Novel Antitubercular 6-Dialkylaminopyrimidine Carboxamides from Phenotypic Whole-Cell High Throughput Screening of a SoftFocus Library: Structure–Activity Relationship and Target Identification Studies

A BioFocus DPI SoftFocus library of ∼35 000 compounds was screened against Mycobacterium tuberculosis (Mtb) in order to identify novel hits with antitubercular activity. The hits were evaluated in biology triage assays to exclude compounds suggested to function via frequently encountered promiscuous mechanisms of action including inhibition of the QcrB subunit of the cytochrome bc1 complex, disruption of cell–wall homeostasis, and DNA damage. Among the hits that passed this screening cascade, a 6-dialkylaminopyrimidine carboxamide series was prioritized for hit to lead optimization. Compounds from this series were active against clinical Mtb strains, while no cross-resistance to conventional antituberculosis drugs was observed. This suggested a novel mechanism of action, which was confirmed by chemoproteomic analysis leading to the identification of BCG_3193 and BCG_3827 as putative targets of the series with unknown function. Initial structure–activity relationship studies have resulted in compounds with moderate to potent antitubercular activity and improved physicochemical properties.

[1]  T. Ioerger,et al.  Susceptibility of Mycobacterium tuberculosis Cytochrome bd Oxidase Mutants to Compounds Targeting the Terminal Respiratory Oxidase, Cytochrome c , 2017, Antimicrobial Agents and Chemotherapy.

[2]  Thomas R. Ioerger,et al.  Essential but Not Vulnerable: Indazole Sulfonamides Targeting Inosine Monophosphate Dehydrogenase as Potential Leads against Mycobacterium tuberculosis. , 2017, ACS infectious diseases.

[3]  G. Poce,et al.  MmpL3 is the flippase for mycolic acids in mycobacteria , 2017, Proceedings of the National Academy of Sciences.

[4]  D. Schnappinger,et al.  Validation of CoaBC as a Bactericidal Target in the Coenzyme A Pathway of Mycobacterium tuberculosis , 2016, ACS infectious diseases.

[5]  Robert H Bates,et al.  Identification of KasA as the cellular target of an anti-tubercular scaffold , 2016, Nature Communications.

[6]  V. Mizrahi,et al.  Bioluminescent Reporters for Rapid Mechanism of Action Assessment in Tuberculosis Drug Discovery , 2016, Antimicrobial Agents and Chemotherapy.

[7]  P. Wyatt,et al.  Prediction of Drug Penetration in Tuberculosis Lesions. , 2016, ACS infectious diseases.

[8]  Richard E. Lee,et al.  New agents for the treatment of drug-resistant Mycobacterium tuberculosis. , 2016, Advanced drug delivery reviews.

[9]  J. Heyckendorf,et al.  Personalized medicine for patients with MDR-TB. , 2016, The Journal of antimicrobial chemotherapy.

[10]  G. Drewes,et al.  THPP target assignment reveals EchA6 as an essential fatty acid shuttle in mycobacteria , 2016, Nature Microbiology.

[11]  C. Harris,et al.  Aminopyrazolo[1,5-a]pyrimidines as potential inhibitors of Mycobacterium tuberculosis: Structure activity relationships and ADME characterization. , 2015, Bioorganic & medicinal chemistry.

[12]  Paul W Smith,et al.  Perspective: Challenges and opportunities in TB drug discovery from phenotypic screening. , 2015, Bioorganic & medicinal chemistry.

[13]  P. Karakousis,et al.  Future target-based drug discovery for tuberculosis? , 2014, Tuberculosis.

[14]  V. Mizrahi,et al.  Shortening treatment for tuberculosis--to basics. , 2014, The New England journal of medicine.

[15]  Tom L. Blundell,et al.  Respiratory Flexibility in Response to Inhibition of Cytochrome c Oxidase in Mycobacterium tuberculosis , 2014, Antimicrobial Agents and Chemotherapy.

[16]  Christopher B. Cooper,et al.  1,4-Azaindole, a Potential Drug Candidate for Treatment of Tuberculosis , 2014, Antimicrobial Agents and Chemotherapy.

[17]  Bart Hens,et al.  A review of drug solubility in human intestinal fluids: implications for the prediction of oral absorption. , 2014, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.

[18]  Marcus Bantscheff,et al.  Ion coalescence of neutron encoded TMT 10-plex reporter ions. , 2014, Analytical chemistry.

[19]  T. Buclin,et al.  Towards a new combination therapy for tuberculosis with next generation benzothiazinones , 2014, EMBO molecular medicine.

[20]  S. Cole,et al.  Tuberculosis drug discovery in the post-post-genomic era , 2014, EMBO molecular medicine.

[21]  Vijay T. Ahuja,et al.  Azaindoles: noncovalent DprE1 inhibitors from scaffold morphing efforts, kill Mycobacterium tuberculosis and are efficacious in vivo. , 2013, Journal of medicinal chemistry.

[22]  Se Yeon Kim,et al.  Discovery of Q203, a potent clinical candidate for the treatment of tuberculosis , 2013, Nature Medicine.

[23]  D. Menzies,et al.  A Review of the Evidence for Using Bedaquiline (TMC207) to Treat Multi-Drug Resistant Tuberculosis , 2013, Infectious Diseases and Therapy.

[24]  N. Leadbeater,et al.  A Weinreb amide approach to the synthesis of trifluoromethylketones. , 2012, Chemical communications.

[25]  K. Andries,et al.  Discovery and development of SQ109: a new antitubercular drug with a novel mechanism of action. , 2012, Future microbiology.

[26]  L. Dover,et al.  Current status and research strategies in tuberculosis drug development. , 2011, Journal of medicinal chemistry.

[27]  C. Harris,et al.  The Design and Application of Target-Focused Compound Libraries , 2011, Combinatorial chemistry & high throughput screening.

[28]  W. Ren,et al.  Mo(CO)6‐Mediated Carbamoylation of Aryl Halides. , 2011 .

[29]  P. Grandi,et al.  Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes , 2011, Nature Biotechnology.

[30]  G. D. de Souza,et al.  Definition of novel cell envelope associated proteins in Triton X-114 extracts of Mycobacterium tuberculosis H37Rv , 2010, BMC Microbiology.

[31]  J. Falgueyret,et al.  The discovery of odanacatib (MK-0822), a selective inhibitor of cathepsin K. , 2008, Bioorganic & medicinal chemistry letters.

[32]  D. Speijer,et al.  1,2,3-Triazoles as peptide bond isosteres: synthesis and biological evaluation of cyclotetrapeptide mimics. , 2007, Organic & biomolecular chemistry.

[33]  Hinrich W. H. Göhlmann,et al.  A Diarylquinoline Drug Active on the ATP Synthase of Mycobacterium tuberculosis , 2005, Science.

[34]  C Antzelevitch,et al.  The potential for QT prolongation and proarrhythmia by non-antiarrhythmic drugs: clinical and regulatory implications. Report on a policy conference of the European Society of Cardiology. , 2000, European heart journal.

[35]  K Gubernator,et al.  Physicochemical high throughput screening: parallel artificial membrane permeation assay in the description of passive absorption processes. , 1998, Journal of medicinal chemistry.

[36]  L. Soto-Ramírez,et al.  [Treatment of tuberculosis]. , 1997, Gaceta medica de Mexico.