Left-Hand Side Exploration of Novel Bacterial Topoisomerase Inhibitors to Improve Selectivity against hERG Binding Shahul Hameed P,* Praveena Manjrekar, Anandkumar Raichurkar, Vikas Shinde, Jayashree Puttur, Gajanan Shanbhag, Murugan Chinnapattu, Vikas Patil, Suresh Rudrapatana, Sreevalli Sharma, C. N. Naveen Kumar, Radha Nandishaiah, Prashanti Madhavapeddi, D. Sriram, † Suresh Solapure, and Vasan K. Sambandamurthy AstraZeneca India Pvt. Ltd, Avishkar, Bellary Road, Bangalore-560024, India * S Supporting Information ABSTRACT: Structure-activity relationship (SAR) exploration on the left-hand side (LHS) of a novel class of bacterial topoisomerase inhibitors led to a significant improvement in the selectivity against hERG cardiac channel binding with concomitant potent antimycobacterial activity. Bulky polar substituents at the C-7 position of the naphthyridone ring did not disturb its positioning between two base pairs of DNA. Further optimization of the polar substituents on the LHS of the naphthyridone ring led to potent antimycobacterial activity (Mtb MIC = 0.06 μM) against Mycobacterium tuberculosis (Mtb). Additionally, this knowledge provided a robust SAR understanding to mitigate the hERG risk. This compound class inhibits Mtb DNA gyrase and retains its antimycobacterial activity against moxifloxacin-resistant strains of Mtb. Finally, we demonstrate in vivo proof of concept in an acute mouse model of TB following oral administration of compound 19. KEYWORDS: Tuberculosis, type II topoisomerases, DNA gyrase, NBTIs, aminopiperidines, naphthyridones T uberculosis caused by Mycobacterium tuberculosis (Mtb) continues to be a global threat claiming 1.5 million lives each year. 1 For treating drug susceptible TB, the World Health Organization (WHO) recommends a regimen containing four drugs administered for six months. 2 The global emergence of multidrug resistant (MDR) and extremely drug resistant (XDR) strains of Mtb have greatly impeded the TB control and eradication efforts. Patients with MDR or XDR-TB require treatment with a combination of 6-8 drugs for a period of 8-24 months. 3 DNA gyrase, a type II topoisomerase enzyme is involved in DNA replication and repair. This enzyme is essential in all bacteria and is absent in eukaryotes. 4 DNA gyrase catalyzes the critical step of maintaining the various topological forms of DNA during DNA replication. DNA gyrase performs an ATP- dependent reaction to introduce a negative supercoiling into circular DNA. 5 This enzyme exists in a heterotetrameric form, comprising a GyrA and a GyrB subunit (A2B2). The DNA breakage reunion function resides in the GyrA subunit, while the GyrB subunit catalyzes the ATP-dependent hydrolysis to generate the energy required for enzyme activity. Interestingly, the Mtb genome encodes a functional DNA gyrase, but no topoisomerase IV. 6,7 Several inhibitors targeting the DNA gyrase have been reported to exhibit activity against Mtb. A class of inhibitors that target the ATP recognition site of GyrB enzyme and block ATP hydrolysis have shown antimycobacterial activity. Examples of this type include aminopyrazinamides, thiazolopyr- idine ureas, and pyrrolamides. 6,7 A second type of inhibitor that targets the GyrA subunit has been shown to inhibit the DNA breakage-reunion function of the enzyme. This category of inhibitors is represented by fluoroquinolones (FQs), novel bacterial topoisomerase inhibitors (NBTIs), and aminopiper- idines. 6,8-10 The attractiveness of DNA gyrase as a high quality antibacterial target has been validated by the clinical success of several generations of FQs to treat serious bacterial infections. The widespread emergence of FQ-resistant bacterial strains is likely to reduce the clinical value of FQs in the near future. 11 The clinical benefit of combining FQs in the drug regimen to treat TB have been demonstrated in preclinical animal models as well as in TB patients. 12 Numerous reports have highlighted the emergence of Mtb strains resistant to FQs, thereby limiting the life of these drugs in treating TB. The existing body of evidence around the clinical safety and efficacy of FQs, provides an Received: May 19, 2014 Accepted: May 22, 2015 Letter pubs.acs.org/acsmedchemlett © XXXX American Chemical Society A DOI: 10.1021/ml500531p ACS Med. Chem. Lett. XXXX, XXX, XXX-XXX