS Chem Biol 2015; 10:705-14. [PMID: 25427196 DOI: 10.1021/cb5007163] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phenotypic screening of a quinoxaline library against replicating Mycobacterium tuberculosis led to the identification of lead compound Ty38c (3-((4-methoxybenzyl)amino)-6-(trifluoromethyl)quinoxaline-2-carboxylic acid). With an MIC99 and MBC of 3.1 μM, Ty38c is bactericidal and active against intracellular bacteria. To investigate its mechanism of action, we isolated mutants resistant to Ty38c and sequenced their genomes. Mutations were found in rv3405c, coding for the transcriptional repressor of the divergently expressed rv3406 gene. Biochemical studies clearly showed that Rv3406 decarboxylates Ty38c into its inactive keto metabolite. The actual target was then identified by isolating Ty38c-resistant mutants of an M. tuberculosis strain lacking rv3406. Here, mutations were found in dprE1, encoding the decaprenylphosphoryl-d-ribose oxidase DprE1, essential for biogenesis of the mycobacterial cell wall. Genetics, biochemical validation, and X-ray crystallography revealed Ty38c to be a noncovalent, noncompetitive DprE1 inhibitor. Structure-activity relationship studies generated a family of DprE1 inhibitors with a range of IC50's and bactericidal activity. Co-crystal structures of DprE1 in complex with eight different quinoxaline analogs provided a high-resolution interaction map of the active site of this extremely vulnerable target in M. tuberculosis.
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Affiliation(s)
- João Neres
- More Medicines for Tuberculosis (MM4TB) Consortium
- Global
Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ruben C. Hartkoorn
- More Medicines for Tuberculosis (MM4TB) Consortium
- Global
Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Laurent R. Chiarelli
- More Medicines for Tuberculosis (MM4TB) Consortium
- Department
of Biology and Biotecnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Ramakrishna Gadupudi
- Tydock Pharma, srl Via Campi
183, 41125 Modena, Italy
- Department
of Life Sciences, University of Modena and Reggio Emilia, Via Campi
183, 41126 Modena, Italy
| | - Maria Rosalia Pasca
- More Medicines for Tuberculosis (MM4TB) Consortium
- Department
of Biology and Biotecnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Giorgia Mori
- More Medicines for Tuberculosis (MM4TB) Consortium
- Department
of Biology and Biotecnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | | | - Svetlana Savina
- More Medicines for Tuberculosis (MM4TB) Consortium
- A. N. Bakh
Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Vadim Makarov
- More Medicines for Tuberculosis (MM4TB) Consortium
- A. N. Bakh
Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Gaelle S. Kolly
- More Medicines for Tuberculosis (MM4TB) Consortium
- Global
Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Elisabetta Molteni
- More Medicines for Tuberculosis (MM4TB) Consortium
- Department
of Biology and Biotecnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Claudia Binda
- More Medicines for Tuberculosis (MM4TB) Consortium
- Department
of Biology and Biotecnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Neeraj Dhar
- More Medicines for Tuberculosis (MM4TB) Consortium
- Global
Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Stefania Ferrari
- Tydock Pharma, srl Via Campi
183, 41125 Modena, Italy
- Department
of Life Sciences, University of Modena and Reggio Emilia, Via Campi
183, 41126 Modena, Italy
| | - Priscille Brodin
- More Medicines for Tuberculosis (MM4TB) Consortium
- Inserm
U1019 − CNRS UMR 8204, Institut Pasteur de Lille, Université de Lille, 1 rue du Professeur Calmette, 59019, Lille, France
| | - Vincent Delorme
- More Medicines for Tuberculosis (MM4TB) Consortium
- Inserm
U1019 − CNRS UMR 8204, Institut Pasteur de Lille, Université de Lille, 1 rue du Professeur Calmette, 59019, Lille, France
| | - Valérie Landry
- Inserm
U1019 − CNRS UMR 8204, Institut Pasteur de Lille, Université de Lille, 1 rue du Professeur Calmette, 59019, Lille, France
| | | | - Davide Farina
- Department
of Life Sciences, University of Modena and Reggio Emilia, Via Campi
183, 41126 Modena, Italy
| | - Puneet Saxena
- Department
of Life Sciences, University of Modena and Reggio Emilia, Via Campi
183, 41126 Modena, Italy
| | - Florence Pojer
- More Medicines for Tuberculosis (MM4TB) Consortium
- Global
Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Antonio Carta
- Department
of Chemistry and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Rosaria Luciani
- Department
of Life Sciences, University of Modena and Reggio Emilia, Via Campi
183, 41126 Modena, Italy
| | - Alessio Porta
- Department
of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Giuseppe Zanoni
- Department
of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Edda De Rossi
- More Medicines for Tuberculosis (MM4TB) Consortium
- Department
of Biology and Biotecnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Maria Paola Costi
- More Medicines for Tuberculosis (MM4TB) Consortium
- Tydock Pharma, srl Via Campi
183, 41125 Modena, Italy
- Department
of Life Sciences, University of Modena and Reggio Emilia, Via Campi
183, 41126 Modena, Italy
| | - Giovanna Riccardi
- More Medicines for Tuberculosis (MM4TB) Consortium
- Department
of Biology and Biotecnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Stewart T. Cole
- More Medicines for Tuberculosis (MM4TB) Consortium
- Global
Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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32
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Maggi M, Chiarelli LR, Valentini G, Scotti C. Engineering of Helicobacter pylori L-asparaginase: characterization of two functionally distinct groups of mutants. PLoS One 2015; 10:e0117025. [PMID: 25664771 PMCID: PMC4321988 DOI: 10.1371/journal.pone.0117025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/18/2014] [Indexed: 01/19/2023] Open
Abstract
Bacterial L-asparaginases have been used as anti-cancer drugs for over 4 decades though presenting, along with their therapeutic efficacy, several side effects due to their bacterial origin and, seemingly, to their secondary glutaminase activity. Helicobacter pylori type II L-asparaginase possesses interesting features, among which a reduced catalytic efficiency for L-GLN, compared to the drugs presently used in therapy. In the present study, we describe some enzyme variants with catalytic and in vitro cytotoxic activities different from the wild type enzyme. Particularly, replacements on catalytic threonines (T16D and T95E) deplete the enzyme of both its catalytic activities, once more underlining the essential role of such residues. One serendipitous mutant, M121C/T169M, had a preserved efficiency vs L-asparagine but was completely unable to carry out L-glutamine hydrolysis. Interestingly, this variant did not exert any cytotoxic effect on HL-60 cells. The M121C and T169M single mutants had reduced catalytic activities (nearly 2.5- to 4-fold vs wild type enzyme, respectively). Mutant Q63E, endowed with a similar catalytic efficiency versus asparagine and halved glutaminase efficiency with respect to the wild type enzyme, was able to exert a cytotoxic effect comparable to, or higher than, the one of the wild type enzyme when similar asparaginase units were used. These findings may be relevant to determine the role of glutaminase activity of L-asparaginase in the anti-proliferative effect of the drug and to shed light on how to engineer the best asparaginase/glutaminase combination for an ever improved, patients-tailored therapy.
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Affiliation(s)
- Maristella Maggi
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy
- Department of Biology and Biotechnologies “Lazzaro Spallanzani”, Laboratory of Protein Biochemistry, University of Pavia, Pavia, Italy
| | - Laurent R. Chiarelli
- Department of Biology and Biotechnologies “Lazzaro Spallanzani”, Laboratory of Molecular Microbiology, University of Pavia, Pavia, Italy
| | - Giovanna Valentini
- Department of Biology and Biotechnologies “Lazzaro Spallanzani”, Laboratory of Protein Biochemistry, University of Pavia, Pavia, Italy
| | - Claudia Scotti
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy
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33
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Albesa-Jové D, Chiarelli LR, Makarov V, Pasca MR, Urresti S, Mori G, Salina E, Vocat A, Comino N, Mohorko E, Ryabova S, Pfieiffer B, Lopes Ribeiro ALDJ, Rodrigo-Unzueta A, Tersa M, Zanoni G, Buroni S, Altmann KH, Hartkoorn RC, Glockshuber R, Cole ST, Riccardi G, Guerin ME. Rv2466c mediates the activation of TP053 to kill replicating and non-replicating Mycobacterium tuberculosis. ACS Chem Biol 2014; 9:1567-75. [PMID: 24877756 DOI: 10.1021/cb500149m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The emergence of multidrug- and extensively drug-resistant strains of Mycobacterium tuberculosis highlights the need to discover new antitubercular agents. Here we describe the synthesis and characterization of a new series of thienopyrimidine (TP) compounds that kill both replicating and non-replicating M. tuberculosis. The strategy to determine the mechanism of action of these TP derivatives was to generate resistant mutants to the most effective compound TP053 and to isolate the genetic mutation responsible for this phenotype. The only non-synonymous mutation found was a g83c transition in the Rv2466c gene, resulting in the replacement of tryptophan 28 by a serine. The Rv2466c overexpression increased the sensitivity of M. tuberculosis wild-type and resistant mutant strains to TP053, indicating that TP053 is a prodrug activated by Rv2466c. Biochemical studies performed with purified Rv2466c demonstrated that only the reduced form of Rv2466c can activate TP053. The 1.7 Å resolution crystal structure of the reduced form of Rv2466c, a protein whose expression is transcriptionally regulated during the oxidative stress response, revealed a unique homodimer in which a β-strand is swapped between the thioredoxin domains of each subunit. A pronounced groove harboring the unusual active-site motif CPWC might account for the uncommon reactivity profile of the protein. The mutation of Trp28Ser clearly predicts structural defects in the thioredoxin fold, including the destabilization of the dimerization core and the CPWC motif, likely impairing the activity of Rv2466c against TP053. Altogether our experimental data provide insights into the molecular mechanism underlying the anti-mycobacterial activity of TP-based compounds, paving the way for future drug development programmes.
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Affiliation(s)
- David Albesa-Jové
- Unidad
de Biofísica,
Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad
del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Leioa, Bizkaia 48940, Spain
- Departamento
de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Laurent R. Chiarelli
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Vadim Makarov
- A.
N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Maria Rosalia Pasca
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Saioa Urresti
- Unidad
de Biofísica,
Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad
del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Leioa, Bizkaia 48940, Spain
- Departamento
de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Giorgia Mori
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Elena Salina
- A.
N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Anthony Vocat
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland
| | - Natalia Comino
- Unidad
de Biofísica,
Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad
del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Leioa, Bizkaia 48940, Spain
- Departamento
de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Elisabeth Mohorko
- Institute
of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Svetlana Ryabova
- A.
N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Bernhard Pfieiffer
- Department
of Chemistry and Applied Biosciences, Institute of Pharmaceutical
Sciences, ETH Zürich, HCI H405, Wolfgang-Pauli Str. 10, CH-8093 Zürich, Switzerland
| | | | - Ane Rodrigo-Unzueta
- Unidad
de Biofísica,
Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad
del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Leioa, Bizkaia 48940, Spain
- Departamento
de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Montse Tersa
- Unidad
de Biofísica,
Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad
del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Leioa, Bizkaia 48940, Spain
- Departamento
de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Giuseppe Zanoni
- Department
of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Silvia Buroni
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Karl-Heinz Altmann
- Department
of Chemistry and Applied Biosciences, Institute of Pharmaceutical
Sciences, ETH Zürich, HCI H405, Wolfgang-Pauli Str. 10, CH-8093 Zürich, Switzerland
| | - Ruben C. Hartkoorn
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland
| | - Rudi Glockshuber
- Institute
of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Stewart T. Cole
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland
| | - Giovanna Riccardi
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Marcelo E. Guerin
- Unidad
de Biofísica,
Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad
del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Leioa, Bizkaia 48940, Spain
- Departamento
de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
- IKERBASQUE, Basque
Foundation for Science, 48011 Bilbao, Spain
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34
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Naik M, Humnabadkar V, Tantry SJ, Panda M, Narayan A, Guptha S, Panduga V, Manjrekar P, Jena LK, Koushik K, Shanbhag G, Jatheendranath S, Manjunatha MR, Gorai G, Bathula C, Rudrapatna S, Achar V, Sharma S, Ambady A, Hegde N, Mahadevaswamy J, Kaur P, Sambandamurthy VK, Awasthy D, Narayan C, Ravishankar S, Madhavapeddi P, Reddy J, Prabhakar KR, Saralaya R, Chatterji M, Whiteaker J, McLaughlin B, Chiarelli LR, Riccardi G, Pasca MR, Binda C, Neres J, Dhar N, Signorino-Gelo F, McKinney JD, Ramachandran V, Shandil R, Tommasi R, Iyer PS, Narayanan S, Hosagrahara V, Kavanagh S, Dinesh N, Ghorpade SR. 4-Aminoquinolone Piperidine Amides: Noncovalent Inhibitors of DprE1 with Long Residence Time and Potent Antimycobacterial Activity. J Med Chem 2014; 57:5419-34. [DOI: 10.1021/jm5005978] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Laurent R. Chiarelli
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Giovanna Riccardi
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Maria Rosalia Pasca
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Claudia Binda
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - João Neres
- École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Neeraj Dhar
- École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - John D. McKinney
- École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | | | | | | | | | | | - Stefan Kavanagh
- Safety Assessment, AstraZeneca, Alderley
Park, Macclesfield, Cheshire SK10 2NA, United Kingdom
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35
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Chinaglia S, Chiarelli LR, Maggi M, Rodolfi M, Valentini G, Picco AM. Biochemistry of lipolytic enzymes secreted by Penicillium solitum and Cladosporium cladosporioides. Biosci Biotechnol Biochem 2014; 78:245-54. [DOI: 10.1080/09168451.2014.882752] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Two distinct extracellular lipases were obtained from Penicillium solitum 194A, isolated from domestic compost, and Cladosporium cladosporioides 194B, isolated from dairy wastewater. These alkaline enzymes had molecular masses of 42 and 30 kDa, respectively. The P. solitum 194A lipase differed in mass from previously reported enzyme, indicating that it is a novel lipase, and indicating that penicillia can secrete lipase isoenzymes. The C. cladosporioides lipase was more active on esters of medium-chain acids, whereas the P. solitum lipase was more active on longer chained substrates. The C. cladosporioides enzyme displayed higher thermal stability than the P. solitum lipase, preserving full activity up to 48 °C and showing a T50 (10 min) of 60 °C. Their different catalytic properties and good protein stability should make these enzymes suitable for biotechnological applications. Furthermore, the combined use of these two fungal strains may prove to be valuable in lipid-rich waste management.
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Affiliation(s)
- Selene Chinaglia
- Mycology Laboratory, Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Maristella Maggi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Marinella Rodolfi
- Mycology Laboratory, Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Giovanna Valentini
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Anna Maria Picco
- Mycology Laboratory, Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
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36
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Tortorici M, Borrello MT, Tardugno M, Chiarelli LR, Pilotto S, Ciossani G, Vellore NA, Bailey SG, Cowan J, O’Connell M, Crabb SJ, Packham G, Mai A, Baron R, Ganesan A, Mattevi A. Protein recognition by short peptide reversible inhibitors of the chromatin-modifying LSD1/CoREST lysine demethylase. ACS Chem Biol 2013; 8:1677-82. [PMID: 23721412 DOI: 10.1021/cb4001926] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The combinatorial assembly of protein complexes is at the heart of chromatin biology. Lysine demethylase LSD1(KDM1A)/CoREST beautifully exemplifies this concept. The active site of the enzyme tightly associates to the N-terminal domain of transcription factors of the SNAIL1 family, which therefore can competitively inhibit the binding of the N-terminal tail of the histone substrate. Our enzymatic, crystallographic, spectroscopic, and computational studies reveal that LSD1/CoREST can bind to a hexapeptide derived from the SNAIL sequence through recognition of a positively charged α-helical turn that forms upon binding to the enzyme. Variations in sequence and length of this six amino acid ligand modulate affinities enabling the same binding site to differentially interact with proteins that exert distinct biological functions. The discovered short peptide inhibitors exhibit antiproliferative activities and lay the foundation for the development of peptidomimetic small molecule inhibitors of LSD1.
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Affiliation(s)
- Marcello Tortorici
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Maria Teresa Borrello
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich
NR47TJ, United Kingdom
| | - Maria Tardugno
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich
NR47TJ, United Kingdom
- Department
of Drug Chemistry and
Technologies, University “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
| | - Laurent R. Chiarelli
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Simona Pilotto
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Giuseppe Ciossani
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Nadeem A. Vellore
- Department of Medicinal Chemistry,
College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112-5820,
United States
| | - Sarah G. Bailey
- Cancer Research
UK Centre, University
of Southampton, Faculty of Medicine, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, United
Kingdom
| | - Jonathan Cowan
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich
NR47TJ, United Kingdom
| | - Maria O’Connell
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich
NR47TJ, United Kingdom
| | - Simon J. Crabb
- Cancer Research
UK Centre, University
of Southampton, Faculty of Medicine, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, United
Kingdom
| | - Graham Packham
- Cancer Research
UK Centre, University
of Southampton, Faculty of Medicine, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, United
Kingdom
| | - Antonello Mai
- Department
of Drug Chemistry and
Technologies, University “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
| | - Riccardo Baron
- Department of Medicinal Chemistry,
College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112-5820,
United States
| | - A. Ganesan
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich
NR47TJ, United Kingdom
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
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37
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Neres J, Pojer F, Molteni E, Chiarelli LR, Dhar N, Boy-Röttger S, Buroni S, Fullam E, Degiacomi G, Lucarelli AP, Read RJ, Zanoni G, Edmondson DE, De Rossi E, Pasca MR, McKinney JD, Dyson PJ, Riccardi G, Mattevi A, Cole ST, Binda C. Structural basis for benzothiazinone-mediated killing of Mycobacterium tuberculosis. Sci Transl Med 2013; 4:150ra121. [PMID: 22956199 DOI: 10.1126/scitranslmed.3004395] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The benzothiazinone BTZ043 is a tuberculosis drug candidate with nanomolar whole-cell activity. BTZ043 targets the DprE1 catalytic component of the essential enzyme decaprenylphosphoryl-β-D-ribofuranose-2'-epimerase, thus blocking biosynthesis of arabinans, vital components of mycobacterial cell walls. Crystal structures of DprE1, in its native form and in a complex with BTZ043, reveal formation of a semimercaptal adduct between the drug and an active-site cysteine, as well as contacts to a neighboring catalytic lysine residue. Kinetic studies confirm that BTZ043 is a mechanism-based, covalent inhibitor. This explains the exquisite potency of BTZ043, which, when fluorescently labeled, localizes DprE1 at the poles of growing bacteria. Menaquinone can reoxidize the flavin adenine dinucleotide cofactor in DprE1 and may be the natural electron acceptor for this reaction in the mycobacterium. Our structural and kinetic analysis provides both insight into a critical epimerization reaction and a platform for structure-based design of improved inhibitors.
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Affiliation(s)
- João Neres
- Global Health Institute, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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38
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Pey AL, Mesa-Torres N, Chiarelli LR, Valentini G. Structural and energetic basis of protein kinetic destabilization in human phosphoglycerate kinase 1 deficiency. Biochemistry 2013; 52:1160-70. [PMID: 23336698 DOI: 10.1021/bi301565m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein kinetic destabilization is a common feature of many human genetic diseases. Human phosphoglycerate kinase 1 (PGK1) deficiency is a rare genetic disease caused by mutations in the PGK1 protein, which often shows reduced kinetic stability. In this work, we have performed an in-depth characterization of the thermal stability of the wild type and four disease-causing mutants (I47N, L89P, E252A, and T378P) of human PGK1. PGK1 thermal denaturation is a process under kinetic control, and it is described well by a two-state irreversible denaturation model. Kinetic analysis of differential scanning calorimetry profiles shows that the disease-causing mutations decrease PGK1 kinetic stability from ~5-fold (E252A) to ~100000-fold (L89P) compared to that of wild-type PGK1, and in some cases, mutant enzymes are denatured on a time scale of a few minutes at physiological temperature. We show that changes in protein kinetic stability are associated with large differences in enthalpic and entropic contributions to denaturation free energy barriers. It is also shown that the denaturation transition state becomes more nativelike in terms of solvent exposure as the protein is destabilized by mutations (Hammond effect). Unfolding experiments with urea further suggest a scenario in which the thermodynamic stability of PGK1 at least partly determines its kinetic stability. ATP and ADP kinetically stabilize PGK1 enzymes, and kinetic stabilization is nucleotide- and mutant-selective. Overall, our data provide insight into the structural and energetic basis underlying the low kinetic stability displayed by some mutants causing human PGK1 deficiency, which may have important implications for the development of native state kinetic stabilizers for the treatment of this disease.
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Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Granada, Spain.
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39
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Covini D, Tardito S, Bussolati O, Chiarelli LR, Pasquetto MV, Digilio R, Valentini G, Scotti C. Expanding targets for a metabolic therapy of cancer: L-asparaginase. Recent Pat Anticancer Drug Discov 2012; 7:4-13. [PMID: 21854356 DOI: 10.2174/157489212798358001] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 04/28/2011] [Accepted: 04/15/2011] [Indexed: 11/22/2022]
Abstract
The antitumour enzyme L-asparaginase (L-asparagine amidohydrolase, EC 3.5.1.1, ASNase), which catalyses the deamidation of L-asparagine (Asn) to L-aspartic acid and ammonia, has been used for many years in the treatment of acute lymphoblastic leukaemia. Also NK tumours, subtypes of myeloid leukaemias and T-cell lymphomas respond to ASNase, and ovarian carcinomas and other solid tumours have been proposed as additional targets for ASNase, with a potential role for its glutaminase activity. The increasing attention devoted to the antitumour activity of ASNase prompted us to analyse recent patents specifically concerning this enzyme. Here, we first give an overview of metabolic pathways affected by Asn and Gln depletion and, hence, potential targets of ASNase. We then discuss recent published patents concerning ASNases. In particular, we pay attention to novel ASNases, such as the recently characterised ASNase produced by Helicobacter pylori, and those presenting amino acid substitutions aimed at improving enzymatic activity of the classical Escherichia coli enzyme. We detail modifications, such as natural glycosylation or synthetic conjugation with other molecules, for therapeutic purposes. Finally, we analyse patents concerning biotechnological protocols and strategies applied to production of ASNase as well as to its administration and delivery in organisms.
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Affiliation(s)
- Daniele Covini
- Department of Experimental Medicine, Section of General Pathology, University of Pavia, Via Ferrata, 1, 27100 Pavia, Italy
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40
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Molinaro M, Chiarelli LR, Biancone L, Castagneto M, Boschiero L, Pisani F, Sabbatini M, Sandrini S, Arbustini E, Tinelli C, Regazzi M, Schena FP, Segoloni GP. Monitoring of inosine monophosphate dehydrogenase activity and expression during the early period of mycophenolate mofetil therapy in de novo renal transplant patients. Drug Metab Pharmacokinet 2012; 28:109-17. [PMID: 22892445 DOI: 10.2133/dmpk.dmpk-12-rg-048] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Measurement of inosine-monophosphate dehydrogenase (IMPDH) activity or gene expression was used as a further approach in pharmacokinetics (PK)/pharmacodynamic (PD)-guided mycophenolate mofetil (MMF) therapy. Forty-four de novo kidney transplant patients were enrolled; 35 of these completed the study, and were followed for 24 weeks for clinical status, PK parameters, IMPDH activity and IMPDH1/2 gene expression. IMPDH activity and expression were measured in peripheral blood mononuclear cells before transplant and at week 2,4,12 and 24, drawn before (t0) and 2 h (t2 h) after MMF administration. No significant correlation was found between IMPDH activity/expression and PK parameters. For both genes, significant enhancement in t2 h expression was observed, then decreases towards week 24 with a trend following steroid dosages. Seven patients experienced acute rejection (AR) and exhibited significantly higher pre-transplant expression of both IMPDH1 (median 3.42 vs. 0.84; p=0.0025), and IMPDH2 genes (135 vs. 104; p=0.0218) with respect to non-rejecting patients. A significant association was also found between pre-transplant IMPDH1 mRNA and haematological complications (p=0.032). This study suggests that high steroid dosages may influence IMPDH1/2 expression, hampering their use as a PD biomarker, particularly during the early post-transplant period. The measurement of pre-transplant levels of IMPDH1/2 may contribute to prediction of individual drug responsiveness to improve the clinical management of patients in MMF therapy.
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Affiliation(s)
- Mariadelfina Molinaro
- Clinical Pharmacokinetics in Transplantation and Autoimmune Diseases, Foundation IRCCS Policlinico S. Matteo, Pavia, Italy.
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41
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Chiarelli LR, Morera SM, Bianchi P, Fermo E, Zanella A, Galizzi A, Valentini G. Molecular insights on pathogenic effects of mutations causing phosphoglycerate kinase deficiency. PLoS One 2012; 7:e32065. [PMID: 22348148 PMCID: PMC3279470 DOI: 10.1371/journal.pone.0032065] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 01/22/2012] [Indexed: 11/18/2022] Open
Abstract
Phosphoglycerate kinase (PGK) catalyzes an important ATP-generating step in glycolysis. PGK1 deficiency is an uncommon X-linked inherited disorder, generally characterized by various combinations of non-spherocytic hemolytic anemia, neurological dysfunctions, and myopathies. Patients rarely exhibit all three clinical features. To provide a molecular framework to the different pathological manifestations, all known mutations were reviewed and 16 mutant enzymes, obtained as recombinant forms, were functionally and structurally characterized. Most mutations heavily affect thermal stability and to a different extent catalytic efficiency, in line with the remarkably low PGK activity clinically observed in the patients. Mutations grossly impairing protein stability, but moderately affecting kinetic properties (p.I47N, p.L89P, p.C316R, p.S320N, and p.A354P) present the most homogeneous correlation with the clinical phenotype. Patients carrying these mutations display hemolytic anemia and neurological disorders, and,except for p.A354P variant, no myopaty. Variants highly perturbed in both catalytic efficiency (p.G158V, p.D164V, p.K191del, D285V, p.D315N, and p.T378P) and heat stability (all, but p.T378P) result to be mainly associated with myopathy alone. Finally, mutations faintly affecting molecular properties (p.R206P, p.E252A, p.I253T, p.V266M, and p.D268N) correlate with a wide spectrum of clinical symptoms. These are the first studies that correlate the clinical symptoms with the molecular properties of the mutant enzymes. All findings indicate that the different clinical manifestations associated with PGK1 deficiency chiefly depend on the distinctive type of perturbations caused by mutations in the PGK1 gene, highlighting the need for determination of the molecular properties of PGK variants to assist in prognosis and genetic counseling. However, the clinical symptoms can not be understood only on the bases of molecular properties of the mutant enzyme. Different (environmental, metabolic, genetic and/or epigenetic) intervening factors can contribute toward the expression of PGK deficient clinical phenotypes.
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Affiliation(s)
- Laurent R. Chiarelli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università degli Studi di Pavia, Pavia, Italy
| | - Simone M. Morera
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università degli Studi di Pavia, Pavia, Italy
| | - Paola Bianchi
- U.O. Ematologia 2, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Elisa Fermo
- U.O. Ematologia 2, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Alberto Zanella
- U.O. Ematologia 2, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Alessandro Galizzi
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università degli Studi di Pavia, Pavia, Italy
| | - Giovanna Valentini
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università degli Studi di Pavia, Pavia, Italy
- * E-mail:
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Manina G, Bellinzoni M, Pasca MR, Neres J, Milano A, Ribeiro ALDJL, Buroni S, Skovierová H, Dianišková P, Mikušová K, Marák J, Makarov V, Giganti D, Haouz A, Lucarelli AP, Degiacomi G, Piazza A, Chiarelli LR, De Rossi E, Salina E, Cole ST, Alzari PM, Riccardi G. Biological and structural characterization of the Mycobacterium smegmatis nitroreductase NfnB, and its role in benzothiazinone resistance. Mol Microbiol 2011; 77:1172-85. [PMID: 20624223 DOI: 10.1111/j.1365-2958.2010.07277.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Tuberculosis is still a leading cause of death in developing countries, for which there is an urgent need for new pharmacological agents. The synthesis of the novel antimycobacterial drug class of benzothiazinones (BTZs) and the identification of their cellular target as DprE1 (Rv3790), a component of the decaprenylphosphoryl-β-d-ribose 2'-epimerase complex, have been reported recently. Here, we describe the identification and characterization of a novel resistance mechanism to BTZ in Mycobacterium smegmatis. The overexpression of the nitroreductase NfnB leads to the inactivation of the drug by reduction of a critical nitro-group to an amino-group. The direct involvement of NfnB in the inactivation of the lead compound BTZ043 was demonstrated by enzymology, microbiological assays and gene knockout experiments. We also report the crystal structure of NfnB in complex with the essential cofactor flavin mononucleotide, and show that a common amino acid stretch between NfnB and DprE1 is likely to be essential for the interaction with BTZ. We performed docking analysis of NfnB-BTZ in order to understand their interaction and the mechanism of nitroreduction. Although Mycobacterium tuberculosis seems to lack nitroreductases able to inactivate these drugs, our findings are valuable for the design of new BTZ molecules, which may be more effective in vivo.
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Affiliation(s)
- Giulia Manina
- Dipartimento di Genetica e Microbiologia, Università degli Studi di Pavia, via Ferrata, 1, 27100 Pavia, Italy
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Bovi M, Carrizo ME, Capaldi S, Perduca M, Chiarelli LR, Galliano M, Monaco HL. Structure of a lectin with antitumoral properties in king bolete (Boletus edulis) mushrooms. Glycobiology 2011; 21:1000-9. [DOI: 10.1093/glycob/cwr012] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Lucarelli AP, Buroni S, Pasca MR, Rizzi M, Cavagnino A, Valentini G, Riccardi G, Chiarelli LR. Mycobacterium tuberculosis phosphoribosylpyrophosphate synthetase: biochemical features of a crucial enzyme for mycobacterial cell wall biosynthesis. PLoS One 2010; 5:e15494. [PMID: 21085589 PMCID: PMC2981568 DOI: 10.1371/journal.pone.0015494] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 10/02/2010] [Indexed: 12/03/2022] Open
Abstract
The selection and soaring spread of Mycobacterium tuberculosis multidrug-resistant (MDR-TB) and extensively drug-resistant strains (XDR-TB) is a severe public health problem. Currently, there is an urgent need for new drugs for tuberculosis treatment, with novel mechanisms of action and, moreover, the necessity to identify new drug targets. Mycobacterial phosphoribosylpyrophosphate synthetase (MtbPRPPase) is a crucial enzyme involved in the biosynthesis of decaprenylphosphoryl-arabinose, an essential precursor for the mycobacterial cell wall biosynthesis. Moreover, phosphoribosylpyrophosphate, which is the product of the PRPPase catalyzed reaction, is the precursor for the biosynthesis of nucleotides and of some amino acids such as histidine and tryptophan. In this context, the elucidation of the molecular and functional features of MtbPRPPase is mandatory. MtbPRPPase was obtained as a recombinant form, purified to homogeneity and characterized. According to its hexameric form, substrate specificity and requirement of phosphate for activity, the enzyme proved to belong to the class I of PRPPases. Although the sulfate mimicked the phosphate, it was less effective and required higher concentrations for the enzyme activation. MtbPRPPase showed hyperbolic response to ribose 5-phosphate, but sigmoidal behaviour towards Mg-ATP. The enzyme resulted to be allosterically activated by Mg2+ or Mn2+ and inhibited by Ca2+ and Cu2+ but, differently from other characterized PRPPases, it showed a better affinity for the Mn2+ and Cu2+ ions, indicating a different cation binding site geometry. Moreover, the enzyme from M. tuberculosis was allosterically inhibited by ADP, but less sensitive to inhibition by GDP. The characterization of M. tuberculosis PRPPase provides the starting point for the development of inhibitors for antitubercular drug design.
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Affiliation(s)
- Anna P Lucarelli
- Dipartimento di Genetica e Microbiologia, Università degli Studi di Pavia, Pavia, Italy
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Chiarelli LR, Molinaro M, Libetta C, Tinelli C, Cosmai L, Valentini G, Dal Canton A, Regazzi M. Inosine monophosphate dehydrogenase variability in renal transplant patients on long-term mycophenolate mofetil therapy. Br J Clin Pharmacol 2010; 69:38-50. [PMID: 20078611 DOI: 10.1111/j.1365-2125.2009.03542.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT * Mycophenolic acid (MPA) is a potent, selective and reversible inhibitor of inosine 5'-monophosphate dehydrogenase (IMPDH), the rate-limiting enzyme for de novo guanosine triphosphate biosynthesis. * The large IMPDH interindividual variability could be responsible for the differences in therapeutic effects and side-effects observed with MPA. * Induction of IMPDH activity has been observed in whole blood during immunosuppressive therapy. WHAT THIS STUDY ADDS * Our data were acquired in long-term mycophenolate mofetil-treated renal transplant recipients on different combinations of immunosuppressive agents (ciclosporin, tacrolimus, sirolimus) and with different treatment duration (up to 8.8 years post transplant). * The increasing trend in IMPDH activity that we observed throughout our 12-month observation period was significantly higher in rejecting than in nonrejecting subjects. AIMS Long-term mycophenolate mofetil (MMF) therapy may induce inosine 5'-monophosphate dehydrogenase (IMPDH) activity in peripheral blood mononuclear cells (PBMCs), thus decreasing MMF immunosuppressive properties. Pharmacodynamic monitoring was used to investigate whether biological activity is altered after long-term therapy. METHODS IMPDH activity was measured in PBMC samples from 54 stable kidney transplant patients, already on MMF (for at least 3 months), before (t(0)) and 2 h after (t(2)) MMF morning dose administration; levels were monitored for up to 15 months, together with total mycophenolic acid (MPA) and free MPA concentrations. RESULTS During the 15 months' monitoring, t(0) IMPDH activity in transplant recipients increased from 5.9 +/- 3.7 nmol h(-1) mg(-1)[95% confidence interval (CI) 4.9, 6.9] to 9.0 +/- 3.9 nmol h(-1) mg(-1) (95% CI 7.2, 10.8), with an intra- and interpatient variability of 28% and 42%. Five patients experienced acute rejection during the follow-up: t(0) IMPDH activity was increased during rejection vs. nonrejection, and the trend was significantly higher in rejecting than in nonrejecting subjects for the whole monitoring period. CONCLUSIONS Even though a correlation has been found between IMPDH activity and rejection, its efficacy as a predictive tool in long-term transplant outcomes may be affected by high interpatient variability; on the other hand, continuous monitoring of the IMPDH trend could make an effective prognostic parameter of rejection. Other trials also including pre-transplant data on both IMPDH expression and activity are warranted to better assess their role as biomarkers for MPA effect in clinical practice.
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Affiliation(s)
- Laurent R Chiarelli
- Department of Biochemistry, University of Pavia, Pharmacokinetics Unit, Pavia, Italy
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Forneris F, Orru R, Bonivento D, Chiarelli LR, Mattevi A. ThermoFAD, a Thermofluor-adapted flavin ad hoc detection system for protein folding and ligand binding. FEBS J 2009; 276:2833-40. [PMID: 19459938 DOI: 10.1111/j.1742-4658.2009.07006.x] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In living organisms, genes encoding proteins that contain flavins as a prosthetic group constitute approximately 2-3% of the total. The fluorescence of flavin cofactors in these proteins is a property that is widely employed for biochemical characterisation. Here, we present a modified Thermofluor approach called ThermoFAD (Thermofluor-adapted flavin ad hoc detection system), which simplifies identification of optimal purification and storage conditions as well as high-affinity ligands. In this technique, the flavin cofactor is used as an intrinsic probe to monitor protein folding and stability, taking advantage of the different fluorescent properties of flavin-containing proteins between the folded and denatured state. The main advantage of the method is that it allows a large amount of biochemical data to be obtained using very small amounts of protein sample and standard laboratory equipment. We have explored several cases that demonstrate the reliability and versatility of this technique when applied to globular flavoenzymes, membrane-anchored flavoproteins, and macromolecular complexes. The information gathered from ThermoFAD analysis can be very valuable for any biochemical and biophysical analysis, including crystallisation. The method is likely to be applicable to other classes of proteins that possess endogenous fluorescent cofactors and prosthetic groups.
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Affiliation(s)
- Federico Forneris
- Department of Genetics and Microbiology, University of Pavia, Italy.
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Cappelletti D, Chiarelli LR, Pasquetto MV, Stivala S, Valentini G, Scotti C. Helicobacter pyloril-asparaginase: a promising chemotherapeutic agent. Biochem Biophys Res Commun 2008; 377:1222-6. [PMID: 18983825 DOI: 10.1016/j.bbrc.2008.10.118] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2008] [Accepted: 10/25/2008] [Indexed: 01/28/2023]
Abstract
Bacterial L-asparaginases are amidohydrolases that catalyse the conversion of L-asparagine to L-aspartate and ammonia and are used as anti-cancer drugs. The current members of this class of drugs have several toxic side effects mainly due to their associated glutaminase activity. In the present study, we report the molecular cloning, biochemical characterisation and in vitro cytotoxicity of a novel L-asparaginase from the pathogenic strain Helicobacter pylori CCUG 17874. The recombinant enzyme showed a strong preference for L-asparagine over L-glutamine and, in contrast to most L-asparaginases, it exhibited a sigmoidal behaviour towards L-glutamine. The enzyme preserved full activity after 2 h incubation at 45 degrees C. In vitro cytotoxicity assays revealed that different cell lines displayed a variable sensitivity towards the enzyme, AGS and MKN28 gastric epithelial cells being the most affected. These findings may be relevant both for the interpretation of the mechanisms underlying H. pylori associated diseases and for biomedical applications.
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Affiliation(s)
- Donata Cappelletti
- Department of Experimental Medicine, Section of General Pathology, University of Pavia, Piazza Botta, 10, 27100 Pavia, Italy
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Abrusci P, Chiarelli LR, Galizzi A, Fermo E, Bianchi P, Zanella A, Valentini G. Erythrocyte adenylate kinase deficiency: characterization of recombinant mutant forms and relationship with nonspherocytic hemolytic anemia. Exp Hematol 2007; 35:1182-9. [PMID: 17662886 DOI: 10.1016/j.exphem.2007.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 04/19/2007] [Accepted: 05/07/2007] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Red cell adenylate kinase (AK) deficiency is a rare hereditary erythroenzymopathy associated with moderate to severe nonspherocytic hemolytic anemia and, in some cases, with mental retardation and psychomotor impairment. To date, diagnosis of AK deficiency depends upon demonstration of low enzyme activity in red blood cells and detection of mutations in AK1 gene. To investigate the molecular bases of the AK deficiency, we characterized five variants of AK1 isoenzyme-bearing mutations (118G>A, 190G>A, 382C>T, 418-420del, and 491A>G) found in AK-deficient patients with chronic hemolytic anemia. MATERIALS AND METHODS The complete AK1 cDNA was obtained by standard procedures and using as template the reticulocyte RNA. The cDNA was cloned in a plasmid vector and the enzyme was expressed in Escherichia coli BL21(DE3)pLysS, and purified by standard protocols to homogeneity. DNA mutants bearing point mutations were obtained from the cloned wild-type cDNA using standard methods of site-directed mutagenesis, whereas the DNA mutant with deletion of codon 140 was obtained by a two-step method. RESULTS Four mutant enzymes (Gly40Arg, Gly64Arg, Arg128Trp, Asp140del) were severely affected in activity, displaying a catalytic efficiency of four orders of magnitude lower than the wild-type; one (Tyr164Cys) was grossly perturbed in protein stability. CONCLUSIONS The altered properties displayed by the mutant enzymes support the cause-effect relationship between AK1 mutations and hemolytic anemia.
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Affiliation(s)
- Patrizia Abrusci
- Dipartimento di Biochimica A. Castellani, Università degli Studi di Pavia, Pavia, Italy
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Chiarelli LR, Fermo E, Zanella A, Valentini G. Hereditary erythrocyte pyrimidine 5'-nucleotidase deficiency: a biochemical, genetic and clinical overview. ACTA ACUST UNITED AC 2006; 11:67-72. [PMID: 16522554 DOI: 10.1080/10245330500276667] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Pyrimidine 5' -nucleotidase (P5'N-1) deficiency is the third most common enzyme abnormality after glucose 6-phosphate dehydrogenase and pyruvate kinase causing hereditary non-spherocytic hemolytic anemia. The disease is transmitted as an autosomal recessive trait. The degree of hemolysis is generally mild-to moderate. The hallmark of this enzyme deficiency is the presence of pronounced basophylic stippling in red blood cell peripheral blood smear together with accumulation of pyrimidine nucleotides within erythrocytes. No correlation has been found between residual activity and degree of hemolysis. The structural human gene for P5'N-1 is now available and fifteen different mutations had been identified so far. More recently, a functional analysis of P5'N-1 mutants had been performed providing a rationale for the pathological effects of the mutations. All mutations investigated affect amino acid residues unambiguously essential for the catalytic efficiency and/or protein stability, suggesting drastic reduction of the enzyme activity in red blood cells of patients affected by the disorder. Nevertheless, some patients exhibit high residual P5'N-1 activity, suggesting that P5'N-1 deficiency is compensate by other nucleotidases and/or alternative pathways in nucleotide metabolism. No specific therapy for P5'N-1 deficiency is now available.
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Affiliation(s)
- Laurent R Chiarelli
- Department of Biochemistry, A. Castellani, University of Pavia, Via Taramelli 3/b. 27100 Pavia, Italy
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Comincini S, Chiarelli LR, Zelini P, Del Vecchio I, Azzalin A, Arias A, Ferrara V, Rognoni P, Dipoto A, Nano R, Valentini G, Ferretti L. Nuclear mRNA retention and aberrant doppel protein expression in human astrocytic tumor cells. Oncol Rep 2006; 16:1325-32. [PMID: 17089057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Doppel (Dpl) is a paralogue of the mammalian Prion (PrP) protein. It is abundant in testis and, unlike PrP, it is expressed at low levels in the adult central nervous system (CNS). Besides, Dpl overexpression correlates with some prion-disease pathological features, such as ataxia and death of cerebellar neurons. Recently, ectopic expression of doppel was found in two different tumor types, specifically in glial and haematological cancers. In this study the doppel gene (PRND) mRNA and protein expression in PRT-HU2 and IPDDC-A2 astrocytoma-derived cell lines was investigated. Northern blot analysis revealed two equally abundant PRND mRNA isoforms, while real-time PCR, on nuclear and cytoplasmic RNA fractions, and cRNA in situ hybridization, on astrocytoma cells and bioptical specimens, showed a nuclear retention of PRND transcripts. Western blot analysis showed that the amount of protein expressed is low compared to the level of mRNA. Moreover deglycosylation studies indicated that Dpl undergoes unusual glycosylation processes. Immunohistochemistry experiments demonstrated that Dpl was mainly localised in the cytoplasm of the astrocytic tumor cells, and that it failed to be GPI-anchored to the cell membrane. This unusual cellular localization was also confirmed through EGFP-Dpl expression in astrocytomas; on the contrary, HeLa cells exhibited the expected Dpl membrane localization. Our findings suggest an aberrant doppel gene expression pattern, characterized by a substantial nuclear retention of the transcript, an altered post-translational modification of the protein and an unusual cytoplasmic localization.
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Affiliation(s)
- Sergio Comincini
- Dipartimento di Genetica e Microbiologia, Università di Pavia, 27100 Pavia, Italy.
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