ACS Publications. Most Trusted. Most Cited. Most Read
My Activity

Figure 1Loading Img

Binding of the Antitubercular Pro-Drug Isoniazid in the Heme Access Channel of Catalase-Peroxidase (KatG). A Combined Structural and Metadynamics Investigation

View Author Information
Unitat de Química Física, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
§ IRB Barcelona, Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
Institute for Computational Molecular Science, Temple University, 1900 N. 12th Street, Philadelphia, PA 19122, United States
Institut de Biologia Molecular (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
@ 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
*E-mail: [email protected]. Tel: +34 93 4039254. Fax: +34 93 3397878.
Cite this: J. Phys. Chem. B 2014, 118, 11, 2924–2931
Publication Date (Web):February 26, 2014
Copyright © 2014 American Chemical Society

    Article Views





    Read OnlinePDF (4 MB)
    Supporting Info (1)»


    Abstract Image

    Isonicotinic acid hydrazide (isoniazid or INH) is a front line antitubercular pro-drug that is converted to its active form, isonicotinyl-NAD, by the bacterial catalase-peroxidase KatG. Understanding the role of KatG in the INH activation process has been hampered by a lack of knowledge of the actual drug binding site. In this work, we have investigated the binding of INH in the main access channel of KatG with a combination of molecular dynamics, using an enhanced-sampling technique (metadynamics), X-ray crystallography, and site-directed mutagenesis. The metadynamics simulations show that there are several weak drug binding sites along the access channel. Moreover, the simulations evidence that complete entrance to the heme active site is impeded by an aspartate residue (D141) located above the heme. This has been confirmed by structural and functional analysis of the D141A mutant, leading to the first X-ray crystallography evidence of INH at the heme access channel.

    Supporting Information

    Jump To

    Further details of the calculations and inhibition data. This material is available free of charge via the Internet at

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system:

    Cited By

    This article is cited by 26 publications.

    1. Diogo Vila-Viçosa, Bruno L. Victor, Jorge Ramos, Diana Machado, Miguel Viveiros, Jacek Switala, Peter C. Loewen, Ruben Leitão, Filomena Martins, and Miguel Machuqueiro . Insights on the Mechanism of Action of INH-C10 as an Antitubercular Prodrug. Molecular Pharmaceutics 2017, 14 (12) , 4597-4605.
    2. Miguel Machuqueiro , Bruno Victor , Jacek Switala , Jacylyn Villanueva , Carme Rovira , Ignacio Fita , Peter C. Loewen . The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine. Biochemistry 2017, 56 (17) , 2271-2281.
    3. Jacopo Sgrignani, Marcella Iannuzzi, and Alessandra Magistrato . Role of Water in the Puzzling Mechanism of the Final Aromatization Step Promoted by the Human Aromatase Enzyme. Insights from QM/MM MD Simulations. Journal of Chemical Information and Modeling 2015, 55 (10) , 2218-2226.
    4. Vitor H. Teixeira, Cristina Ventura, Ruben Leitão, Clara Ràfols, Elisabeth Bosch, Filomena Martins, and Miguel Machuqueiro . Molecular Details of INH-C10 Binding to wt KatG and Its S315T Mutant. Molecular Pharmaceutics 2015, 12 (3) , 898-909.
    5. Somanna Ajjamada Nachappa, Sumana M. Neelambike, Nallur B. Ramachandra. Differential expression of the Mycobacterium tuberculosis heat shock protein genes in response to drug-induced stress. Tuberculosis 2022, 134 , 102201.
    6. Shahinda S. R. Alsayed, Shichun Lun, Alan Payne, William R. Bishai, Hendra Gunosewoyo. Facile synthesis and antimycobacterial activity of isoniazid, pyrazinamide and ciprofloxacin derivatives. Chemical Biology & Drug Design 2021, 97 (6) , 1137-1150.
    7. Salma Jamal, Mohd. Khubaib, Rishabh Gangwar, Sonam Grover, Abhinav Grover, Seyed E. Hasnain. Artificial Intelligence and Machine learning based prediction of resistant and susceptible mutations in Mycobacterium tuberculosis. Scientific Reports 2020, 10 (1)
    8. Sy-Bing Choi, Beow Keat Yap, Yee Siew Choong, Habibah Wahab. Molecular Dynamics Simulations in Drug Discovery. 2019, 652-665.
    9. Ameeruddin Nusrath Unissa, George Priya Doss C, Thirumal Kumar, Swathi Sukumar, Appisetty Ramya Lakshmi, Luke Elizabeth Hanna. Significance of catalase-peroxidase (KatG) mutations in mediating isoniazid resistance in clinical strains of Mycobacterium tuberculosis. Journal of Global Antimicrobial Resistance 2018, 15 , 111-120.
    10. Hessam Sepasi Tehrani, Ali Akbar Moosavi-Movahedi. Catalase and its mysteries. Progress in Biophysics and Molecular Biology 2018, 140 , 5-12.
    11. Stephanie Portelli, Jody E. Phelan, David B. Ascher, Taane G. Clark, Nicholas Furnham. Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis. Scientific Reports 2018, 8 (1)
    12. Somanna Ajjamada Nachappa, Sumana M. Neelambike, Chokkanna Amruthavalli, Nallur B. Ramachandra. Detection of First-Line Drug Resistance Mutations and Drug–Protein Interaction Dynamics from Tuberculosis Patients in South India. Microbial Drug Resistance 2018, 24 (4) , 377-385.
    13. Vanessa Vega-García, Adelaida Díaz-Vilchis, Juan Pablo Saucedo-Vázquez, Alejandro Solano-Peralta, Enrique Rudiño-Piñera, Wilhelm Hansberg. Structure, kinetics, molecular and redox properties of a cytosolic and developmentally regulated fungal catalase-peroxidase. Archives of Biochemistry and Biophysics 2018, 640 , 17-26.
    14. Juan Duan, Chuncai Hu, Jiafan Guo, Lianxian Guo, Jia Sun, Zuguo Zhao. A molecular dynamics study of the complete binding process of meropenem to New Delhi metallo-β-lactamase 1. Physical Chemistry Chemical Physics 2018, 20 (9) , 6409-6420.
    15. Julie Laborde, Céline Deraeve, Vania Bernardes-Génisson. Update of Antitubercular Prodrugs from a Molecular Perspective: Mechanisms of Action, Bioactivation Pathways, and Associated Resistance. ChemMedChem 2017, 12 (20) , 1657-1676.
    16. Gaurava Srivastava, Shubhandra Tripathi, Akhil Kumar, Ashok Sharma. Molecular investigation of active binding site of isoniazid (INH) and insight into resistance mechanism of S315T-MtKatG in Mycobacterium tuberculosis. Tuberculosis 2017, 105 , 18-27.
    17. Arethusa Lobo Pimentel, Regiane Bertin de Lima Scodro, Katiany Rizzieri Caleffi-Ferracioli, Vera Lúcia Dias Siqueira, Paula Aline Zanetti Campanerut-Sá, Luciana Dias Ghiraldi Lopes, Aryadne Larissa de Almeida, Rosilene Fressatti Cardoso, Flavio Augusto Vicente Seixas. Mutations in catalase-peroxidase KatG from isoniazid resistant Mycobacterium tuberculosis clinical isolates: insights from molecular dynamics simulations. Journal of Molecular Modeling 2017, 23 (4)
    18. Gargi Datta, Luisa M. Nieto, Rebecca M. Davidson, Carolina Mehaffy, Caroline Pederson, Karen M. Dobos, Michael Strong. Longitudinal whole genome analysis of pre and post drug treatment Mycobacterium tuberculosis isolates reveals progressive steps to drug resistance. Tuberculosis 2016, 98 , 50-55.
    19. Zhi-Hua Pei, Ting Xie, Qing-Yong Yang, Qing-Ye Zhang, Hong-Yu Zhang. Novel Isoniazid- and Ethionamide-resistance loci in mycobacterium tuberculosis identified by phenome-wide association scans. 2015, 1129-1132.
    20. Bernhard Gasselhuber, Christa Jakopitsch, Marcel Zámocký, Paul G. Furtmüller, Christian Obinger. Mechanistic Aspects of Catalase-peroxidase. 2015, 156-180.
    21. Hanna Kwon, Peter C. E. Moody, Emma L. Raven. Understanding the Reactivity and Interactions of Peroxidases with Substrates. 2015, 47-60.
    22. Ignacio Fita, Xavi Carpena, Peter C. Loewen. Catalase-peroxidase (KatG) Structure and Function. 2015, 133-155.
    23. Ignacio Fita, Peter C Loewen, Xavi Carpena. Catalase‐Peroxidase: KatG. 2015, 1-14.
    24. Saori Kamachi, Kei Hirabayashi, Masahiro Tamoi, Shigeru Shigeoka, Toshiji Tada, Kei Wada. The crystal structure of isoniazid-bound KatG catalase-peroxidase from Synechococcus elongatus PCC7942. FEBS Journal 2015, 282 (1) , 54-64.
    25. Saori Kamachi, Kei Hirabayashi, Masahiro Tamoi, Shigeru Shigeoka, Toshiji Tada, Kei Wada. Crystal structure of the catalase–peroxidase KatG W78F mutant from Synechococcus elongatus PCC7942 in complex with the antitubercular pro‐drug isoniazid. FEBS Letters 2015, 589 (1) , 131-137.
    26. Iñaki de Diego, Florian Veillard, Maryta N. Sztukowska, Tibisay Guevara, Barbara Potempa, Anja Pomowski, James A. Huntington, Jan Potempa, F. Xavier Gomis-Rüth. Structure and Mechanism of Cysteine Peptidase Gingipain K (Kgp), a Major Virulence Factor of Porphyromonas gingivalis in Periodontitis. Journal of Biological Chemistry 2014, 289 (46) , 32291-32302.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Your Mendeley pairing has expired. Please reconnect