Jan Konecny

PC13 – Jan Konecny

Biomedical Research Center, University Hospital Hradec Kralove, Czech Republic

jan.konecny@fnhk.cz

Optimization of pyrrolo[3,2-d]pyrimidine derivatives as antitubercular agents through drug-driven design
Konecny Jan ¹, Finger Vladimir ^1,2, Novak Martin ¹, Roh Jaroslav ² and Korabecny Jan ¹ ¹ Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic ² Faculty of Pharmacy in Hradec Kralove, Charles University, Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
Abstract Tuberculosis (TB) remains one of the ten leading causes of death worldwide and is caused by the infectious pathogen Mycobacterium tuberculosis (Mtb). According to the World Health Organization (WHO), approximately 10.7 million new TB cases and 1.23 million deaths were reported in 2025.[1] One of the major obstacles in TB therapy is the growing prevalence of Mtb strains resistant to both first-line drugs (isoniazid, pyrazinamide, ethambutol, and rifampicin) and second-line agents (fluoroquinolones, amikacin, bedaquiline, pretomanid, delamanid, etc.). This alarming trend underscores the urgent need to develop new anti-TB drugs with novel mechanisms of action to improve treatment outcomes and overcome drug resistance. In our previous work, we identified a purine-based compound, K2032, with strong anti-TB activity, demonstrating a minimum inhibitory concentration (MIC₉₉) of 1 μM against the H₃₇Rv strain (for comparison, isoniazid exhibits an MIC₉₉ of 0.5 μM). Whole-genome sequencing of resistant strains revealed that K2032 functions as a noncovalent inhibitor of DprE1. In a subsequent study, we employed a scaffold-hopping strategy to simplify the purine core to a 5H-pyrrolo[3,2-d]pyrimidine scaffold. Within this compound series, we discovered the highly potent derivative K2653, which showed high activity against both drug-susceptible Mtb strains (MIC₉₉ = 2 μM) and extensively drug-resistant Mtb strains (MIC₉₉ = 2 μM). However, K2653 displayed approximately 20-fold higher cytotoxicity (IC₅₀ in HepG2 cells = 3.5 μM) compared with the most potent purine derivative, K2032 (IC₅₀ in HepG2 cells = 63.8 μM). In vivo pharmacokinetic studies conducted in rats enabled the identification of plasma metabolites responsible for the increased toxicity of K2653. Through targeted structural modifications, including the incorporation of deuterium into the K2653 scaffold, we successfully improved its cytotoxicity profile.[2] This study was supported by the Czech Science Foundation project (No. 25-16937S).
References [1] Global Tuberculosis Report 2025, (n.d.). https://www.who.int/teams/global-programme-on-tuberculosis-and-lung-health/tb-reports/global-tuberculosis-report-2025 (accessed March 9, 2026). [2] V. Finger, M. Vrbicky, L. Muckova, L. Prchal, M. Novak, J. Marek, O. Soukup, M. Hympanova, A. Sorf, M. Benkova, J. Bartacek, P. Drabina, M. Kufa, O. Kovar, L. Fikejzlová, M. Hruby, O. Ozhelevska, J. Jagob, J. Zdarova-Karasova, J. Odvarkova, I. Kaderavková, T. Rozsypal, K. Ewa Greber, K. Ciura, J. Janousek, M. Kratky, I.C. Igreja Sa, P. Bostik, R. Sleha, J. Roh, J. Korabecny, Novel antitubercular agents based on 2,4-disubstituted 5-(aryl-2-ylmethyl)-5H-pyrrolo[3,2-d]pyrimidines, Biomed Pharmacother 191 (2025) 118537. https://doi.org/10.1016/j.biopha.2025.118537.