Mycobactin Analogues with Excellent Pharmacokinetic Profile Demonstrate Potent Antitubercular Specific Activity and Exceptional Efflux Pump Inhibition.

In this study, we have designed and synthesized pyrazoline analogues that partially mimic the structure of mycobactin, to address the requirement of novel therapeutics to tackle the emerging global challenge of antimicrobial resistance (AMR). Our investigation resulted in the identification of novel lead compounds 44 and 49 as potential mycobactin biosynthesis inhibitors against mycobacteria. Moreover, candidates efficiently eradicated intracellularly surviving mycobacteria. Thermofluorimetric analysis and molecular dynamics simulations suggested that compounds 44 and 49 bind to salicyl-AMP ligase (MbtA), a key enzyme in the mycobactin biosynthetic pathway. To the best of our knowledge, these are the first rationally designed mycobactin inhibitors to demonstrate an excellent in vivo pharmacokinetic profile. In addition, these compounds also exhibited more potent whole-cell efflux pump inhibition than known efflux pump inhibitors verapamil and chlorpromazine. Results from this study pave the way for the development of 3-(2-hydroxyphenyl)-5-(aryl)-pyrazolines as a new weapon against superbug-associated AMR challenges.

[1]  S. Bhakta,et al.  The Mycobactin Biosynthesis Pathway: A Prospective Therapeutic Target in the Battle against Tuberculosis. , 2020, Journal of medicinal chemistry.

[2]  L. Chiarelli,et al.  Shedding X-ray Light on the Role of Magnesium in the Activity of Mycobacterium tuberculosis Salicylate Synthase (MbtI) for Drug Design , 2020, Journal of medicinal chemistry.

[3]  S. Bhakta,et al.  Flavonoids as Novel Efflux Pump Inhibitors and Antimicrobials Against Both Environmental and Pathogenic Intracellular Mycobacterial Species , 2020, Molecules.

[4]  S. Bhakta,et al.  Exploration of 5‐(5‐nitrothiophen‐2‐yl)‐4,5‐dihydro‐1H‐pyrazoles as selective, multitargeted antimycobacterial agents , 2020, Chemical biology & drug design.

[5]  Marek Orzechowski,et al.  Large-Scale Chemical-Genetic Strategy Enables the Design of Antimicrobial Combination Chemotherapy in Mycobacteria , 2019, ACS infectious diseases.

[6]  G. Wells,et al.  Integrated Target‐Based and Phenotypic Screening Approaches for the Identification of Anti‐Tubercular Agents That Bind to the Mycobacterial Adenylating Enzyme MbtA , 2019, ChemMedChem.

[7]  M. T. B. Geller,et al.  Molecular , 2019, Modern Pathology.

[8]  Aniruddha Molla,et al.  Borax Catalysed Domino Synthesis of Highly Functionalised Spirooxindole and Chromenopyridine Derivatives: X‐Ray Structure, Hirshfeld Surface Analysis and Molecular Docking Studies , 2018, ChemistrySelect.

[9]  J. Falkinham.  Challenges of NTM Drug Development , 2018, Front. Microbiol..

[10]  L. Kremer,et al.  The diverse family of MmpL transporters in mycobacteria: from regulation to antimicrobial developments , 2017, Molecular microbiology.

[11]  D. Do,et al.  On the consistency of NVT, NPT, μVT and Gibbs ensembles in the framework of kinetic Monte Carlo – Fluid phase equilibria and adsorption of pure component systems , 2017 .

[12]  William L. Jorgensen,et al.  LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands , 2017, Nucleic Acids Res..

[13]  K. Chibale,et al.  Design, Synthesis, and Evaluation of Novel Hybrid Efflux Pump Inhibitors for Use against Mycobacterium tuberculosis. , 2016, ACS infectious diseases.

[14]  S. Bhakta,et al.  Design and Synthesis of 1-((1,5-Bis(4-chlorophenyl)-2-methyl-1H-pyrrol-3-yl)methyl)-4-methylpiperazine (BM212) and N-Adamantan-2-yl-N'-((E)-3,7-dimethylocta-2,6-dienyl)ethane-1,2-diamine (SQ109) Pyrrole Hybrid Derivatives: Discovery of Potent Antitubercular Agents Effective against Multidrug-Resista , 2016, Journal of medicinal chemistry.

[15]  S. Bhakta,et al.  HT‐SPOTi: A Rapid Drug Susceptibility Test (DST) to Evaluate Antibiotic Resistance Profiles and Novel Chemicals for Anti‐Infective Drug Discovery , 2016, Current protocols in microbiology.

[16]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

[17]  C. Partch,et al.  Analysis of Protein Stability and Ligand Interactions by Thermal Shift Assay , 2015, Current protocols in protein science.

[18]  B. D. de Jong,et al.  Acquired Resistance of Mycobacterium tuberculosis to Bedaquiline , 2014, PloS one.

[19]  Rajendra Kumar,et al.  g_mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations , 2014, J. Chem. Inf. Model..

[20]  F. Jiang,et al.  Residue-specific force field based on the protein coil library. RSFF1: modification of OPLS-AA/L. , 2014, The journal of physical chemistry. B.

[21]  A. Sonawane,et al.  Evaluation of antibacterial and cytotoxic activity of Artemisia nilagirica and Murraya koenigii leaf extracts against mycobacteria and macrophages , 2014, BMC Complementary and Alternative Medicine.

[22]  M. Niederweis,et al.  Self-poisoning of Mycobacterium tuberculosis by interrupting siderophore recycling , 2014, Proceedings of the National Academy of Sciences.

[23]  M. Niederweis,et al.  Discovery of a Siderophore Export System Essential for Virulence of Mycobacterium tuberculosis , 2013, PLoS pathogens.

[24]  Marcus D. Hanwell,et al.  Avogadro: an advanced semantic chemical editor, visualization, and analysis platform , 2012, Journal of Cheminformatics.

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

[26]  S. Bhakta,et al.  An integrated surrogate model for screening of drugs against Mycobacterium tuberculosis. , 2012, The Journal of antimicrobial chemotherapy.

[27]  M. Vedadi,et al.  Thermal denaturation assays in chemical biology. , 2012, Assay and drug development technologies.

[28]  U. Kishore,et al.  Mycobacterium tuberculosis: immune evasion, latency and reactivation. , 2012, Immunobiology.

[29]  S. Worgall,et al.  Chemical scaffolds with structural similarities to siderophores of nonribosomal peptide-polyketide origin as novel antimicrobials against Mycobacterium tuberculosis and Yersinia pestis. , 2011, Bioorganic & medicinal chemistry letters.

[30]  Jan de Sonneville,et al.  A High-Throughput Screen for Tuberculosis Progression , 2011, PloS one.

[31]  A. Gray,et al.  Antimycobacterial terpenoids from Juniperus communis L. (Cuppressaceae). , 2009, Journal of ethnopharmacology.

[32]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[33]  A. Gulick.  Conformational dynamics in the Acyl-CoA synthetases, adenylation domains of non-ribosomal peptide synthetases, and firefly luciferase. , 2009, ACS chemical biology.

[34]  T. Schaberg,et al.  Multidrug- and Extensively Drug-Resistant Tuberculosis, Germany , 2008, Emerging infectious diseases.

[35]  L. Quadri,et al.  Small molecules with structural similarities to siderophores as novel antimicrobials against Mycobacterium tuberculosis and Yersinia pestis. , 2008, Bioorganic & medicinal chemistry letters.

[36]  D. Sarkar,et al.  A simple whole cell based high throughput screening protocol using Mycobacterium bovis BCG for inhibitors against dormant and active tubercle bacilli. , 2008, Journal of microbiological methods.

[37]  L. Quadri.  Strategic paradigm shifts in the antimicrobial drug discovery process of the 21st century. , 2007, Infectious disorders drug targets.

[38]  S. Gibbons,et al.  Antibacterial activity of two canthin‐6‐one alkaloids from Allium neapolitanum , 2007, Phytotherapy research : PTR.

[39]  Andrew M Gulick,et al.  Biochemical and crystallographic analysis of substrate binding and conformational changes in acetyl-CoA synthetase. , 2007, Biochemistry.

[40]  F. Blasi,et al.  125 years after Robert Koch's discovery of the tubercle bacillus: the new XDR-TB threat. Is “science” enough to tackle the epidemic? , 2007, European Respiratory Journal.

[41]  Derek S. Tan,et al.  Small-molecule inhibition of siderophore biosynthesis in Mycobacterium tuberculosis and Yersinia pestis , 2005, Nature chemical biology.

[42]  P. Brennan,et al.  Structures of the glycopeptidolipid antigens from serovars in the Mycobacterium avium/Mycobacterium intracellulare/Mycobacterium scrofulaceum serocomplex. , 2005, European journal of biochemistry.

[43]  Greg L. Hura,et al.  Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. , 2004, The Journal of chemical physics.

[44]  A. Brigo,et al.  The Poisson–Boltzmann equation for biomolecular electrostatics: a tool for structural biology , 2002, Journal of molecular recognition : JMR.

[45]  P. Brennan.  Foreword from the Co-Editor-in-Chief , 2001 .

[46]  H. Su,et al.  The salicylate-derived mycobactin siderophores of Mycobacterium tuberculosis are essential for growth in macrophages. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[47]  S T Cole,et al.  Analysis of the proteome of Mycobacterium tuberculosis in silico. , 1999, Tubercle and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

[48]  D. Williams,et al.  Determination of the structure of exochelin MN, the extracellular siderophore from Mycobacterium neoaurum. , 1995, Chemistry & biology.

[49]  M. Daffé,et al.  Structures of the glycopeptidolipid antigens of Mycobacterium abscessus and Mycobacterium chelonae and possible chemical basis of the serological cross-reactions in the Mycobacterium fortuitum complex. , 1994, Microbiology.

[50]  M. Karplus,et al.  Molecular dynamics simulations in biology , 1990, Nature.

[51]  T. Richmond,et al.  Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. , 1984, Journal of molecular biology.

[52]  C. Ratledge,et al.  Iron transport in Mycobacterium smegmatis: the location of mycobactin by electron microscopy. , 1982, Journal of general microbiology.

[53]  G. Snow.  Mycobactins: iron-chelating growth factors from mycobacteria , 1970 .

[54]  S. Bhakta,et al.  Rapid methods for testing inhibitors of mycobacterial growth. , 2010, Methods in molecular biology.

[55]  A. Lucarelli,et al.  Azole resistance in Mycobacterium tuberculosis is mediated by the MmpS5-MmpL5 efflux system. , 2009, Tuberculosis.

[56]  C. Ratledge.  Iron, mycobacteria and tuberculosis. , 2004, Tuberculosis.

[57]  M. Miller,et al.  Iron chelators from mycobacteria (1954-1999) and potential therapeutic applications. , 2000, Natural product reports.

[58]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.

[59]  H. Nikaido,et al.  The envelope of mycobacteria. , 1995, Annual review of biochemistry.

[60]  H. Berman,et al.  Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank , 2022 .