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Uribe-Vázquez B, Díaz-Vilchis A, Avila-Linares A, Saab-Rincón G, Marín-Tovar Y, Flores H, Pastor N, Huerta-Miranda G, Rudiño-Piñera E, Soberón X. Characterization of a catalase-peroxidase variant (L333V-KatG) identified in an INH-resistant Mycobacterium tuberculosis clinical isolate. Biochem Biophys Rep 2024; 37:101649. [PMID: 38318524 PMCID: PMC10839757 DOI: 10.1016/j.bbrep.2024.101649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/24/2023] [Accepted: 01/15/2024] [Indexed: 02/07/2024] Open
Abstract
Mycobacterium tuberculosis catalase-peroxidase (Mt-KatG) is a bifunctional heme-dependent enzyme that has been shown to activate isoniazid (INH), the widely used antibiotic against tuberculosis (TB). The L333V-KatG variant has been associated with INH resistance in clinical M. tuberculosis isolates from Mexico. To understand better the mechanisms of INH activation, its catalytic properties (catalase, peroxidase, and IN-NAD formation) and crystal structure were compared with those of the wild-type enzyme (WT-KatG). The rate of IN-NAD formation mediated by WT-KatG was 23% greater than L333V-KatG when INH concentration is varied. In contrast to WT-KatG, the crystal structure of the L333V-KatG variant has a perhydroxy modification of the indole nitrogen of W107 from MYW adduct. L333V-KatG shows most of the active site residues in a similar position to WT-KatG; only R418 is in the R-conformation instead of the double R and Y conformation present in WT-KatG. L333V-KatG shows a small displacement respect to WT-KatG in the helix from R385 to L404 towards the mutation site, an increase in length of the coordination bond between H270 and heme Fe, and a longer H-bond between proximal D381 and W321, compared to WT-KatG; these small displacements could explain the altered redox potential of the heme, and result in a less active and stable enzyme.
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Affiliation(s)
- Brenda Uribe-Vázquez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, México
| | - Adelaida Díaz-Vilchis
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, UNAM, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, México
| | - Aylin Avila-Linares
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, UNAM, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, México
| | - Gloria Saab-Rincón
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, México
| | - Yerli Marín-Tovar
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, UNAM, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, México
| | - Humberto Flores
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, México
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, UAEM, Avenida Universidad 1001, Colonia Chamilpa, 62209, Cuernavaca, Morelos, México
| | - Guillermo Huerta-Miranda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, México
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, UNAM, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, México
| | - Xavier Soberón
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, México
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2
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Marquês JT, Frazão De Faria C, Reis M, Machado D, Santos S, Santos MDS, Viveiros M, Martins F, De Almeida RFM. In vitro Evaluation of Isoniazid Derivatives as Potential Agents Against Drug-Resistant Tuberculosis. Front Pharmacol 2022; 13:868545. [PMID: 35600870 PMCID: PMC9114799 DOI: 10.3389/fphar.2022.868545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
The upsurge of multidrug-resistant tuberculosis has toughened the challenge to put an end to this epidemic by 2030. In 2020 the number of deaths attributed to tuberculosis increased as compared to 2019 and newly identified multidrug-resistant tuberculosis cases have been stably close to 3%. Such a context stimulated the search for new and more efficient antitubercular compounds, which culminated in the QSAR-oriented design and synthesis of a series of isoniazid derivatives active against Mycobacterium tuberculosis. From these, some prospective isonicotinoyl hydrazones and isonicotinoyl hydrazides are studied in this work. To evaluate if the chemical derivatizations are generating compounds with a good performance concerning several in vitro assays, their cytotoxicity against human liver HepG2 cells was determined and their ability to bind human serum albumin was thoroughly investigated. For the two new derivatives presented in this study, we also determined their lipophilicity and activity against both the wild type and an isoniazid-resistant strain of Mycobacterium tuberculosis carrying the most prevalent mutation on the katG gene, S315T. All compounds were less cytotoxic than many drugs in clinical use with IC50 values after a 72 h challenge always higher than 25 µM. Additionally, all isoniazid derivatives studied exhibited stronger binding to human serum albumin than isoniazid itself, with dissociation constants in the order of 10−4–10−5 M as opposed to 10−3 M, respectively. This suggests that their transport and half-life in the blood stream are likely improved when compared to the parent compound. Furthermore, our results are a strong indication that the N′ = C bond of the hydrazone derivatives of INH tested is essential for their enhanced activity against the mutant strain of M. tuberculosis in comparison to both their reduced counterparts and INH.
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Affiliation(s)
- Joaquim Trigo Marquês
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Catarina Frazão De Faria
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Marina Reis
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Instituto Superior de Educação e Ciências (ISEC Lisboa), Lisboa, Portugal
| | - Diana Machado
- Unidade de Microbiologia Medica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Susana Santos
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Maria da Soledade Santos
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Viveiros
- Unidade de Microbiologia Medica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Filomena Martins
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- *Correspondence: Filomena Martins, ; Rodrigo F. M. De Almeida,
| | - Rodrigo F. M. De Almeida
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- *Correspondence: Filomena Martins, ; Rodrigo F. M. De Almeida,
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3
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Nontuberculous Mycobacterial Resistance to Antibiotics and Disinfectants: Challenges Still Ahead. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8168750. [PMID: 35257011 PMCID: PMC8898113 DOI: 10.1155/2022/8168750] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 02/16/2022] [Indexed: 12/11/2022]
Abstract
The mortality incidence from nontuberculous mycobacteria (NTM) infections has been steadily developing globally. These bacterial agents were once thought to be innocent environmental saprophytic that are only dangerous to patients with defective lungs or the immunosuppressed. Nevertheless, the emergence of highly resistant NTM to different antibiotics and disinfectants increased the importance of these agents in the health system. Currently, NTM frequently infect seemingly immunocompetent individuals at rising rates. This is of concern as the resistant NTM are difficult to control and treat. The details behind this NTM development are only beginning to be clarified. The current study will provide an overview of the most important NTM resistance mechanisms to not only antibiotics but also the most commonly used disinfectants. Such evaluations can open new doors to improving control strategies and reducing the risk of NTM infection. Moreover, further studies are crucial to uncover this association.
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Hegde P, Boshoff HIM, Rusman Y, Aragaw WW, Salomon CE, Dick T, Aldrich CC. Reinvestigation of the structure-activity relationships of isoniazid. Tuberculosis (Edinb) 2021; 129:102100. [PMID: 34116482 PMCID: PMC8324568 DOI: 10.1016/j.tube.2021.102100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/24/2021] [Accepted: 05/30/2021] [Indexed: 11/19/2022]
Abstract
Isoniazid (INH) remains a cornerstone for treatment of drug susceptible tuberculosis (TB), yet the quantitative structure-activity relationships for INH are not well documented in the literature. In this paper, we have evaluated a systematic series of INH analogs against contemporary Mycobacterium tuberculosis strains from different lineages and a few non-tuberculous mycobacteria (NTM). Deletion of the pyridyl nitrogen atom, isomerization of the pyridine nitrogen to other positions, replacement of the pyridine ring with isosteric heterocycles, and modification of the hydrazide moiety of INH abolishes antitubercular activity. Similarly, substitution of the pyridine ring at the 3-position is not tolerated while substitution at the 2-position is permitted with 2-methyl-INH 9 displaying antimycobacterial activity comparable to INH. To assess the specific activity of this series of INH analogs against mycobacteria, we assayed them against a panel of gram-positive and gram-negative bacteria, as well as a few fungi. As expected INH and its analogs display a narrow spectrum of activity and are inactive against all non-mycobacterial strains evaluated, except for 4, which has modest inhibitory activity against Cryptococcus neoformans. Our findings provide an updated analysis of the structure-activity relationship of INH that we hope will serve as useful resource for the community.
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Affiliation(s)
- Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Yudi Rusman
- Center for Drug Design, University of Minnesota, Minneapolis, MN, 55455, USA
| | | | - Christine E Salomon
- Center for Drug Design, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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5
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Munir A, Wilson MT, Hardwick SW, Chirgadze DY, Worrall JAR, Blundell TL, Chaplin AK. Using cryo-EM to understand antimycobacterial resistance in the catalase-peroxidase (KatG) from Mycobacterium tuberculosis. Structure 2021; 29:899-912.e4. [PMID: 33444527 PMCID: PMC8355310 DOI: 10.1016/j.str.2020.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/27/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022]
Abstract
Resolution advances in cryoelectron microscopy (cryo-EM) now offer the possibility to visualize structural effects of naturally occurring resistance mutations in proteins and also of understanding the binding mechanisms of small drug molecules. In Mycobacterium tuberculosis the multifunctional heme enzyme KatG is indispensable for activation of isoniazid (INH), a first-line pro-drug for treatment of tuberculosis. We present a cryo-EM methodology for structural and functional characterization of KatG and INH resistance variants. The cryo-EM structure of the 161 kDa KatG dimer in the presence of INH is reported to 2.7 Å resolution allowing the observation of potential INH binding sites. In addition, cryo-EM structures of two INH resistance variants, identified from clinical isolates, W107R and T275P, are reported. In combination with electronic absorbance spectroscopy our cryo-EM approach reveals how these resistance variants cause disorder in the heme environment preventing heme uptake and retention, providing insight into INH resistance. A cryo-EM structure to 2.7 Å resolution of M. tuberculosis KatG with isoniazid Cryo-EM is able to visualize multiple dynamic binding modes of isoniazid to KatG Structural disorder in isoniazid resistance mutations is observed Structural disorder of the resistance mutations results in the lack of heme retention
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Affiliation(s)
- Asma Munir
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Steven W Hardwick
- CryoEM Facility, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Dimitri Y Chirgadze
- CryoEM Facility, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
| | - Amanda K Chaplin
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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6
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Santos MSC, Matos AM, Reis M, Martins F. Lipophilicity assessment of some isoniazid derivatives active against Mycobacterium tuberculosis. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.124820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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7
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Reyes YIA, Franco FC. DFT study on the effect of proximal residues on the Mycobacterium tuberculosis catalase-peroxidase (katG) heme compound I intermediate and its bonding interaction with isoniazid. Phys Chem Chem Phys 2019; 21:16515-16525. [PMID: 31298238 DOI: 10.1039/c9cp01465a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Isoniazid (INH) is converted into isonicotinyl radical through its interaction with the catalase-peroxidase (katG) enzyme present in the cells of Mycobacterium tuberculosis (M. tb.), the bacteria that causes the tuberculosis disease. This process is important because resistance of M. tb. cells to INH treatment has been associated with the failure of completion of this process. However, this process is poorly understood and there are a variety of conflicting theories about the details of the mechanism of this process. One theory suggests that INH binds to katG and transfers a single electron to the heme while the heme is in its two electron oxidized state, compound I [Fe(iv)Por˙+] (CpdI). In this study, DFT calculations at the UB3LYP/6-31g(d)-LANL2DZ level of theory are used to study the M. tb. katG CpdI molecule. Different models of the M. tb. CpdI molecule were prepared and the calculations revealed the impact of Trp321 on the electronic properties of the heme. Without Trp321 the heme assumed a triradical state with single electrons on the πxy and πyz orbitals of Fe and another on the a2u orbital of the porphyrin ring that can either be coupled with the first two, to assume a quartet state, or decoupled to form a doublet state. With Trp321, however, a transfer of an electron from the πTrp orbital to a2u porphyrin orbital leads to loss of radical character of the porphyrin and leaves the Trp321 group with a radical character. INH was observed to have strong interaction with CpdI and the absence of Trp321 significantly decreased the binding energy by 2 kcal mol-1 explaining the importance of Trp321 in the binding of INH. The results in this study show the importance of Trp321 in the binding of INH and its effect on its electronic properties, which is consistent with previous experimental findings that mutation of Trp321 results in an increase in drug resistance.
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Affiliation(s)
- Yves Ira A Reyes
- Chemistry Department, De La Salle University, 2401 Taft Avenue, 0922 Manila, Philippines.
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8
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Wolf NM, Lee H, Choules MP, Pauli GF, Phansalkar R, Anderson JR, Gao W, Ren J, Santarsiero BD, Lee H, Cheng J, Jin YY, Ho NA, Duc NM, Suh JW, Abad-Zapatero C, Cho S. High-Resolution Structure of ClpC1-Rufomycin and Ligand Binding Studies Provide a Framework to Design and Optimize Anti-Tuberculosis Leads. ACS Infect Dis 2019; 5:829-840. [PMID: 30990022 DOI: 10.1021/acsinfecdis.8b00276] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Addressing the urgent need to develop novel drugs against drug-resistant Mycobacterium tuberculosis ( M. tb) strains, ecumicin (ECU) and rufomycin I (RUFI) are being explored as promising new leads targeting cellular proteostasis via the caseinolytic protein ClpC1. Details of the binding topology and chemical mode of (inter)action of these cyclopeptides help drive further development of novel potency-optimized entities as tuberculosis drugs. ClpC1 M. tb protein constructs with mutations driving resistance to ECU and RUFI show reduced binding affinity by surface plasmon resonance (SPR). Despite certain structural similarities, ECU and RUFI resistant mutation sites did not overlap in their SPR binding patterns. SPR competition experiments show ECU prevents RUFI binding, whereas RUFI partially inhibits ECU binding. The X-ray structure of the ClpC1-NTD-RUFI complex reveals distinct differences compared to the previously reported ClpC1-NTD-cyclomarin A structure. Surprisingly, the complex structure revealed that the epoxide moiety of RUFI opened and covalently bound to ClpC1-NTD via the sulfur atom of Met1. Furthermore, RUFI analogues indicate that the epoxy group of RUFI is critical for binding and bactericidal activity. The outcomes demonstrate the significance of ClpC1 as a novel target and the importance of SAR analysis of identified macrocyclic peptides for drug discovery.
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Affiliation(s)
- Nina M. Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Hyun Lee
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Biophysics Core at the Research Resource Center, University of Illinois at Chicago, 1100 S. Ashland Street, Chicago, Illinois 60612, United States
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Mary P. Choules
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Guido F. Pauli
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Rasika Phansalkar
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Jeffrey R. Anderson
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Wei Gao
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Jinhong Ren
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Bernard D. Santarsiero
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Hanki Lee
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Jinhua Cheng
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
- Division of Bioscience and Bioinformatics, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Ying-Yu Jin
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
- Division of Bioscience and Bioinformatics, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Ngoc Anh Ho
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Nguyen Minh Duc
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Joo-Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
- Division of Bioscience and Bioinformatics, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Celerino Abad-Zapatero
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
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9
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Loewen P, De Silva PM, Donald LJ, Switala J, Villanueva J, Fita I, Kumar A. KatG-Mediated Oxidation Leading to Reduced Susceptibility of Bacteria to Kanamycin. ACS OMEGA 2018; 3:4213-4219. [PMID: 29732452 PMCID: PMC5928485 DOI: 10.1021/acsomega.8b00356] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
Resistance to antibiotics has become a serious problem for society, and there are increasing efforts to understand the reasons for and sources of resistance. Bacterial-encoded enzymes and transport systems, both innate and acquired, are the most frequent culprits for the development of resistance, although in Mycobacterium tuberculosis, the catalase-peroxidase, KatG, has been linked to the activation of the antitubercular drug isoniazid. While investigating a possible link between aminoglycoside antibiotics and the induction of oxidative bursts, we observed that KatG reduces susceptibility to aminoglycosides. Investigation revealed that kanamycin served as an electron donor for the peroxidase reaction, reducing the oxidized ferryl intermediates of KatG to the resting state. Loss of electrons from kanamycin was accompanied by the addition of a single oxygen atom to the aminoglycoside. The oxidized form of kanamycin proved to be less effective as an antibiotic. Kanamycin inhibited the crystallization of KatG, but the smaller, structurally related glycoside maltose did cocrystallize with KatG, providing a suggestion as to the possible binding site of kanamycin.
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Affiliation(s)
- Peter
C. Loewen
- Department
of Microbiology, University of Manitoba, 45 Chancellor’s Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - P. Malaka De Silva
- Department
of Microbiology, University of Manitoba, 45 Chancellor’s Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Lynda J. Donald
- Department
of Microbiology, University of Manitoba, 45 Chancellor’s Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Jacek Switala
- Department
of Microbiology, University of Manitoba, 45 Chancellor’s Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Jacylyn Villanueva
- Department
of Microbiology, University of Manitoba, 45 Chancellor’s Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Ignacio Fita
- Instituto
de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Baldiri i Reixac 10-12, 08028 Barcelona, Spain
| | - Ayush Kumar
- Department
of Microbiology, University of Manitoba, 45 Chancellor’s Circle, Winnipeg, Manitoba R3T 2N2, Canada
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10
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Vila-Viçosa D, Victor BL, Ramos J, Machado D, Viveiros M, Switala J, Loewen PC, Leitão R, Martins F, Machuqueiro M. Insights on the Mechanism of Action of INH-C 10 as an Antitubercular Prodrug. Mol Pharm 2017; 14:4597-4605. [PMID: 29091448 DOI: 10.1021/acs.molpharmaceut.7b00719] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tuberculosis remains one of the top causes of death worldwide, and combating its spread has been severely complicated by the emergence of drug-resistance mutations, highlighting the need for more effective drugs. Despite the resistance to isoniazid (INH) arising from mutations in the katG gene encoding the catalase-peroxidase KatG, most notably the S315T mutation, this compound is still one of the most powerful first-line antitubercular drugs, suggesting further pursuit of the development of tailored INH derivatives. The N'-acylated INH derivative with a long alkyl chain (INH-C10) has been shown to be more effective than INH against the S315T variant of Mycobacterium tuberculosis, but the molecular details of this activity enhancement are still unknown. In this work, we show that INH N'-acylation significantly reduces the rate of production of both isonicotinoyl radical and isonicotinyl-NAD by wild type KatG, but not by the S315T variant of KatG mirroring the in vivo effectiveness of the compound. Restrained and unrestrained MD simulations of INH and its derivatives at the water/membrane interface were performed and showed a higher preference of INH-C10 for the lipidic phase combined with a significantly higher membrane permeability rate (27.9 cm s-1), compared with INH-C2 or INH (3.8 and 1.3 cm s-1, respectively). Thus, we propose that INH-C10 is able to exhibit better minimum inhibitory concentration (MIC) values against certain variants because of its better ability to permeate through the lipid membrane, enhancing its availability inside the cell. MIC values of INH and INH-C10 against two additional KatG mutations (S315N and D735A) revealed that some KatG variants are able to process INH faster than INH-C10 into an effective antitubercular form (wt and S315N), while others show similar reaction rates (S315T and D735A). Altogether, our results highlight the potential of increased INH lipophilicity for treating INH-resistant strains.
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Affiliation(s)
- Diogo Vila-Viçosa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa , 1749-016 Lisboa, Portugal
| | - Bruno L Victor
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa , 1749-016 Lisboa, Portugal
| | - Jorge Ramos
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa , 1349-008 Lisboa, Portugal
| | - Diana Machado
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa , 1349-008 Lisboa, Portugal
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa , 1349-008 Lisboa, Portugal
| | - Jacek Switala
- Department of Microbiology, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
| | - Peter C Loewen
- Department of Microbiology, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
| | - Ruben Leitão
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa , 1749-016 Lisboa, Portugal.,Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa , R. Conselheiro Emídio Navarro, 1, 1959-007, Lisboa, Portugal
| | - Filomena Martins
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa , 1749-016 Lisboa, Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa , 1749-016 Lisboa, Portugal
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11
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Laborde J, Deraeve C, Bernardes-Génisson V. Update of Antitubercular Prodrugs from a Molecular Perspective: Mechanisms of Action, Bioactivation Pathways, and Associated Resistance. ChemMedChem 2017; 12:1657-1676. [DOI: 10.1002/cmdc.201700424] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/12/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Julie Laborde
- CNRS; LCC (Laboratoire de Chimie de Coordination); 205, route de Narbonne, BP 44099 31077 Toulouse, Cedex 4 France
- Université de Toulouse; UPS, INPT; 31077 Toulouse, Cedex 4 France
| | - Céline Deraeve
- CNRS; LCC (Laboratoire de Chimie de Coordination); 205, route de Narbonne, BP 44099 31077 Toulouse, Cedex 4 France
- Université de Toulouse; UPS, INPT; 31077 Toulouse, Cedex 4 France
| | - Vania Bernardes-Génisson
- CNRS; LCC (Laboratoire de Chimie de Coordination); 205, route de Narbonne, BP 44099 31077 Toulouse, Cedex 4 France
- Université de Toulouse; UPS, INPT; 31077 Toulouse, Cedex 4 France
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12
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Njuma OJ, Davis I, Ndontsa EN, Krewall JR, Liu A, Goodwin DC. Mutual synergy between catalase and peroxidase activities of the bifunctional enzyme KatG is facilitated by electron hole-hopping within the enzyme. J Biol Chem 2017; 292:18408-18421. [PMID: 28972181 DOI: 10.1074/jbc.m117.791202] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 09/22/2017] [Indexed: 11/06/2022] Open
Abstract
KatG is a bifunctional, heme-dependent enzyme in the front-line defense of numerous bacterial and fungal pathogens against H2O2-induced oxidative damage from host immune responses. Contrary to the expectation that catalase and peroxidase activities should be mutually antagonistic, peroxidatic electron donors (PxEDs) enhance KatG catalase activity. Here, we establish the mechanism of synergistic cooperation between these activities. We show that at low pH values KatG can fully convert H2O2 to O2 and H2O only if a PxED is present in the reaction mixture. Stopped-flow spectroscopy results indicated rapid initial rates of H2O2 disproportionation slowing concomitantly with the accumulation of ferryl-like heme states. These states very slowly returned to resting (i.e. ferric) enzyme, indicating that they represented catalase-inactive intermediates. We also show that an active-site tryptophan, Trp-321, participates in off-pathway electron transfer. A W321F variant in which the proximal tryptophan was replaced with a non-oxidizable phenylalanine exhibited higher catalase activity and less accumulation of off-pathway heme intermediates. Finally, rapid freeze-quench EPR experiments indicated that both WT and W321F KatG produce the same methionine-tyrosine-tryptophan (MYW) cofactor radical intermediate at the earliest reaction time points and that Trp-321 is the preferred site of off-catalase protein oxidation in the native enzyme. Of note, PxEDs did not affect the formation of the MYW cofactor radical but could reduce non-productive protein-based radical species that accumulate during reaction with H2O2 Our results suggest that catalase-inactive intermediates accumulate because of off-mechanism oxidation, primarily of Trp-321, and PxEDs stimulate KatG catalase activity by preventing the accumulation of inactive intermediates.
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Affiliation(s)
- Olive J Njuma
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312
| | - Ian Davis
- the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249-0698, and.,the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Elizabeth N Ndontsa
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312
| | - Jessica R Krewall
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312
| | - Aimin Liu
- the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249-0698, and
| | - Douglas C Goodwin
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312,
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13
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Srivastava G, Tripathi S, Kumar A, Sharma A. Molecular investigation of active binding site of isoniazid (INH) and insight into resistance mechanism of S315T-MtKatG in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2017; 105:18-27. [DOI: 10.1016/j.tube.2017.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 12/19/2022]
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14
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Machuqueiro M, Victor B, Switala J, Villanueva J, Rovira C, Fita I, Loewen PC. The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine. Biochemistry 2017; 56:2271-2281. [DOI: 10.1021/acs.biochem.6b01276] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miguel Machuqueiro
- Centro de Química
e Bioquímica, Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Bruno Victor
- Centro de Química
e Bioquímica, Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Jacek Switala
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T
2N2, Canada
| | - Jacylyn Villanueva
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T
2N2, Canada
| | - Carme Rovira
- Departament de Química
Organica and Institut de Química Teòrica i Computacional
(IQTCUB), Universtat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Ignacio Fita
- Institut de Biología
Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Baldiri
i Reixac 10-12, 08028 Barcelona, Spain
| | - Peter C. Loewen
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T
2N2, Canada
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15
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Furkan M, Rizvi A, Alam MT, Naeem A. Peroxidase improves the activity of catalase by preventing aggregation during TFE-induced denaturation. J Biomol Struct Dyn 2017; 36:551-560. [DOI: 10.1080/07391102.2017.1287007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Mohammad Furkan
- Faculty of Life Sciences, Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Asim Rizvi
- Faculty of Life Sciences, Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Md Tauqir Alam
- Faculty of Life Sciences, Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Aabgeena Naeem
- Faculty of Life Sciences, Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
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16
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Abel zur Wiesch P, Clarelli F, Cohen T. Using Chemical Reaction Kinetics to Predict Optimal Antibiotic Treatment Strategies. PLoS Comput Biol 2017; 13:e1005321. [PMID: 28060813 PMCID: PMC5257006 DOI: 10.1371/journal.pcbi.1005321] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 01/23/2017] [Accepted: 12/19/2016] [Indexed: 11/19/2022] Open
Abstract
Identifying optimal dosing of antibiotics has proven challenging-some antibiotics are most effective when they are administered periodically at high doses, while others work best when minimizing concentration fluctuations. Mechanistic explanations for why antibiotics differ in their optimal dosing are lacking, limiting our ability to predict optimal therapy and leading to long and costly experiments. We use mathematical models that describe both bacterial growth and intracellular antibiotic-target binding to investigate the effects of fluctuating antibiotic concentrations on individual bacterial cells and bacterial populations. We show that physicochemical parameters, e.g. the rate of drug transmembrane diffusion and the antibiotic-target complex half-life are sufficient to explain which treatment strategy is most effective. If the drug-target complex dissociates rapidly, the antibiotic must be kept constantly at a concentration that prevents bacterial replication. If antibiotics cross bacterial cell envelopes slowly to reach their target, there is a delay in the onset of action that may be reduced by increasing initial antibiotic concentration. Finally, slow drug-target dissociation and slow diffusion out of cells act to prolong antibiotic effects, thereby allowing for less frequent dosing. Our model can be used as a tool in the rational design of treatment for bacterial infections. It is easily adaptable to other biological systems, e.g. HIV, malaria and cancer, where the effects of physiological fluctuations of drug concentration are also poorly understood.
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Affiliation(s)
- Pia Abel zur Wiesch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, Oslo, Norway
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Fabrizio Clarelli
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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17
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Brossier F, Boudinet M, Jarlier V, Petrella S, Sougakoff W. Comparative study of enzymatic activities of new KatG mutants from low- and high-level isoniazid-resistant clinical isolates of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2016; 100:15-24. [DOI: 10.1016/j.tube.2016.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 05/08/2016] [Accepted: 06/05/2016] [Indexed: 11/29/2022]
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18
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Cui ZJ, Yang QY, Zhang HY, Zhu Q, Zhang QY. Bioinformatics Identification of Drug Resistance-Associated Gene Pairs in Mycobacterium tuberculosis. Int J Mol Sci 2016; 17:ijms17091417. [PMID: 27618895 PMCID: PMC5037696 DOI: 10.3390/ijms17091417] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/16/2016] [Accepted: 08/22/2016] [Indexed: 12/27/2022] Open
Abstract
Tuberculosis is a chronic infectious disease caused by Mycobacterium tuberculosis (Mtb). Due to the extensive use of anti-tuberculosis drugs and the development of mutations, the emergence and spread of multidrug-resistant tuberculosis is recognized as one of the most dangerous threats to global tuberculosis control. Some single mutations have been identified to be significantly linked with drug resistance. However, the prior research did not take gene-gene interactions into account, and the emergence of transmissible drug resistance is connected with multiple genetic mutations. In this study we use the bioinformatics software GBOOST (The Hong Kong University, Clear Water Bay, Kowloon, Hong Kong, China) to calculate the interactions of Single Nucleotide Polymorphism (SNP) pairs and identify gene pairs associated with drug resistance. A large part of the non-synonymous mutations in the drug target genes that were included in the screened gene pairs were confirmed by previous reports, which lent sound solid credits to the effectiveness of our method. Notably, most of the identified gene pairs containing drug targets also comprise Pro-Pro-Glu (PPE) family proteins, suggesting that PPE family proteins play important roles in the drug resistance of Mtb. Therefore, this study provides deeper insights into the mechanisms underlying anti-tuberculosis drug resistance, and the present method is useful for exploring the drug resistance mechanisms for other microorganisms.
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Affiliation(s)
- Ze-Jia Cui
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qing-Yong Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qiang Zhu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qing-Ye Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
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19
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Kumar V, Sobhia ME. Molecular dynamics-based investigation of InhA substrate binding loop for diverse biological activity of direct InhA inhibitors. J Biomol Struct Dyn 2016; 34:2434-52. [DOI: 10.1080/07391102.2015.1118410] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Vivek Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar 160 062, Punjab, India
| | - M. Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar 160 062, Punjab, India
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20
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Abel Zur Wiesch P, Abel S, Gkotzis S, Ocampo P, Engelstädter J, Hinkley T, Magnus C, Waldor MK, Udekwu K, Cohen T. Classic reaction kinetics can explain complex patterns of antibiotic action. Sci Transl Med 2016; 7:287ra73. [PMID: 25972005 DOI: 10.1126/scitranslmed.aaa8760] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Finding optimal dosing strategies for treating bacterial infections is extremely difficult, and improving therapy requires costly and time-intensive experiments. To date, an incomplete mechanistic understanding of drug effects has limited our ability to make accurate quantitative predictions of drug-mediated bacterial killing and impeded the rational design of antibiotic treatment strategies. Three poorly understood phenomena complicate predictions of antibiotic activity: post-antibiotic growth suppression, density-dependent antibiotic effects, and persister cell formation. We show that chemical binding kinetics alone are sufficient to explain these three phenomena, using single-cell data and time-kill curves of Escherichia coli and Vibrio cholerae exposed to a variety of antibiotics in combination with a theoretical model that links chemical reaction kinetics to bacterial population biology. Our model reproduces existing observations, has a high predictive power across different experimental setups (R(2) = 0.86), and makes several testable predictions, which we verified in new experiments and by analyzing published data from a clinical trial on tuberculosis therapy. Although a variety of biological mechanisms have previously been invoked to explain post-antibiotic growth suppression, density-dependent antibiotic effects, and especially persister cell formation, our findings reveal that a simple model that considers only binding kinetics provides a parsimonious and unifying explanation for these three complex, phenotypically distinct behaviours. Current antibiotic and other chemotherapeutic regimens are often based on trial and error or expert opinion. Our "chemical reaction kinetics"-based approach may inform new strategies, which are based on rational design.
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Affiliation(s)
- Pia Abel Zur Wiesch
- Division of Global Health Equity, Brigham and Women's Hospital and Harvard Medical School, 641 Huntington Avenue, Boston, MA 02115, USA. Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, New Haven, CT 06510, USA.
| | - Sören Abel
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA. Department of Pharmacy, UiT, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Spyridon Gkotzis
- Department of Neuroscience, Karolinska Institutet, Retzius väg 8, 17177 Stockholm, Sweden
| | - Paolo Ocampo
- Institute of Integrative Biology, ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland. Department of Environmental Microbiology, EAWAG, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Jan Engelstädter
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Trevor Hinkley
- School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
| | - Carsten Magnus
- Institute of Medical Virology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA. Howard Hughes Medical Institute, 181 Longwood Avenue, Boston, MA 02115, USA
| | - Klas Udekwu
- Department of Neuroscience, Karolinska Institutet, Retzius väg 8, 17177 Stockholm, Sweden
| | - Ted Cohen
- Division of Global Health Equity, Brigham and Women's Hospital and Harvard Medical School, 641 Huntington Avenue, Boston, MA 02115, USA. Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, New Haven, CT 06510, USA. Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
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21
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Identification of novel loci associated with mycobacterial isoniazid resistance. Tuberculosis (Edinb) 2016; 96:21-6. [DOI: 10.1016/j.tube.2015.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/24/2015] [Accepted: 09/28/2015] [Indexed: 11/19/2022]
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22
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Loewen PC, Villanueva J, Switala J, Donald LJ, Ivancich A. Unprecedented access of phenolic substrates to the heme active site of a catalase: substrate binding and peroxidase-like reactivity of Bacillus pumilus catalase monitored by X-ray crystallography and EPR spectroscopy. Proteins 2015; 83:853-66. [PMID: 25663126 DOI: 10.1002/prot.24777] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/19/2015] [Accepted: 01/28/2015] [Indexed: 11/09/2022]
Abstract
Heme-containing catalases and catalase-peroxidases catalyze the dismutation of hydrogen peroxide as their predominant catalytic activity, but in addition, individual enzymes support low levels of peroxidase and oxidase activities, produce superoxide, and activate isoniazid as an antitubercular drug. The recent report of a heme enzyme with catalase, peroxidase and penicillin oxidase activities in Bacillus pumilus and its categorization as an unusual catalase-peroxidase led us to investigate the enzyme for comparison with other catalase-peroxidases, catalases, and peroxidases. Characterization revealed a typical homotetrameric catalase with one pentacoordinated heme b per subunit (Tyr340 being the axial ligand), albeit in two orientations, and a very fast catalatic turnover rate (kcat = 339,000 s(-1) ). In addition, the enzyme supported a much slower (kcat = 20 s(-1) ) peroxidatic activity utilizing substrates as diverse as ABTS and polyphenols, but no oxidase activity. Two binding sites, one in the main access channel and the other on the protein surface, accommodating pyrogallol, catechol, resorcinol, guaiacol, hydroquinone, and 2-chlorophenol were identified in crystal structures at 1.65-1.95 Å. A third site, in the heme distal side, accommodating only pyrogallol and catechol, interacting with the heme iron and the catalytic His and Arg residues, was also identified. This site was confirmed in solution by EPR spectroscopy characterization, which also showed that the phenolic oxygen was not directly coordinated to the heme iron (no low-spin conversion of the Fe(III) high-spin EPR signal upon substrate binding). This is the first demonstration of phenolic substrates directly accessing the heme distal side of a catalase.
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Affiliation(s)
- Peter C Loewen
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
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23
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Teixeira VH, Ventura C, Leitão R, Ràfols C, Bosch E, Martins F, Machuqueiro M. Molecular Details of INH-C10 Binding to wt KatG and Its S315T Mutant. Mol Pharm 2015; 12:898-909. [DOI: 10.1021/mp500736n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Vitor H. Teixeira
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Cristina Ventura
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Instituto Superior de Educação e Ciências, Alameda das Linhas de Torres 179, 1750 Lisboa, Portugal
| | - Ruben Leitão
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Área
Departamental de Engenharia Química, Instituto Superior de
Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro
Emídio Navarro, 1, 1959-007 Lisboa, Portugal
| | - Clara Ràfols
- Departament
de Química Analítica and Institut de Biomedicina (IBUB), Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Elisabeth Bosch
- Departament
de Química Analítica and Institut de Biomedicina (IBUB), Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Filomena Martins
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Miguel Machuqueiro
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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24
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Bogdándi V, Lente G, Fábián I. Kinetics of the oxidation of isoniazid with the hypochlorite ion. RSC Adv 2015. [DOI: 10.1039/c5ra13540k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Isoniazid is oxidized within 1–10 seconds by the hypochlorite ion in a process that is first order with respect to both reactants and shows somewhat complicated stoichiometry.
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Affiliation(s)
- Virág Bogdándi
- Department of Inorganic and Analytical Chemistry
- University of Debrecen
- Debrecen
- Hungary
| | - Gábor Lente
- Department of Inorganic and Analytical Chemistry
- University of Debrecen
- Debrecen
- Hungary
| | - István Fábián
- Department of Inorganic and Analytical Chemistry
- University of Debrecen
- Debrecen
- Hungary
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25
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Kamachi S, Hirabayashi K, Tamoi M, Shigeoka S, Tada T, Wada K. Crystal structure of the catalase-peroxidase KatG W78F mutant from Synechococcus elongatus PCC7942 in complex with the antitubercular pro-drug isoniazid. FEBS Lett 2014; 589:131-7. [PMID: 25479089 DOI: 10.1016/j.febslet.2014.11.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/21/2014] [Accepted: 11/23/2014] [Indexed: 10/24/2022]
Abstract
Isoniazid (INH) is a pro-drug that has been extensively used to treat tuberculosis. INH is activated by the heme enzyme catalase-peroxidase (KatG), but the mechanism of the activation is poorly understood, in part because the INH binding site has not been clearly established. Here, we observed that a single-residue mutation of KatG from Synechococcus elongatus PCC7942 (SeKatG), W78F, enhances INH activation. The crystal structure of INH-bound KatG-W78F revealed that INH binds to the heme pocket. The results of a thermal-shift assay implied that the flexibility of the SeKatG molecule is increased by the W78F mutation, allowing the INH molecule to easily invade the heme pocket through the access channel on the γ-edge side of the heme.
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Affiliation(s)
- Saori Kamachi
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Kei Hirabayashi
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan; Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Masahiro Tamoi
- Faculty of Agriculture, Kinki University, Nakamachi, Nara 631-8505, Japan
| | - Shigeru Shigeoka
- Faculty of Agriculture, Kinki University, Nakamachi, Nara 631-8505, Japan
| | - Toshiji Tada
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.
| | - Kei Wada
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan.
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26
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Sousa EHS, de Mesquita Vieira FG, Butler JS, Basso LA, Santiago DS, Diógenes IC, Lopes LGDF, Sadler PJ. [Fe(CN)5(isoniazid)]3−: An iron isoniazid complex with redox behavior implicated in tuberculosis therapy. J Inorg Biochem 2014; 140:236-44. [DOI: 10.1016/j.jinorgbio.2014.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/04/2014] [Accepted: 08/05/2014] [Indexed: 01/07/2023]
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27
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Kamachi S, Hirabayashi K, Tamoi M, Shigeoka S, Tada T, Wada K. The crystal structure of isoniazid-bound KatG catalase-peroxidase from Synechococcus elongatus PCC7942. FEBS J 2014; 282:54-64. [PMID: 25303560 DOI: 10.1111/febs.13102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 09/26/2014] [Accepted: 10/06/2014] [Indexed: 11/28/2022]
Abstract
Isoniazid (INH) is one of the most effective antibiotics against tuberculosis. INH is a prodrug that is activated by KatG. Although extensive studies have been performed in order to understand the mechanism of KatG, even the binding site of INH in KatG remains controversial. In this study, we determined the crystal structure of KatG from Synechococcus elongatus PCC7942 (SeKatG) in a complex with INH at 2.12-Å resolution. Three INH molecules were bound to the molecular surface. One INH molecule was bound at the entrance to the ε-edge side of heme (designated site 1), another was bound at the entrance to the γ-edge side of heme (site 2), and another was bound to the loop structures in front of the heme propionate side chain (site 3). All of the interactions between KatG and the bound INH seemed to be weak, being mediated mainly by van der Waals contacts. Structural comparisons revealed that the identity and configuration of the residues in site 1 were very similar among SeKatG, Burkholderia pseudomallei KatG, and Mycobacterium tuberculosis KatG. In contrast, sites 2 and 3 were structurally diverse among the three proteins. Thus, site 1 is probably the common KatG INH-binding site. A static enzymatic analysis and thermal shift assay suggested that the INH-activating reaction does not proceed in site 1, but rather that this site may function as an initial trapping site for the INH molecule. Database: The atomic coordinates and structure factors have been deposited in the Protein Data Bank under the accession number 3WXO.
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Affiliation(s)
- Saori Kamachi
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
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28
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Zhao X, Hersleth HP, Zhu J, Andersson KK, Magliozzo RS. Access channel residues Ser315 and Asp137 in Mycobacterium tuberculosis catalase-peroxidase (KatG) control peroxidatic activation of the pro-drug isoniazid. Chem Commun (Camb) 2014; 49:11650-2. [PMID: 24185282 DOI: 10.1039/c3cc47022a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peroxidatic activation of the anti-tuberculosis pro-drug isoniazid by Mycobacterium tuberculosis catalase-peroxidase (KatG) is regulated by gating residues of a heme access channel. The steric restriction at the bottleneck of this channel is alleviated by replacement of residue Asp137 with Ser, according to crystallographic and kinetic studies.
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Affiliation(s)
- Xiangbo Zhao
- Department of Chemistry, Brooklyn College and The Graduate Center of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA.
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29
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Miner KD, Pfister TD, Hosseinzadeh P, Karaduman N, Donald LJ, Loewen PC, Lu Y, Ivancich A. Identifying the elusive sites of tyrosyl radicals in cytochrome c peroxidase: implications for oxidation of substrates bound at a site remote from the heme. Biochemistry 2014; 53:3781-9. [PMID: 24901481 PMCID: PMC4063442 DOI: 10.1021/bi500353p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The location of the Trp radical and the catalytic function of the [Fe(IV)═O Trp₁₉₁(•+)] intermediate in cytochrome c peroxidase (CcP) are well-established; however, the unambiguous identification of the site(s) for the formation of tyrosyl radical(s) and their possible biological roles remain elusive. We have now performed a systematic investigation of the location and reactivity of the Tyr radical(s) using multifrequency Electron Paramagnetic Resonance (EPR) spectroscopy combined with multiple-site Trp/Tyr mutations in CcP. Two tyrosines, Tyr71 and Tyr236, were identified as those contributing primarily to the EPR spectrum of the tyrosyl radical, recorded at 9 and 285 GHz. The EPR characterization also showed that the heme distal-side Trp51 is involved in the intramolecular electron transfer between Tyr71 and the heme and that formation of Tyr₇₁(•) and Tyr₂₃₆(•) is independent of the [Fe(IV)═O Trp₁₉₁(•+)] intermediate. Tyr71 is located in an optimal position to mediate the oxidation of substrates binding at a site, more than 20 Å from the heme, which has been reported recently in the crystal structures of CcP with bound guaicol and phenol [Murphy, E. J., et al. (2012) FEBS J. 279, 1632-1639]. The possibility of discriminating the radical intermediates by their EPR spectra allowed us to identify Tyr₇₁(•) as the reactive species with the guaiacol substrate. Our assignment of the surface-exposed Tyr236 as the other radical site agrees well with previous studies based on MNP labeling and protein cross-linking [Tsaprailis, G., and English, A. M. (2003) JBIC, J. Biol. Inorg. Chem. 8, 248-255] and on its covalent modification upon reaction of W191G CcP with 2-aminotriazole [Musah, R. A., and Goodin, D. B. (1997) Biochemistry 36, 11665-11674]. Accordingly, while Tyr71 acts as a true reactive intermediate for the oxidation of certain small substrates that bind at a site remote from the heme, the surface-exposed Tyr236 would be more likely related to oxidative stress signaling, as previously proposed. Our findings reinforce the view that CcP is the monofunctional peroxidase that most closely resembles its ancestor enzymes, the catalase-peroxidases, in terms of the higher complexity of the peroxidase reaction [Colin, J., et al. (2009) J. Am. Chem. Soc. 131, 8557-8563]. The strategy used to identify the elusive Tyr radical sites in CcP may be applied to other heme enzymes containing a large number of Tyr and Trp residues and for which Tyr (or Trp) radicals have been proposed to be involved in their peroxidase or peroxidase-like reaction.
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Affiliation(s)
- Kyle D Miner
- CNRS, Unité de Recherche Mixte CNRS/CEA/Université Paris-Sud (UMR 8221), Laboratoire de Bioénergétique, Métalloprotéines et Stress. Centre d'Etudes de Saclay, iBiTec-S, 91191 Gif-sur-Yvette, France
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30
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Loewen PC, Carpena X, Vidossich P, Fita I, Rovira C. An Ionizable Active-Site Tryptophan Imparts Catalase Activity to a Peroxidase Core. J Am Chem Soc 2014; 136:7249-52. [DOI: 10.1021/ja502794e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Peter C. Loewen
- Department
of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | | | - Pietro Vidossich
- Departament
de Química, Edifici Cn., Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | | | - Carme Rovira
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08020 Barcelona, Spain
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31
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Vidossich P, Loewen PC, Carpena X, Fiorin G, Fita I, Rovira C. Binding of the Antitubercular Pro-Drug Isoniazid in the Heme Access Channel of Catalase-Peroxidase (KatG). A Combined Structural and Metadynamics Investigation. J Phys Chem B 2014; 118:2924-31. [DOI: 10.1021/jp4123425] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pietro Vidossich
- Unitat de Química
Física, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Peter C. Loewen
- Department
of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Xavi Carpena
- IRB Barcelona, Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Giacomo Fiorin
- Institute for
Computational Molecular Science, Temple University, 1900 N. 12th Street, Philadelphia, PA 19122, United States
| | - Ignacio Fita
- Institut de Biologia
Molecular (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Carme Rovira
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
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32
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Kamachi S, Wada K, Tamoi M, Shigeoka S, Tada T. The 2.2 Å resolution structure of the catalase-peroxidase KatG from Synechococcus elongatus PCC7942. Acta Crystallogr F Struct Biol Commun 2014; 70:288-93. [PMID: 24598912 PMCID: PMC3944687 DOI: 10.1107/s2053230x14002052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 01/29/2014] [Indexed: 03/24/2024] Open
Abstract
The crystal structure of catalase-peroxidase from Synechococcus elongatus PCC7942 (SeKatG) was solved by molecular replacement and refined to an Rwork of 16.8% and an Rfree of 20.6% at 2.2 Å resolution. The asymmetric unit consisted of only one subunit of the catalase-peroxidase molecule, including a protoporphyrin IX haem moiety and two sodium ions. A typical KatG covalent adduct was formed, Met248-Tyr222-Trp94, which is a key structural element for catalase activity. The crystallographic equivalent subunit was created by a twofold symmetry operation to form the functional dimer. The overall structure of the dimer was quite similar to other KatGs. One sodium ion was located close to the proximal Trp314. The location and configuration of the proximal cation site were very similar to those of typical peroxidases such as ascorbate peroxidase. These features may provide a structural basis for the behaviour of the radical localization/delocalization during the course of the enzymatic reaction.
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Affiliation(s)
- Saori Kamachi
- School of Graduate Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Kei Wada
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki, Miyazaki 889-1692, Japan
| | - Masahiro Tamoi
- Faculty of Agriculture, Kinki University, Nara, Nara 631-8505, Japan
| | - Shigeru Shigeoka
- Faculty of Agriculture, Kinki University, Nara, Nara 631-8505, Japan
| | - Toshiji Tada
- School of Graduate Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
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33
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Njuma OJ, Ndontsa EN, Goodwin DC. Catalase in peroxidase clothing: Interdependent cooperation of two cofactors in the catalytic versatility of KatG. Arch Biochem Biophys 2013; 544:27-39. [PMID: 24280274 DOI: 10.1016/j.abb.2013.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 11/11/2013] [Accepted: 11/15/2013] [Indexed: 11/26/2022]
Abstract
Catalase-peroxidase (KatG) is found in eubacteria, archaea, and lower eukaryotae. The enzyme from Mycobacterium tuberculosis has received the greatest attention because of its role in activation of the antitubercular pro-drug isoniazid, and the high frequency with which drug resistance stems from mutations to the katG gene. Generally, the catalase activity of KatGs is striking. It rivals that of typical catalases, enzymes with which KatGs share no structural similarity. Instead, catalatic turnover is accomplished with an active site that bears a strong resemblance to a typical peroxidase (e.g., cytochrome c peroxidase). Yet, KatG is the only member of its superfamily with such capability. It does so using two mutually dependent cofactors: a heme and an entirely unique Met-Tyr-Trp (MYW) covalent adduct. Heme is required to generate the MYW cofactor. The MYW cofactor allows KatG to leverage heme intermediates toward a unique mechanism for H2O2 oxidation. This review evaluates the range of intermediates identified and their connection to the diverse catalytic processes KatG facilitates, including mechanisms of isoniazid activation.
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Affiliation(s)
- Olive J Njuma
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA
| | - Elizabeth N Ndontsa
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA
| | - Douglas C Goodwin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA.
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34
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Ivancich A, Donald LJ, Villanueva J, Wiseman B, Fita I, Loewen PC. Spectroscopic and kinetic investigation of the reactions of peroxyacetic acid with Burkholderia pseudomallei catalase-peroxidase, KatG. Biochemistry 2013; 52:7271-82. [PMID: 24044787 DOI: 10.1021/bi400963j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Catalase-peroxidases or KatGs can utilize organic peroxyacids and peroxides instead of hydrogen peroxide to generate the high-valent ferryl-oxo intermediates involved in the catalase and peroxidase reactions. In the absence of peroxidatic one-electron donors, the ferryl intermediates generated with a low excess (10-fold) of peroxyacetic acid (PAA) slowly decay to the ferric resting state after several minutes, a reaction that is demonstrated in this work by both stopped-flow UV-vis absorption measurements and EPR spectroscopic characterization of Burkholderia pseudomallei KatG (BpKatG). EPR spectroscopy showed that the [Fe(IV)═O Trp330(•+)], [Fe(IV)═O Trp139(•)], and [Fe(IV)═O Trp153(•)] intermediates of the peroxidase-like cycle of BpKatG ( Colin, J. Wiseman, B. Switala, J. Loewen, P. C. Ivancich, A. ( 2009 ) J. Am. Chem. Soc. 131 , 8557 - 8563 ), formed with a low excess of PAA at low temperature, are also generated with a high excess (1000-fold) of PAA at room temperature. However, under high excess conditions, there is a rapid conversion to a persistent [Fe(IV)═O] intermediate. Analysis of tryptic peptides of BpKatG by mass spectrometry before and after treatment with PAA showed that specific tryptophan (including W330, W139, and W153), methionine (including Met264 of the M-Y-W adduct), and cysteine residues are either modified with one, two, or three oxygen atoms or could not be identified in the spectrum because of other undetermined modifications. It was concluded that these oxidized residues were the source of electrons used to reduce the excess of PAA to acetic acid and return the enzyme to the ferric state. Treatment of BpKatG with PAA also caused a loss of catalase activity towards certain substrates, consistent with oxidative disruption of the M-Y-W adduct, and a loss of peroxidase activity, consistent with accumulation of the [Fe(IV)═O] intermediate and the oxidative modification of the W330, W139, and W153. PAA, but not H2O2 or tert-butyl hydroperoxide, also caused subunit cross-linking.
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Affiliation(s)
- Anabella Ivancich
- CNRS, Unité de Recherche Mixte CNRS/CEA/Université Paris Sud (UMR 8221), Laboratoire de Bioénergétique, Métalloprotéines et Stress, Centre d'Etudes de Saclay/iBiTec-S , 91191 Gif-sur-Yvette, France
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35
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Chim N, Owens CP, Contreras H, Goulding CW. Withdrawn. Infect Disord Drug Targets 2012:CDTID-EPUB-20121116-2. [PMID: 23167715 PMCID: PMC3695056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Withdrawn by the publisher.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Cedric P. Owens
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Heidi Contreras
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Celia W. Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine CA 92697, USA
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36
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Forbes LV, Furtmüller PG, Khalilova I, Turner R, Obinger C, Kettle AJ. Isoniazid as a substrate and inhibitor of myeloperoxidase: Identification of amine adducts and the influence of superoxide dismutase on their formation. Biochem Pharmacol 2012; 84:949-60. [DOI: 10.1016/j.bcp.2012.07.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 07/17/2012] [Accepted: 07/18/2012] [Indexed: 12/01/2022]
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37
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Zámocký M, García-Fernández Q, Gasselhuber B, Jakopitsch C, Furtmüller PG, Loewen PC, Fita I, Obinger C, Carpena X. High conformational stability of secreted eukaryotic catalase-peroxidases: answers from first crystal structure and unfolding studies. J Biol Chem 2012; 287:32254-62. [PMID: 22822072 PMCID: PMC3442556 DOI: 10.1074/jbc.m112.384271] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 07/03/2012] [Indexed: 11/06/2022] Open
Abstract
Catalase-peroxidases (KatGs) are bifunctional heme enzymes widely spread in archaea, bacteria, and lower eukaryotes. Here we present the first crystal structure (1.55 Å resolution) of an eukaryotic KatG, the extracellular or secreted enzyme from the phytopathogenic fungus Magnaporthe grisea. The heme cavity of the homodimeric enzyme is similar to prokaryotic KatGs including the unique distal (+)Met-Tyr-Trp adduct (where the Trp is further modified by peroxidation) and its associated mobile arginine. The structure also revealed several conspicuous peculiarities that are fully conserved in all secreted eukaryotic KatGs. Peculiarities include the wrapping at the dimer interface of the N-terminal elongations from the two subunits and cysteine residues that cross-link the two subunits. Differential scanning calorimetry and temperature- and urea-mediated unfolding followed by UV-visible, circular dichroism, and fluorescence spectroscopy combined with site-directed mutagenesis demonstrated that secreted eukaryotic KatGs have a significantly higher conformational stability as well as a different unfolding pattern when compared with intracellular eukaryotic and prokaryotic catalase-peroxidases. We discuss these properties with respect to the structure as well as the postulated roles of this metalloenzyme in host-pathogen interactions.
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Affiliation(s)
- Marcel Zámocký
- From the Department of Chemistry, Division of Biochemistry, BOKU, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
- the Laboratory of Molecular Microbiology, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
| | - Queralt García-Fernández
- the Institute for Research in Biomedicine (IRB Barcelona) and Institut de Biologia Molecular de Barcelona (IBMB) from Consell Superior d'Investigacions Científiques (CSIC), Parc Científic, 08028 Barcelona, Spain, and
| | - Bernhard Gasselhuber
- From the Department of Chemistry, Division of Biochemistry, BOKU, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Christa Jakopitsch
- From the Department of Chemistry, Division of Biochemistry, BOKU, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Paul G. Furtmüller
- From the Department of Chemistry, Division of Biochemistry, BOKU, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Peter C. Loewen
- the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Ignacio Fita
- the Institute for Research in Biomedicine (IRB Barcelona) and Institut de Biologia Molecular de Barcelona (IBMB) from Consell Superior d'Investigacions Científiques (CSIC), Parc Científic, 08028 Barcelona, Spain, and
| | - Christian Obinger
- From the Department of Chemistry, Division of Biochemistry, BOKU, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Xavi Carpena
- the Institute for Research in Biomedicine (IRB Barcelona) and Institut de Biologia Molecular de Barcelona (IBMB) from Consell Superior d'Investigacions Científiques (CSIC), Parc Científic, 08028 Barcelona, Spain, and
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38
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Ndontsa EN, Moore RL, Goodwin DC. Stimulation of KatG catalase activity by peroxidatic electron donors. Arch Biochem Biophys 2012; 525:215-22. [DOI: 10.1016/j.abb.2012.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/25/2012] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
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Brown-Elliott BA, Nash KA, Wallace RJ. Antimicrobial susceptibility testing, drug resistance mechanisms, and therapy of infections with nontuberculous mycobacteria. Clin Microbiol Rev 2012; 25:545-82. [PMID: 22763637 PMCID: PMC3416486 DOI: 10.1128/cmr.05030-11] [Citation(s) in RCA: 335] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Within the past 10 years, treatment and diagnostic guidelines for nontuberculous mycobacteria have been recommended by the American Thoracic Society (ATS) and the Infectious Diseases Society of America (IDSA). Moreover, the Clinical and Laboratory Standards Institute (CLSI) has published and recently (in 2011) updated recommendations including suggested antimicrobial and susceptibility breakpoints. The CLSI has also recommended the broth microdilution method as the gold standard for laboratories performing antimicrobial susceptibility testing of nontuberculous mycobacteria. This article reviews the laboratory, diagnostic, and treatment guidelines together with established and probable drug resistance mechanisms of the nontuberculous mycobacteria.
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40
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Mishra S, Imlay J. Why do bacteria use so many enzymes to scavenge hydrogen peroxide? Arch Biochem Biophys 2012; 525:145-60. [PMID: 22609271 DOI: 10.1016/j.abb.2012.04.014] [Citation(s) in RCA: 263] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 04/13/2012] [Accepted: 04/14/2012] [Indexed: 12/16/2022]
Abstract
Hydrogen peroxide (H(2)O(2)) is continuously formed by the autoxidation of redox enzymes in aerobic cells, and it also enters from the environment, where it can be generated both by chemical processes and by the deliberate actions of competing organisms. Because H(2)O(2) is acutely toxic, bacteria elaborate scavenging enzymes to keep its intracellular concentration at nanomolar levels. Mutants that lack such enzymes grow poorly, suffer from high rates of mutagenesis, or even die. In order to understand how bacteria cope with oxidative stress, it is important to identify the key enzymes involved in H(2)O(2) degradation. Catalases and NADH peroxidase (Ahp) are primary scavengers in many bacteria, and their activities and physiological impacts have been unambiguously demonstrated through phenotypic analysis and through direct measurements of H(2)O(2) clearance in vivo. Yet a wide variety of additional enzymes have been proposed to serve similar roles: thiol peroxidase, bacterioferritin comigratory protein, glutathione peroxidase, cytochrome c peroxidase, and rubrerythrins. Each of these enzymes can degrade H(2)O(2) in vitro, but their contributions in vivo remain unclear. In this review we examine the genetic, genomic, regulatory, and biochemical evidence that each of these is a bonafide scavenger of H(2)O(2) in the cell. We also consider possible reasons that bacteria might require multiple enzymes to catalyze this process, including differences in substrate specificity, compartmentalization, cofactor requirements, kinetic optima, and enzyme stability. It is hoped that the resolution of these issues will lead to an understanding of stress resistance that is more accurate and perceptive.
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Affiliation(s)
- Surabhi Mishra
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
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41
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Thirty years of heme catalases structural biology. Arch Biochem Biophys 2011; 525:102-10. [PMID: 22209752 DOI: 10.1016/j.abb.2011.12.011] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 12/13/2011] [Accepted: 12/15/2011] [Indexed: 11/23/2022]
Abstract
About thirty years ago the crystal structures of the heme catalases from Penicillium vitale (PVC) and, a few months later, from bovine liver (BLC) were published. Both enzymes were compact tetrameric molecules with subunits that, despite their size differences and the large phylogenetic separation between the two organisms, presented a striking structural similarity for about 460 residues. The high conservation, confirmed in all the subsequent structures determined, suggested a strong pressure to preserve a functional catalase fold, which is almost exclusively found in these mono-functional heme catalases. However, even in the absence of the catalase fold an efficient catalase activity is also found in the heme containing catalase-peroxidase proteins. The structure of these broad substrate range enzymes, reported for the first time less than ten years ago from the halophilic archaebacterium Haloarcula marismortui (HmCPx) and from the bacterium Burkholderia pseudomallei (BpKatG), showed a heme pocket closely related to that of plant peroxidases, though with a number of unique modifications that enable the catalase reaction. Despite the wealth of structural information already available, for both monofunctional catalases and catalase-peroxidases, a number of unanswered major questions require continuing structural research with truly innovative approaches.
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Torres E, Moreno E, Ancizu S, Barea C, Galiano S, Aldana I, Monge A, Pérez-Silanes S. New 1,4-di-N-oxide-quinoxaline-2-ylmethylene isonicotinic acid hydrazide derivatives as anti-Mycobacterium tuberculosis agents. Bioorg Med Chem Lett 2011; 21:3699-703. [DOI: 10.1016/j.bmcl.2011.04.072] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 04/15/2011] [Accepted: 04/19/2011] [Indexed: 11/30/2022]
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Organic hydroperoxide resistance protein and ergothioneine compensate for loss of mycothiol in Mycobacterium smegmatis mutants. J Bacteriol 2011; 193:1981-90. [PMID: 21335456 DOI: 10.1128/jb.01402-10] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The mshA::Tn5 mutant of Mycobacterium smegmatis does not produce mycothiol (MSH) and was found to markedly overproduce both ergothioneine and an ~15-kDa protein determined to be organic hydroperoxide resistance protein (Ohr). An mshA(G32D) mutant lacking MSH overproduced ergothioneine but not Ohr. Comparison of the mutant phenotypes with those of the wild-type strain indicated the following: Ohr protects against organic hydroperoxide toxicity, whereas ergothioneine does not; an additional MSH-dependent organic hydroperoxide peroxidase exists; and elevated isoniazid resistance in the mutant is associated with both Ohr and the absence of MSH. Purified Ohr showed high activity with linoleic acid hydroperoxide, indicating lipid hydroperoxides as the likely physiologic targets. The reduction of oxidized Ohr by NADH was shown to be catalyzed by lipoamide dehydrogenase and either lipoamide or DlaT (SucB). Since free lipoamide and lipoic acid levels were shown to be undetectable in M. smegmatis, the bound lipoyl residues of DlaT are the likely source of the physiological dithiol reductant for Ohr. The pattern of occurrence of homologs of Ohr among bacteria suggests that the ohr gene has been distributed by lateral transfer. The finding of multiple Ohr homologs with various sequence identities in some bacterial genomes indicates that there may be multiple physiologic targets for Ohr proteins.
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