Bioisosteric Design Identifies Inhibitors of Mycobacterium tuberculosis DNA Gyrase ATPase Activity

• Published in: Journal of chemical information and modeling Vol. 63; no. 9; pp. 2707 - 2718
• Main Authors: Kamsri, Bundit, Pakamwong, Bongkochawan, Thongdee, Paptawan, Phusi, Naruedon, Kamsri, Pharit, Punkvang, Auradee, Ketrat, Sombat, Saparpakorn, Patchreenart, Hannongbua, Supa, Sangswan, Jidapa, Suttisintong, Khomson, Sureram, Sanya, Kittakoop, Prasat, Hongmanee, Poonpilas, Santanirand, Pitak, Leanpolchareanchai, Jiraporn, Goudar, Kirsty E., Spencer, James, Mulholland, Adrian J., Pungpo, Pornpan
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 08-05-2023
• Subjects: Adenosine; Adenosine Triphosphatases - chemistry; Adenylyl Imidodiphosphate - therapeutic use; Antitubercular Agents - chemistry; Antitubercular Agents - pharmacology; Binding; Caco-2 Cells; Chemical bonds; Computational Chemistry; DNA; DNA Gyrase - chemistry; Humans; Hydrogen bonds; Inhibitors; Molecular dynamics; Mycobacterium tuberculosis - genetics; Optimization; Topoisomerase II Inhibitors - chemistry; Topoisomerase II Inhibitors - pharmacology; Topoisomerase II Inhibitors - therapeutic use; Tuberculosis
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.2c01376

Mutations in DNA gyrase confer resistance to fluoroquinolones, second-line antibiotics for Mycobacterium tuberculosis infections. Identification of new agents that inhibit M. tuberculosis DNA gyrase ATPase activity is one strategy to overcome this. Here, bioisosteric designs using known inhibitors as templates were employed to define novel inhibitors of M. tuberculosis DNA gyrase ATPase activity. This yielded the modified compound R3-13 with improved drug-likeness compared to the template inhibitor that acted as a promising ATPase inhibitor against M. tuberculosis DNA gyrase. Utilization of compound R3-13 as a virtual screening template, supported by subsequent biological assays, identified seven further M. tuberculosis DNA gyrase ATPase inhibitors with IC50 values in the range of 0.42–3.59 μM. The most active compound 1 showed an IC50 value of 0.42 μM, 3-fold better than the comparator ATPase inhibitor novobiocin (1.27 μM). Compound 1 showed noncytotoxicity to Caco-2 cells at concentrations up to 76-fold higher than its IC50 value. Molecular dynamics simulations followed by decomposition energy calculations identified that compound 1 occupies the binding pocket utilized by the adenosine group of the ATP analogue AMPPNP in the M. tuberculosis DNA gyrase GyrB subunit. The most prominent contribution to the binding of compound 1 to M. tuberculosis GyrB subunit is made by residue Asp79, which forms two hydrogen bonds with the OH group of this compound and also participates in the binding of AMPPNP. Compound 1 represents a potential new scaffold for further exploration and optimization as a M. tuberculosis DNA gyrase ATPase inhibitor and candidate anti-tuberculosis agent.