Kannan Murugan

Aminopyrazinamides: Novel and Specific GyrB Inhibitors that Kill Replicating and Nonreplicating Mycobacterium tuberculosis

Aminopyrazinamides originated from a high throughput screen targeting the Mycobacterium smegmatis (Msm) GyrB ATPase. This series displays chemical tractability, robust structure-activity relationship, and potent antitubercular activity. The crystal structure of Msm GyrB in complex with one of the aminopyrazinamides revealed promising attributes of specificity against other broad spectrum pathogens and selectivity against eukaryotic kinases due to novel interactions at hydrophobic pocket, unlike other known GyrB inhibitors. The aminopyrazinamides display excellent mycobacterial kill under in vitro, intracellular, and hypoxic conditions.

Triaminopyrimidine is a fast-killing and long-acting antimalarial clinical candidate

The widespread emergence of Plasmodium falciparum (Pf) strains resistant to frontline agents has fuelled the search for fast-acting agents with novel mechanism of action. Here, we report the discovery and optimization of novel antimalarial compounds, the triaminopyrimidines (TAPs), which emerged from a phenotypic screen against the blood stages of Pf. The clinical candidate (compound 12) is efficacious in a mouse model of Pf malaria with an ED99 <30 mg kg−1 and displays good in vivo safety margins in guinea pigs and rats. With a predicted half-life of 36 h in humans, a single dose of 260 mg might be sufficient to maintain therapeutic blood concentration for 4–5 days. Whole-genome sequencing of resistant mutants implicates the vacuolar ATP synthase as a genetic determinant of resistance to TAPs. Our studies highlight the potential of TAPs for single-dose treatment of Pf malaria in combination with other agents in clinical development.

Structure Guided Lead Generation for M. Tuberculosis Thymidylate Kinase (Mtb Tmk): Discovery of 3-Cyanopyridone and 1,6-Naphthyridin-2-One as Potent Inhibitors.

M. tuberculosis thymidylate kinase (Mtb TMK) has been shown in vitro to be an essential enzyme in DNA synthesis. In order to identify novel leads for Mtb TMK, we performed a high throughput biochemical screen and an NMR based fragment screen through which we discovered two novel classes of inhibitors, 3-cyanopyridones and 1,6-naphthyridin-2-ones, respectively. We describe three cyanopyridone subseries that arose during our hit to lead campaign, along with cocrystal structures of representatives with Mtb TMK. Structure aided optimization of the cyanopyridones led to single digit nanomolar inhibitors of Mtb TMK. Fragment based lead generation, augmented by crystal structures and the SAR from the cyanopyridones, enabled us to drive the potency of our 1,6-naphthyridin-2-one fragment hit from 500 μM to 200 nM while simultaneously improving the ligand efficiency. Cyanopyridone derivatives containing sulfoxides and sulfones showed cellular activity against M. tuberculosis. To the best of our knowledge, these compounds are the first reports of non-thymidine-like inhibitors of Mtb TMK.

Nitroarenes as Antitubercular Agents: Stereoelectronic Modulation to Mitigate Mutagenicity

Nitroarenes are less preferred in drug discovery due to their potential to be mutagenic. However, several nitroarenes were shown to be promising antitubercular agents with specific modes of action, namely, nitroimidazoles and benzothiazinones. The nitro group in these compounds is activated through different mechanisms, both enzymatic and non‐enzymatic, in mycobacteria prior to binding to the target of interest. From a whole‐cell screening program, we identified a novel lead nitrobenzothiazole (BT) series that acts by inhibition of decaprenylphosphoryl‐β‐d‐ribose 2′‐epimerase (DprE1) of Mycobacterium tuberculosis (Mtb). The lead was found to be mutagenic to start with. Our efforts to mitigate mutagenicity resulted in the identification of 6‐methyl‐7‐nitro‐5‐(trifluoromethyl)‐1,3‐benzothiazoles (cBTs), a novel class of antitubercular agents that are non‐mutagenic and exhibit an improved safety profile. The methyl group ortho to the nitro group decreases the electron affinity of the series, and is hence responsible for the non‐mutagenic nature of these compounds. Additionally, the co‐crystal structure of cBT in complex with Mtb DprE1 established the mode of binding. This investigation led to a new non‐mutagenic antitubercular agent and demonstrates that the mutagenic nature of nitroarenes can be solved by modulation of stereoelectronic properties.

Synthesis of novel benzoxaborinin-4-ones and its application in indolin-2-ones synthesis using a Suzuki–Miyaura reaction protocol

We herein discuss the synthesis of novel benzoxaborinin-4-one from substituted isatins and 2-acetyl phenylboronic acid. Furthermore, we have demonstrated the application of these boronic acids to synthesize indolin-2-ones (Z isomer) regioselectively using Suzuki–Miyaura reaction.

Abstract 5578: Small molecule modulators to understand the role of IDO1 and TDO2 in cancer

Introduction: Tumor immune escape mechanisms have been established as suitable targets for cancer therapy. Among these, tryptophan catabolism plays a central role in creating an immunosuppressive environment, leading to tolerance to potentially immunogenic tumor antigens. Tryptophan catabolism is initiated by either indoleamine 2,3-dioxygenase (IDO1/2) or tryptophan 2,3-dioxygenase 2 (TDO2), resulting in biostatic tryptophan starvation and l-kynurenine production. Recent literature has shown that IDO1 and TDO2 are expressed in multiple tumors, including solid tumors and play key roles in tumor progression other than immune escape. It has also been shown that IDO1 and TDO2 play distinct roles in driving the downstream effectors suggesting that their roles are perhaps non-redundant. Therefore, we developed series of novel small molecule modulators against IDO1 and TDO2 to understand their role in disease biology for multiple indications including cancer, depression and autoimmune disorders. Methods: Rational design approaches were used to design novel IDO1 and TDO2 specific modulators; Potency of these inhibitors was assessed in the in vitro assays using purified IDO1 and TDO2 enzymes and in IDO1 and TDO2 over-expressing HEK293T cells by measuring the formation of kynurenine. Results: In the in vitro biochemical assay using purified human TDO2, one of the NCEs from inhibitor series showed an IC50 of 0.09 μM against TDO2. Against purified human IDO1, this compound was inactive up to 30 μM, thereby showing >300-fold selectivity against IDO1. This TDO2 inhibitory activity translated well in TDO2-overexpressing HEK293 cells and, these NCEs inhibited kynurenine formation with an EC50 of ~2.5 μM. A second chemical series showed comparable dual inhibition of IDO1 and TDO2 activity. One of the molecules from this series showed IC50 of 0.2 and 0.08 μM in the biochemical assay and 1.7 and 0.8 μM in the cell based assay against IDO1 and TDO2, respectively. In addition, another series of NCEs showed strong activation of IDO1 and TDO2 activity. As compared to untreated control, formation of kynurenine was increased in a dose-dependent manner as observed by increase in fluorescence up to of 3-10 folds. One of the compounds from this series showed an EC50 of ~20- 30 μM in the biochemical assay as well as in 293T-based assay. Further mechanistic studies to understand the immune modulatory activity of these selective TDO2 modulators is underway. These tool compounds are being further optimized for potency and ADME properties to be developed as potential drug candidates. Conclusion: To our knowledge such IDO1 and TDO2 specific small molecule activators have not been reported earlier. Therefore, these activators and inhibitors would serve as useful tool compounds in understanding the specific role(s) of IDO1 and TDO2 in disease biology and would also provide us the opportunity to target this pathway for various diseases, including cancer. Citation Format: Shivani Rao Garapaty, Dhanalakshmi Sivanandhan, Guru Pavan Kumar Seerapu, Surendra Naidu, Shalini Chakelam, Pradeep Nagaraj, Reshma Das, Saravanan Vadivelu, Pravin Iyer, Chandrika Mulakala, Kannan Murugan, Somnath Mondal, Anjali Gautam, Saravanan Kandan, Manish Kumar Thakur, Sridharan Rajagopal, Sriram Rajagopal. Small molecule modulators to understand the role of IDO1 and TDO2 in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5578. doi:10.1158/1538-7445.AM2017-5578