Fragment-based drug discovery strategy reveals an unprecedented allosteric binding site in Mycobacterium tuberculosis DNA gyrase
Year: 2026
Type: article
Abstract: Tuberculosis remains a serious public health threat and the leading infectious cause of death worldwide. Tuberculosis treatment requires at least four antimicrobial drugs and is associated with adverse effects and prolonged therapy, compromising adherence and increasing the risk of drug resistance. Therefore, developing new antitubercular therapies remains essential. Mycobacterium tuberculosis , the primary etiological agent of tuberculosis, lacks topoisomerase IV, making DNA gyrase its sole type II topoisomerase and an attractive drug target. Although fluoroquinolones such as moxifloxacin are used to treat tuberculosis, resistance has limited their effectiveness. Here, we applied a fragment-based drug discovery approach to identify and validate low-affinity compounds targeting M. tuberculosis DNA gyrase as starting points for inhibitor development. Using complementary biophysical and biochemical techniques, we identified five compounds that bind DNA gyrase and inhibit DNA supercoiling and DNA cleavage activities. These compounds interfere with early steps of the gyrase catalytic cycle, likely by blocking conformational changes required for DNA cleavage. The cryo-electron microscopy structure of DNA gyrase in complex with the most potent compound revealed binding near the GyrA–GyrB interface and extensive conformational changes in the GyrB TOPRIM domain. These findings provide a foundation for developing antitubercular agents with a novel mechanism of action
Institutions: Universidade de São Paulo, Lyon 1 Université, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Inserm, Laboratoire de Biologie et Modélisation de la Cellule, Vanderbilt University, Université Paris-Saclay, Microbiologie moléculaire et biochimie structurale, Institut de Biologie Intégrative de la Cellule
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $4,650
Funders: Sanofi, Equipex, Agence Nationale de la Recherche, European Synchrotron Radiation Facility, Fundação de Amparo à Pesquisa do Estado de São Paulo, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Centre National de la Recherche Scientifique, École Normale Supérieure de Lyon, National Institutes of Health, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases
Awards: Biology of Bacteria and Bacteriophages Research Center, G22113365, Structural, functional characterization, and fragment screening for dihydrofolate reductase from invasive pathogenic fungi, G5644312937, G692793031, G7293590401, National instrumentation in cryo electron microscopy, Resistance to antimicrobials in Mycobacterium tuberculosis: structural, biophysical and biochemical analysis of missense mutations, G8794115671, Chemical Biology of Infectious Diseases (CBID) Training Program, Mechanistic Studies of Type II Topoisomerases and Topoisomerase-Targeted Agents, Mechanistic Studies of Gyrase/Topoisomerase IV-Targeted Antibacterials
OpenAlex ID: W7214745058