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Gupta VK, Vaishnavi VV, Arrieta-Ortiz ML, P S A, K M J, Jeyasankar S, Raghunathan V, Baliga NS, Agarwal R. 3D Hydrogel Culture System Recapitulates Key Tuberculosis Phenotypes and Demonstrates Pyrazinamide Efficacy. Adv Healthc Mater 2024:e2304299. [PMID: 38655817 DOI: 10.1002/adhm.202304299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/29/2024] [Indexed: 04/26/2024]
Abstract
The mortality caused by tuberculosis (TB) infections is a global concern, and there is a need to improve understanding of the disease. Current in vitro infection models to study the disease have limitations such as short investigation durations and divergent transcriptional signatures. This study aims to overcome these limitations by developing a 3D collagen culture system that mimics the biomechanical and extracellular matrix (ECM) of lung microenvironment (collagen fibers, stiffness comparable to in vivo conditions) as the infection primarily manifests in the lungs. The system incorporates Mycobacterium tuberculosis (Mtb) infected human THP-1 or primary monocytes/macrophages. Dual RNA sequencing reveals higher mammalian gene expression similarity with patient samples than 2D macrophage infections. Similarly, bacterial gene expression more accurately recapitulates in vivo gene expression patterns compared to bacteria in 2D infection models. Key phenotypes observed in humans, such as foamy macrophages and mycobacterial cords, are reproduced in the model. This biomaterial system overcomes challenges associated with traditional platforms by modulating immune cells and closely mimicking in vivo infection conditions, including showing efficacy with clinically relevant concentrations of anti-TB drug pyrazinamide, not seen in any other in vitro infection model, making it reliable and readily adoptable for tuberculosis studies and drug screening.
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Affiliation(s)
- Vishal K Gupta
- Department of Bioengineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
| | - Vijaya V Vaishnavi
- Department of Bioengineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
| | | | - Abhirami P S
- Department of Bioengineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
| | - Jyothsna K M
- Department of Electrical Communication Engineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
| | - Sharumathi Jeyasankar
- Department of Bioengineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
| | - Varun Raghunathan
- Department of Electrical Communication Engineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
| | - Nitin S Baliga
- Institute of Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Rachit Agarwal
- Department of Bioengineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
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2
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Sarathy JP, Aldrich CC, Go ML, Dick T. PROTAC antibiotics: the time is now. Expert Opin Drug Discov 2023; 18:363-370. [PMID: 37027333 PMCID: PMC10540314 DOI: 10.1080/17460441.2023.2178413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/06/2023] [Indexed: 02/24/2023]
Abstract
INTRODUCTION Novel antibiotics are needed to keep antibiotic resistance at bay and to improve treatment of the many drug-susceptible infections for which current therapies achieve poor cure rates. While revolutionizing human therapeutics, the concept of targeted protein degradation (TPD) by bifunctional proteolysis targeting chimeras (PROTACs) has not yet been applied to the discovery of antibiotics. A major obstacle precluding successful translation of this strategy to antibiotic development is that bacteria lack the E3 ligase-proteasome system exploited by human PROTACs to facilitate target degradation. AREAS COVERED The authors describe the serendipitous discovery of the first monofunctional target-degrading antibiotic pyrazinamide, supporting TPD as a viable and novel approach in antibiotic discovery. They then discuss the rational design, mechanism, and activity of the first bifunctional antibacterial target degrader BacPROTAC, enabling a generalizable approach to TPD in bacteria. EXPERT OPINION BacPROTACs demonstrate that linking a target directly to a bacterial protease complex can promote target degradation. BacPROTACs successfully bypass the 'middleman' E3 ligase, providing an entry strategy for the generation of antibacterial PROTACs. We speculate that antibacterial PROTACs will not only expand the target space but may also improve treatment by allowing dosage reduction, stronger bactericidal activity and activity against drug-tolerant 'persisters.'
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Affiliation(s)
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Mei-Lin Go
- Department of Chemistry and Department of Pharmacy, National University of Singapore, Singapore
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
- Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA
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3
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Hegde PV, Aragaw WW, Cole MS, Jachak G, Ragunathan P, Sharma S, Harikishore A, Grüber G, Dick T, Aldrich CC. Structure activity relationship of pyrazinoic acid analogs as potential antimycobacterial agents. Bioorg Med Chem 2022; 74:117046. [PMID: 36228522 PMCID: PMC10551889 DOI: 10.1016/j.bmc.2022.117046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/02/2022]
Abstract
Tuberculosis (TB) remains a leading cause of infectious disease-related mortality and morbidity. Pyrazinamide (PZA) is a critical component of the first-line TB treatment regimen because of its sterilizing activity against non-replicating Mycobacterium tuberculosis (Mtb), but its mechanism of action has remained enigmatic. PZA is a prodrug converted by pyrazinamidase encoded by pncA within Mtb to the active moiety, pyrazinoic acid (POA) and PZA resistance is caused by loss-of-function mutations to pyrazinamidase. We have recently shown that POA induces targeted protein degradation of the enzyme PanD, a crucial component of the coenzyme A biosynthetic pathway essential in Mtb. Based on the newly identified mechanism of action of POA, along with the crystal structure of PanD bound to POA, we designed several POA analogs using structure for interpretation to improve potency and overcome PZA resistance. We prepared and tested ring and carboxylic acid bioisosteres as well as 3, 5, 6 substitutions on the ring to study the structure activity relationships of the POA scaffold. All the analogs were evaluated for their whole cell antimycobacterial activity, and a few representative molecules were evaluated for their binding affinity, towards PanD, through isothermal titration calorimetry. We report that analogs with ring and carboxylic acid bioisosteres did not significantly enhance the antimicrobial activity, whereas the alkylamino-group substitutions at the 3 and 5 position of POA were found to be up to 5 to 10-fold more potent than POA. Further development and mechanistic analysis of these analogs may lead to a next generation POA analog for treating TB.
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Affiliation(s)
- Pooja V Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Wassihun W Aragaw
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Malcolm S Cole
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Gorakhnath Jachak
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Sachin Sharma
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Amaravadhi Harikishore
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore.
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA; Departmentof Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA; Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA.
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA.
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4
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Rajendran A, Palaniyandi K. Mutations Associated with Pyrazinamide Resistance in Mycobacterium tuberculosis: A Review and Update. Curr Microbiol 2022; 79:348. [PMID: 36209317 DOI: 10.1007/s00284-022-03032-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/06/2022] [Indexed: 11/03/2022]
Abstract
Pyrazinamide (PZA) has remained a keystone of tuberculosis (TB) therapy, and it possesses high imperative sterilizing action that can facilitate reduction in the present chemotherapy regimen. The combination of PZA works both with first- and second-line TB drugs, notably fluoroquinolones, clofazimine, bedaquiline, delamanid and pretomanid. Pyrazinamide inhibits various targets that are involved in different cellular processes like energy production (pncA), trans-translation (rpsA) and pantothenate/coenzyme A (panD) which are required for persistence of the pathogen. It is well known that pncA gene encoding pyrazinamidase is involved in the transition of PZA into the active form of pyrazinoic acid, which implies that mutation in the pncA gene can develop PZA resistance in Mycobacterium tuberculosis (M. tuberculosis) strain leading to a major clinical and public health concern. Therefore, it is very crucial to understand its resistance mechanism and to detect it precisely to help in the management of the disease. Scope of this review is to have a deep understanding of molecular mechanism of PZA resistance with its multiple targets which would help study the association of mutations and its resistance in M. tuberculosis. This will in turn help learn about the resistance of PZA and develop more accurate molecular diagnostic tool for drug-resistant TB in future TB therapy.
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Affiliation(s)
- Ananthi Rajendran
- Department of Immunology, ICMR-National Institute for Research in Tuberculosis, #1, Mayor Sathyamoorthy Road, Chetpet, Chennai, 600031, India
| | - Kannan Palaniyandi
- Department of Immunology, ICMR-National Institute for Research in Tuberculosis, #1, Mayor Sathyamoorthy Road, Chetpet, Chennai, 600031, India.
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Saw W, Leow CY, Harikishore A, Shin J, Cole MS, Aragaw WW, Ragunathan P, Hegde P, Aldrich CC, Dick T, Grüber G. Structural and Mechanistic Insights into Mycobacterium abscessus Aspartate Decarboxylase PanD and a Pyrazinoic Acid-Derived Inhibitor. ACS Infect Dis 2022; 8:1324-1335. [PMID: 35731701 PMCID: PMC10517418 DOI: 10.1021/acsinfecdis.2c00133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis (Mtb) aspartate decarboxylase PanD is required for biosynthesis of the essential cofactor coenzyme A and targeted by the first line drug pyrazinamide (PZA). PZA is a prodrug that is converted by a bacterial amidase into its bioactive form pyrazinoic acid (POA). Employing structure-function analyses we previously identified POA-based inhibitors of Mtb PanD showing much improved inhibitory activity against the enzyme. Here, we performed the first structure-function studies on PanD encoded by the nontuberculous mycobacterial lung pathogen Mycobacterium abscessus (Mab), shedding light on the differences and similarities of Mab and Mtb PanD. Solution X-ray scattering data provided the solution structure of the entire tetrameric Mab PanD, which in comparison to the structure of the derived C-terminal truncated Mab PanD1-114 mutant revealed the orientation of the four flexible C-termini relative to the catalytic core. Enzymatic studies of Mab PanD1-114 explored the essentiality of the C-terminus for catalysis. A library of recombinant Mab PanD mutants based on structural information and PZA/POA resistant PanD mutations in Mtb illuminated critical residues involved in the substrate tunnel and enzymatic activity. Using our library of POA analogues, we identified (3-(1-naphthamido)pyrazine-2-carboxylic acid) (analogue 2) as the first potent inhibitor of Mab PanD. The inhibitor shows mainly electrostatic- and hydrogen bonding interaction with the target enzyme as explored by isothermal titration calorimetry and confirmed by docking studies. The observed unfavorable entropy indicates that significant conformational changes are involved in the binding process of analogue 2 to Mab PanD. In contrast to PZA and POA, which are whole-cell inactive, analogue 2 exerts appreciable antibacterial activity against the three subspecies of Mab.
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Affiliation(s)
- Wuan–Geok Saw
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Chen Yen Leow
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Amaravadhi Harikishore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Malcolm S. Cole
- University of Minnesota, College of Pharmacy, Department of Medicinal Chemistry 8-101 Weaver-Densford Hall 308 Harvard St. SE, Minneapolis, MN 55455, USA
| | - Wassihun Wedajo Aragaw
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, New Jersey 07110, USA
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Pooja Hegde
- University of Minnesota, College of Pharmacy, Department of Medicinal Chemistry 8-101 Weaver-Densford Hall 308 Harvard St. SE, Minneapolis, MN 55455, USA
| | - Courtney C. Aldrich
- University of Minnesota, College of Pharmacy, Department of Medicinal Chemistry 8-101 Weaver-Densford Hall 308 Harvard St. SE, Minneapolis, MN 55455, USA
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, New Jersey 07110, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, 123 Metro Boulevard, Nutley, New Jersey 07110, USA
- Department of Microbiology and Immunology, Georgetown University, 3900 Reservoir Road NW Medical-Dental Building, Washington, DC 20007, USA
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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de Vries LE, Lunghi M, Krishnan A, Kooij TWA, Soldati-Favre D. Pantothenate and CoA biosynthesis in Apicomplexa and their promise as antiparasitic drug targets. PLoS Pathog 2021; 17:e1010124. [PMID: 34969059 PMCID: PMC8717973 DOI: 10.1371/journal.ppat.1010124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Apicomplexa phylum comprises thousands of distinct intracellular parasite species, including coccidians, haemosporidians, piroplasms, and cryptosporidia. These parasites are characterized by complex and divergent life cycles occupying a variety of host niches. Consequently, they exhibit distinct adaptations to the differences in nutritional availabilities, either relying on biosynthetic pathways or by salvaging metabolites from their host. Pantothenate (Pan, vitamin B5) is the precursor for the synthesis of an essential cofactor, coenzyme A (CoA), but among the apicomplexans, only the coccidian subgroup has the ability to synthesize Pan. While the pathway to synthesize CoA from Pan is largely conserved across all branches of life, there are differences in the redundancy of enzymes and possible alternative pathways to generate CoA from Pan. Impeding the scavenge of Pan and synthesis of Pan and CoA have been long recognized as potential targets for antimicrobial drug development, but in order to fully exploit these critical pathways, it is important to understand such differences. Recently, a potent class of pantothenamides (PanAms), Pan analogs, which target CoA-utilizing enzymes, has entered antimalarial preclinical development. The potential of PanAms to target multiple downstream pathways make them a promising compound class as broad antiparasitic drugs against other apicomplexans. In this review, we summarize the recent advances in understanding the Pan and CoA biosynthesis pathways, and the suitability of these pathways as drug targets in Apicomplexa, with a particular focus on the cyst-forming coccidian, Toxoplasma gondii, and the haemosporidian, Plasmodium falciparum.
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Affiliation(s)
- Laura E. de Vries
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Matteo Lunghi
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Aarti Krishnan
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Taco W. A. Kooij
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Dominique Soldati-Favre
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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7
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Comparative Performance of Genomic Methods for the Detection of Pyrazinamide Resistance and Heteroresistance in Mycobacterium tuberculosis. J Clin Microbiol 2021; 60:e0190721. [PMID: 34757831 PMCID: PMC8769725 DOI: 10.1128/jcm.01907-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Pyrazinamide is an important component of both drug-susceptible and drug-resistant tuberculosis treatment regimens. Although approximately 50% of rifampin-resistant isolates are also resistant to pyrazinamide, pyrazinamide susceptibility testing is not routinely performed due to the challenging nature of the assay. We investigated the diagnostic accuracy of genotypic and phenotypic methods and explored the occurrence of pyrazinamide heteroresistance. We assessed pyrazinamide susceptibility among 358 individuals enrolled in the South African EXIT-RIF cohort using Sanger and targeted deep sequencing (TDS) of the pncA gene, whole-genome sequencing (WGS), and phenotypic drug susceptibility testing. We calculated the diagnostic accuracy of the different methods and investigated the prevalence and clinical impact of pncA heteroresistance. True pyrazinamide susceptibility status was assigned to each isolate using the Köser classification and expert rules. We observed 100% agreement across genotypic methods for detection of pncA fixed mutations; only TDS confidently identified three isolates (0.8%) with minor variants. For the 355 (99.2%) isolates that could be assigned true pyrazinamide status with confidence, phenotypic DST had a sensitivity of 96.5% (95% confidence interval [CI], 93.8 to 99.3%) and specificity of 100% (95% CI, 100 to 100%), both Sanger sequencing and WGS had a sensitivity of 97.1% (95% CI, 94.6 to 99.6%) and specificity of 97.8% (95% CI, 95.7 to 99.9%), and TDS had sensitivity of 98.8% (95% CI, 97.2 to 100%) and specificity of 97.8% (95% CI, 95.7 to 99.9%). We demonstrate high sensitivity and specificity for pyrazinamide susceptibility testing among all assessed genotypic methods. The prevalence of pyrazinamide heteroresistance in Mycobacterium tuberculosis isolates was lower than that identified for other first-line drugs.
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Activity of Pyrazinamide against Mycobacterium tuberculosis at Neutral pH in PZA-S1 Minimal Medium. Antibiotics (Basel) 2021; 10:antibiotics10080909. [PMID: 34438959 PMCID: PMC8388709 DOI: 10.3390/antibiotics10080909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/14/2021] [Accepted: 07/22/2021] [Indexed: 11/17/2022] Open
Abstract
Susceptibility testing of tuberculosis (TB) drugs on Mycobacterium tuberculosis is essential for the rapid detection of strains resistant to the drugs, providing the patient with effective treatment, and preventing the spread of drug-resistant TB strains. Pyrazinamide (PZA) is one of the first-line agents used for the treatment of TB. However, current phenotypic PZA susceptibility testing is unreliable due to its performance in acidic pH conditions. The aims of this study were to develop minimal media to determine the activity of PZA at a neutral pH at 37 °C to avoid problems caused by an acidic pH, which is currently used in PZA susceptibility tests, and to identify PZA-resistant M. tuberculosis in media with reproducibility and accuracy. Different minimal media were used to determine the activity of PZA using the broth microdilution method with M. tuberculosis H37Ra as the reference strain. The PZA-S1 minimal medium was proposed as the most suitable medium. PZA inhibited the growth of M. tuberculosis in PZA-S1 at a neutral pH of 6.8, which is the optimal pH for M. tuberculosis growth. Moreover, PZA showed activity at a neutral pH on a PZA-S1 agar plate when using the disk diffusion method. PZA-resistant M. tuberculosis could be identified at a neutral pH in PZA-S1 minimal medium. This study establishes valuable information regarding the testing of PZA’s susceptibility in relation to M. tuberculosis at a neutral pH of 6.8 with reliability and accuracy in clinical settings.
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Ragunathan P, Cole M, Latka C, Aragaw WW, Hegde P, Shin J, Subramanian Manimekalai MS, Rishikesan S, Aldrich CC, Dick T, Grüber G. Mycobacterium tuberculosis PanD Structure-Function Analysis and Identification of a Potent Pyrazinoic Acid-Derived Enzyme Inhibitor. ACS Chem Biol 2021; 16:1030-1039. [PMID: 33984234 DOI: 10.1021/acschembio.1c00131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A common strategy employed in antibacterial drug discovery is the targeting of biosynthetic processes that are essential and specific for the pathogen. Specificity in particular avoids undesirable interactions with potential enzymatic counterparts in the human host, and it ensures on-target toxicity. Synthesis of pantothenate (Vitamine B5), which is a precursor of the acyl carrier coenzyme A, is an example of such a pathway. In Mycobacterium tuberculosis (Mtb), which is the causative agent of tuberculosis (TB), pantothenate is formed by pantothenate synthase, utilizing D-pantoate and β-Ala as substrates. β-Ala is mainly formed by the decarboxylation of l-aspartate, generated by the decarboxylase PanD, which is a homo-oliogomer in solution. Pyrazinoic acid (POA), which is the bioactive form of the TB prodrug pyrazinamide, binds and inhibits PanD activity weakly. Here, we generated a library of recombinant Mtb PanD mutants based on structural information and PZA/POA resistance mutants. Alterations in oligomer formation, enzyme activity, and/or POA binding were observed in respective mutants, providing insights into essential amino acids for Mtb PanD's proper structural assembly, decarboxylation activity and drug interaction. This information provided the platform for the design of novel POA analogues with modifications at position 3 of the pyrazine ring. Analogue 2, which incorporates a bulky naphthamido group at this position, displayed a 1000-fold increase in enzyme inhibition, compared to POA, along with moderately improved antimycobacterial activity. The data demonstrate that an improved understanding of mechanistic and enzymatic features of key metabolic enzymes can stimulate design of more-potent PanD inhibitors.
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Affiliation(s)
- Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Malcolm Cole
- University of Minnesota, College of Pharmacy, Department of Medicinal Chemistry 8-101 Weaver-Densford Hall 308 Harvard St. SE, Minneapolis, Minnesota 55455, United States
| | - Chitra Latka
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Wassihun Wedajo Aragaw
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, New Jersey 07110, United States
| | - Pooja Hegde
- University of Minnesota, College of Pharmacy, Department of Medicinal Chemistry 8-101 Weaver-Densford Hall 308 Harvard St. SE, Minneapolis, Minnesota 55455, United States
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | | | - Sankaranarayanan Rishikesan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Courtney C. Aldrich
- University of Minnesota, College of Pharmacy, Department of Medicinal Chemistry 8-101 Weaver-Densford Hall 308 Harvard St. SE, Minneapolis, Minnesota 55455, United States
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, New Jersey 07110, United States
- Department of Medical Sciences, Hackensack Meridian School of Medicine, 123 Metro Boulevard, Nutley, New Jersey 07110, United States
- Department of Microbiology and Immunology, Georgetown University, 3900 Reservoir Road NW Medical-Dental Building, Washington, District of Columbia 20007, United States
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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Atypical Genetic Basis of Pyrazinamide Resistance in Monoresistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 2021; 65:AAC.01916-20. [PMID: 33722890 PMCID: PMC8315952 DOI: 10.1128/aac.01916-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
Pyrazinamide (PZA) is a widely used antitubercular chemotherapeutic. Typically, PZA resistance (PZA-R) emerges in Mycobacterium tuberculosis strains with existing resistance to isoniazid and rifampin (i.e., multidrug resistance [MDR]) and is conferred by loss-of-function pncA mutations that inhibit conversion to its active form, pyrazinoic acid (POA). PZA-R departing from this canonical scenario is poorly understood. Here, we genotyped pncA and purported alternative PZA-R genes (panD, rpsA, and clpC1) with long-read sequencing of 19 phenotypically PZA-monoresistant isolates collected in Sweden and compared their phylogenetic and genomic characteristics to a large set of MDR PZA-R (MDRPZA-R) isolates. We report the first association of ClpC1 mutations with PZA-R in clinical isolates, in the ClpC1 promoter (clpC1p−138) and the N terminus of ClpC1 (ClpC1Val63Ala). Mutations have emerged in both these regions under POA selection in vitro, and the N-terminal region of ClpC1 has been implicated further, through its POA-dependent efficacy in PanD proteolysis. ClpC1Val63Ala mutants spanned 4 Indo-Oceanic sublineages. Indo-Oceanic isolates invariably harbored ClpC1Val63Ala and were starkly overrepresented (odds ratio [OR] = 22.2, P < 0.00001) among PZA-monoresistant isolates (11/19) compared to MDRPZA-R isolates (5/80). The genetic basis of Indo-Oceanic isolates’ overrepresentation in PZA-monoresistant tuberculosis (TB) remains undetermined, but substantial circumstantial evidence suggests that ClpC1Val63Ala confers low-level PZA resistance. Our findings highlight ClpC1 as potentially clinically relevant for PZA-R and reinforce the importance of genetic background in the trajectory of resistance development.
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11
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Pyrazinamide Susceptibility Is Driven by Activation of the SigE-Dependent Cell Envelope Stress Response in Mycobacterium tuberculosis. mBio 2021; 13:e0043921. [PMID: 35100871 PMCID: PMC8805019 DOI: 10.1128/mbio.00439-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Pyrazinamide (PZA) plays a crucial role in first-line tuberculosis drug therapy. Unlike other antimicrobial agents, PZA is active against Mycobacterium tuberculosis only at low pH. The basis for this conditional drug susceptibility remains undefined. In this study, we utilized a genome-wide approach to interrogate potentiation of PZA action. We found that mutations in numerous genes involved in central metabolism as well as cell envelope maintenance and stress response are associated with PZA resistance. Further, we demonstrate that constitutive activation of the cell envelope stress response can drive PZA susceptibility independent of environmental pH. Consequently, exposure to peptidoglycan synthesis inhibitors, such as beta-lactams and d-cycloserine, potentiate PZA action through triggering this response. These findings illuminate a regulatory mechanism for conditional PZA susceptibility and reveal new avenues for enhancing potency of this important drug through targeting activation of the cell envelope stress response. IMPORTANCE For decades, pyrazinamide has served as a cornerstone of tuberculosis therapy. Unlike any other antitubercular drug, pyrazinamide requires an acidic environment to exert its action. Despite its importance, the driver of this conditional susceptibility has remained unknown. In this study, a genome-wide approach revealed that pyrazinamide action is governed by the cell envelope stress response. This observation was validated by orthologous approaches that demonstrate that a central player of this response, SigE, is both necessary and sufficient for potentiation of pyrazinamide action. Moreover, constitutive activation of this response through deletion of the anti-sigma factor gene rseA or exposure of bacilli to drugs that target the cell wall was found to potently drive pyrazinamide susceptibility independent of environmental pH. These findings force a paradigm shift in our understanding of pyrazinamide action and open new avenues for improving diagnostic and therapeutic tools for tuberculosis.
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12
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Butman HS, Kotzé TJ, Dowd CS, Strauss E. Vitamin in the Crosshairs: Targeting Pantothenate and Coenzyme A Biosynthesis for New Antituberculosis Agents. Front Cell Infect Microbiol 2020; 10:605662. [PMID: 33384970 PMCID: PMC7770189 DOI: 10.3389/fcimb.2020.605662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Despite decades of dedicated research, there remains a dire need for new drugs against tuberculosis (TB). Current therapies are generations old and problematic. Resistance to these existing therapies results in an ever-increasing burden of patients with disease that is difficult or impossible to treat. Novel chemical entities with new mechanisms of action are therefore earnestly required. The biosynthesis of coenzyme A (CoA) has long been known to be essential in Mycobacterium tuberculosis (Mtb), the causative agent of TB. The pathway has been genetically validated by seminal studies in vitro and in vivo. In Mtb, the CoA biosynthetic pathway is comprised of nine enzymes: four to synthesize pantothenate (Pan) from l-aspartate and α-ketoisovalerate; five to synthesize CoA from Pan and pantetheine (PantSH). This review gathers literature reports on the structure/mechanism, inhibitors, and vulnerability of each enzyme in the CoA pathway. In addition to traditional inhibition of a single enzyme, the CoA pathway offers an antimetabolite strategy as a promising alternative. In this review, we provide our assessment of what appear to be the best targets, and, thus, which CoA pathway enzymes present the best opportunities for antitubercular drug discovery moving forward.
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Affiliation(s)
- Hailey S. Butman
- Department of Chemistry, George Washington University, Washington, DC, United States
| | - Timothy J. Kotzé
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, Washington, DC, United States
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
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13
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Gopal P, Sarathy JP, Yee M, Ragunathan P, Shin J, Bhushan S, Zhu J, Akopian T, Kandror O, Lim TK, Gengenbacher M, Lin Q, Rubin EJ, Grüber G, Dick T. Pyrazinamide triggers degradation of its target aspartate decarboxylase. Nat Commun 2020; 11:1661. [PMID: 32245967 PMCID: PMC7125159 DOI: 10.1038/s41467-020-15516-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 03/16/2020] [Indexed: 11/28/2022] Open
Abstract
Pyrazinamide is a sterilizing first-line tuberculosis drug. Genetic, metabolomic and biophysical analyses previously demonstrated that pyrazinoic acid, the bioactive form of the prodrug pyrazinamide (PZA), interrupts biosynthesis of coenzyme A in Mycobacterium tuberculosis by binding to aspartate decarboxylase PanD. While most drugs act by inhibiting protein function upon target binding, we find here that pyrazinoic acid is only a weak enzyme inhibitor. We show that binding of pyrazinoic acid to PanD triggers degradation of the protein by the caseinolytic protease ClpC1-ClpP. Thus, the old tuberculosis drug pyrazinamide exerts antibacterial activity by acting as a target degrader, a mechanism of action that has recently emerged as a successful strategy in drug discovery across disease indications. Our findings provide the basis for the rational discovery of next generation PZA. It has been shown that the bioactive component of pyrazinamide, pyrazinoic acid (POA), blocks coenzyme A biosynthesis in M. tuberculosis by binding to the aspartate decarboxylase PanD. Here the authors show that pyrazinamide triggers degradation of PanD by stimulating its degradation by the caseinolytic protease Clp.
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Affiliation(s)
- Pooja Gopal
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,MSD Translational Medicine Research Centre, Merck Research Laboratories, Singapore, Singapore
| | - Jickky Palmae Sarathy
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michelle Yee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Tatos Akopian
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Olga Kandror
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Teck Kwang Lim
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Martin Gengenbacher
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.,Department of Medical Sciences, Hackensack Meridian Medical School at Seton Hall University, Nutley, NJ, USA
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA. .,Department of Medical Sciences, Hackensack Meridian Medical School at Seton Hall University, Nutley, NJ, USA.
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14
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Abstract
Pyrazinamide (PZA) is a cornerstone antimicrobial drug used exclusively for the treatment of tuberculosis (TB). Due to its ability to shorten drug therapy by 3 months and reduce disease relapse rates, PZA is considered an irreplaceable component of standard first-line short-course therapy for drug-susceptible TB and second-line treatment regimens for multidrug-resistant TB. Despite over 60 years of research on PZA and its crucial role in current and future TB treatment regimens, the mode of action of this unique drug remains unclear. Defining the mode of action for PZA will open new avenues for rational design of novel therapeutic approaches for the treatment of TB. In this review, we discuss the four prevailing models for PZA action, recent developments in modulation of PZA susceptibility and resistance, and outlooks for future research and drug development.
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15
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Novel pyrazine based anti-tubercular agents: Design, synthesis, biological evaluation and in silico studies. Bioorg Chem 2020; 96:103610. [DOI: 10.1016/j.bioorg.2020.103610] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 12/02/2019] [Accepted: 01/20/2020] [Indexed: 12/31/2022]
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16
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The molecular basis of pyrazinamide activity on Mycobacterium tuberculosis PanD. Nat Commun 2020; 11:339. [PMID: 31953389 PMCID: PMC6969166 DOI: 10.1038/s41467-019-14238-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/16/2019] [Indexed: 11/18/2022] Open
Abstract
Pyrazinamide has been a mainstay in the multidrug regimens used to treat tuberculosis. It is active against the persistent, non-replicating mycobacteria responsible for the protracted therapy required to cure tuberculosis. Pyrazinamide is a pro-drug that is converted into pyrazinoic acid (POA) by pyrazinamidase, however, the exact target of the drug has been difficult to determine. Here we show the enzyme PanD binds POA in its active site in a manner consistent with competitive inhibition. The active site is not directly accessible to the inhibitor, suggesting the protein must undergo a conformational change to bind the inhibitor. This is consistent with the slow binding kinetics we determined for POA. Drug-resistant mutations cluster near loops that lay on top of the active site. These resistant mutants show reduced affinity and residence time of POA consistent with a model where resistance occurs by destabilizing the closed conformation of the active site. The important tuberculosis drug pyrazinamide (PZA) is converted to its active form pyrazinoic acid (POA) in Mycobacterium tuberculosis (Mtb). Here the authors identify the pantothenate biosynthesis pathway enzyme aspartate decarboxylase (PanD) as the target of PZA and determine the POA bound Mtb PanD crystal structure.
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17
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Gopal P, Grüber G, Dartois V, Dick T. Pharmacological and Molecular Mechanisms Behind the Sterilizing Activity of Pyrazinamide. Trends Pharmacol Sci 2019; 40:930-940. [PMID: 31704175 PMCID: PMC6884696 DOI: 10.1016/j.tips.2019.10.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 11/20/2022]
Abstract
Inclusion of pyrazinamide (PZA) in the tuberculosis (TB) drug regimen during the 1970s enabled a reduction in treatment duration from 12 to 6 months. PZA has this remarkable effect in patients despite displaying poor potency against Mycobacterium tuberculosis (Mtb) in vitro. The pharmacological basis for the in vivo sterilizing activity of the drug has remained obscure and its bacterial target controversial. Recently it was shown that PZA penetrates necrotic caseous TB lung lesions and kills nongrowing, drug-tolerant bacilli. Furthermore, it was uncovered that PZA inhibits bacterial Coenzyme A biosynthesis. It may block this pathway by triggering degradation of its target, aspartate decarboxylase. The elucidation of the pharmacological and molecular mechanisms of PZA provides the basis for the rational discovery of the next-generation PZA with improved in vitro potency while maintaining attractive pharmacological properties.
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Affiliation(s)
- Pooja Gopal
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore; Current address: MSD Translational Medicine Research Centre, Merck Research Laboratories, 8 Biomedical Grove, Singapore 138665, Republic of Singapore.
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, 340 Kingsland Street Building 102, Nutley, NJ 07110, USA; Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, 340 Kingsland Street Building 102, Nutley, NJ 07110, USA; Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, 340 Kingsland Street, Nutley, NJ 07110, USA; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore
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18
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Gopal P, Dick T. Targeted protein degradation in antibacterial drug discovery? PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 152:10-14. [PMID: 31738980 DOI: 10.1016/j.pbiomolbio.2019.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/29/2019] [Accepted: 11/13/2019] [Indexed: 11/25/2022]
Abstract
Drug induced degradation of a target protein is a novel concept in drug discovery. Traditionally drugs modulate activity, as opposed to abundance, of their targets. Degradation inducing ligands act catalytically. Thus, one advantage of target degradation over the classical on-target mechanism is that lower drug concentration may be sufficient to cause the desired cellular effects. The first promoters of target degradation were discovered unintentionally: it turned out that some drugs 'accidently' promote degradation of their target by the cellular proteolytic machinery. Elegant methods were developed to target specific proteins of interest for degradation, thus enabling the rational discovery of degradation inducers. The application of targeted degradation has so far been limited to human cells. Recently, we discovered that an antibacterial drug, the anti-tuberculosis antibiotic pyrazinamide, functions as a promotor of degradation of its bacterial target. Increasing antimicrobial resistance makes the discovery of novel antibiotics more urgent than ever. Can rational target degradation be applied for the discovery of anti-bacterials? Here, we first discuss briefly some historic examples and then recent approaches in rational target degradation for human diseases. Then, we describe how the first anti-bacterial target degradation promoter pyrazinamide triggers removal of its target. Efforts are under way to exploit this specific mechanistic knowledge for the discovery of next generation pyrazinamide. We end with the big - and open - question whether targeted protein degradation as an approach to anti-bacterial drug discovery can be generalized, similar to what has been achieved in the area of drug discovery for human diseases.
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Affiliation(s)
- Pooja Gopal
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA; Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, NJ, USA.
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19
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Lamont EA, Baughn AD. Impact of the host environment on the antitubercular action of pyrazinamide. EBioMedicine 2019; 49:374-380. [PMID: 31669220 PMCID: PMC6945238 DOI: 10.1016/j.ebiom.2019.10.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 10/01/2019] [Accepted: 10/01/2019] [Indexed: 01/05/2023] Open
Abstract
Pyrazinamide remains the only drug in the tuberculosis pharmacopeia to drastically shorten first-line therapy from nine to six months. Due to its unparalleled ability to sterilize non-replicating bacilli and reduce relapse rates, PZA is expected to be irreplaceable in future therapies against tuberculosis. While the molecular target of PZA is unclear, recent pharmacokinetic studies using small animal models and patient samples have highlighted the importance of host metabolism and immune responses in PZA efficacy. Delineating which host factors are important for PZA action will be integral to the design of next-generation therapies to shorten current TB drug regimens as well as to overcome treatment limitations in some patients. In this review, we discuss evidence for influence of the host environment on PZA activity, targets for PZA mechanism of action, recent studies in PZA pharmacokinetics, PZA antagonism and synergy with other first-line anti-TB drugs, and implications for future research.
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Affiliation(s)
- Elise A Lamont
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Anthony D Baughn
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, 55455, USA.
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20
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Anthony RM, den Hertog AL, van Soolingen D. 'Happy the man, who, studying nature's laws, Thro' known effects can trace the secret cause.' Do we have enough pieces to solve the pyrazinamide puzzle? J Antimicrob Chemother 2019. [PMID: 29528413 DOI: 10.1093/jac/dky060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A low pH was assumed to be required for the activity of pyrazinoic acid (the active form of pyrazinamide) against Mycobacterium tuberculosis, but recently activity has been demonstrated at neutral pH. Renewed interest in pyrazinamide has led to an increasing number of potential targets and the suspicion that pyrazinamide is a 'dirty drug'. However, it is our opinion that the recent demonstration that pyrazinoic acid is active against PanD provides an alternative explanation for the secret of pyrazinamide's unusual activity. In this article we propose that PanD is the primary target of pyrazinoic acid but expression of pyrazinoic acid susceptibility requires an intact stress response. As the mycobacterial stress response requires the interaction of a number of genes, disruption of any could result in an inability to enter the susceptible phenotype. We believe this model can explain most of the recent observations of the seemingly diverse spectrum of activity of pyrazinamide.
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Affiliation(s)
- R M Anthony
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - A L den Hertog
- Institute for Life Sciences and Chemistry, HU University of Applied Sciences Utrecht, Utrecht, The Netherlands
| | - D van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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21
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Zhong W, Pasunooti KK, Balamkundu S, Wong YH, Nah Q, Gadi V, Gnanakalai S, Chionh YH, McBee ME, Gopal P, Lim SH, Olivier N, Buurman ET, Dick T, Liu CF, Lescar J, Dedon PC. Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37- N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism. J Med Chem 2019; 62:7788-7805. [PMID: 31442049 PMCID: PMC6748665 DOI: 10.1021/acs.jmedchem.9b00582] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Among the >120
modified ribonucleosides in the prokaryotic epitranscriptome,
many tRNA modifications are critical to bacterial survival, which
makes their synthetic enzymes ideal targets for antibiotic development.
Here we performed a structure-based design of inhibitors of tRNA-(N1G37) methyltransferase, TrmD, which is an essential enzyme
in many bacterial pathogens. On the basis of crystal structures of
TrmDs from Pseudomonas aeruginosa and Mycobacterium tuberculosis, we synthesized a series
of thienopyrimidinone derivatives with nanomolar potency against TrmD
in vitro and discovered a novel active site conformational change
triggered by inhibitor binding. This tyrosine-flipping mechanism is
uniquely found in P. aeruginosa TrmD
and renders the enzyme inaccessible to the cofactor S-adenosyl-l-methionine (SAM) and probably to the substrate
tRNA. Biophysical and biochemical structure–activity relationship
studies provided insights into the mechanisms underlying the potency
of thienopyrimidinones as TrmD inhibitors, with several derivatives
found to be active against Gram-positive and mycobacterial pathogens.
These results lay a foundation for further development of TrmD inhibitors
as antimicrobial agents.
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Affiliation(s)
- Wenhe Zhong
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , 636921 Singapore
| | - Kalyan Kumar Pasunooti
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Seetharamsing Balamkundu
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Yee Hwa Wong
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 637551 Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , 636921 Singapore
| | - Qianhui Nah
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Vinod Gadi
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Shanmugavel Gnanakalai
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Yok Hian Chionh
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Megan E McBee
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Pooja Gopal
- Yong Loo Lin School of Medicine , National University of Singapore , 117597 Singapore
| | - Siau Hoi Lim
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 637551 Singapore
| | | | | | - Thomas Dick
- Yong Loo Lin School of Medicine , National University of Singapore , 117597 Singapore
| | - Chuan Fa Liu
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 637551 Singapore
| | - Julien Lescar
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 637551 Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , 636921 Singapore
| | - Peter C Dedon
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore.,Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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22
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Lane T, Russo DP, Zorn KM, Clark AM, Korotcov A, Tkachenko V, Reynolds RC, Perryman AL, Freundlich JS, Ekins AS. Comparing and Validating Machine Learning Models for Mycobacterium tuberculosis Drug Discovery. Mol Pharm 2018; 15:4346-4360. [PMID: 29672063 PMCID: PMC6167198 DOI: 10.1021/acs.molpharmaceut.8b00083] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Tuberculosis is a global health dilemma. In 2016, the WHO reported 10.4 million incidences and 1.7 million deaths. The need to develop new treatments for those infected with Mycobacterium tuberculosis ( Mtb) has led to many large-scale phenotypic screens and many thousands of new active compounds identified in vitro. However, with limited funding, efforts to discover new active molecules against Mtb needs to be more efficient. Several computational machine learning approaches have been shown to have good enrichment and hit rates. We have curated small molecule Mtb data and developed new models with a total of 18,886 molecules with activity cutoffs of 10 μM, 1 μM, and 100 nM. These data sets were used to evaluate different machine learning methods (including deep learning) and metrics and to generate predictions for additional molecules published in 2017. One Mtb model, a combined in vitro and in vivo data Bayesian model at a 100 nM activity yielded the following metrics for 5-fold cross validation: accuracy = 0.88, precision = 0.22, recall = 0.91, specificity = 0.88, kappa = 0.31, and MCC = 0.41. We have also curated an evaluation set ( n = 153 compounds) published in 2017, and when used to test our model, it showed the comparable statistics (accuracy = 0.83, precision = 0.27, recall = 1.00, specificity = 0.81, kappa = 0.36, and MCC = 0.47). We have also compared these models with additional machine learning algorithms showing Bayesian machine learning models constructed with literature Mtb data generated by different laboratories generally were equivalent to or outperformed deep neural networks with external test sets. Finally, we have also compared our training and test sets to show they were suitably diverse and different in order to represent useful evaluation sets. Such Mtb machine learning models could help prioritize compounds for testing in vitro and in vivo.
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Affiliation(s)
- Thomas Lane
- Collaborations Pharmaceuticals, Inc., Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel P. Russo
- Collaborations Pharmaceuticals, Inc., Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ, 08102, USA
| | - Kimberley M. Zorn
- Collaborations Pharmaceuticals, Inc., Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
| | - Alex M. Clark
- Molecular Materials Informatics, Inc., 1900 St. Jacques #302, Montreal H3J 2S1, Quebec, Canada
| | - Alexandru Korotcov
- Science Data Software, LLC, 14914 Bradwill Court, Rockville, MD 20850, USA
| | - Valery Tkachenko
- Science Data Software, LLC, 14914 Bradwill Court, Rockville, MD 20850, USA
| | - Robert C. Reynolds
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, NP 2540 J, 1720 2Avenue South, Birmingham, AL 35294-3300, USA
| | - Alexander L. Perryman
- Department of Pharmacology, Physiology and Neuroscience, Rutgers University-New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Joel S. Freundlich
- Department of Pharmacology, Physiology and Neuroscience, Rutgers University-New Jersey Medical School, Newark, New Jersey 07103, USA
- Division of Infectious Diseases, Department of Medicine, and the Ruy V. Lourenço Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University–New Jersey Medical School, Newark, New Jersey 07103, USA
| | - and Sean Ekins
- Collaborations Pharmaceuticals, Inc., Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
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23
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Genetics and roadblocks of drug resistant tuberculosis. INFECTION GENETICS AND EVOLUTION 2018; 72:113-130. [PMID: 30261266 DOI: 10.1016/j.meegid.2018.09.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 11/22/2022]
Abstract
Considering the extensive evolutionary history of Mycobacterium tuberculosis, anti-Tuberculosis (TB) drug therapy exerts a recent selective pressure. However, in a microorganism devoid of horizontal gene transfer and with a strictly clonal populational structure such as M. tuberculosis the usual, but not sole, path to overcome drug susceptibility is through de novo mutations on a relatively strict set of genes. The possible allelic diversity that can be associated with drug resistance through several mechanisms such as target alteration or target overexpression, will dictate how these genes can become associated with drug resistance. The success demonstrated by this pathogenic microbe in this latter process and its ability to spread is currently one of the major obstacles to an effective TB elimination. This article reviews the action mechanism of the more important anti-TB drugs, including bedaquiline and delamanid, along with new findings on specific resistance mechanisms. With the development, validation and endorsement of new in vitro molecular tests for drug resistance, knowledge on these resistance mechanisms and microevolutionary dynamics leading to the emergence and fixation of drug resistance mutations within the host is highly important. Additionally, the fitness toll imposed by resistance development is also herein discussed together with known compensatory mechanisms. By elucidating the possible mechanisms that enable one strain to reacquire the original fitness levels, it will be theoretically possible to make more informed decisions and develop novel strategies that can force M. tuberculosis microevolutionary trajectory down through a path of decreasing fitness levels.
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24
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Lupoli TJ, Vaubourgeix J, Burns-Huang K, Gold B. Targeting the Proteostasis Network for Mycobacterial Drug Discovery. ACS Infect Dis 2018; 4:478-498. [PMID: 29465983 PMCID: PMC5902792 DOI: 10.1021/acsinfecdis.7b00231] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the world's deadliest infectious diseases and urgently requires new antibiotics to treat drug-resistant strains and to decrease the duration of therapy. During infection, Mtb encounters numerous stresses associated with host immunity, including hypoxia, reactive oxygen and nitrogen species, mild acidity, nutrient starvation, and metal sequestration and intoxication. The Mtb proteostasis network, composed of chaperones, proteases, and a eukaryotic-like proteasome, provides protection from stresses and chemistries of host immunity by maintaining the integrity of the mycobacterial proteome. In this Review, we explore the proteostasis network as a noncanonical target for antibacterial drug discovery.
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Affiliation(s)
- Tania J. Lupoli
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Kristin Burns-Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Ben Gold
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
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25
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Gopal P, Nartey W, Ragunathan P, Sarathy J, Kaya F, Yee M, Setzer C, Manimekalai MSS, Dartois V, Grüber G, Dick T. Pyrazinoic Acid Inhibits Mycobacterial Coenzyme A Biosynthesis by Binding to Aspartate Decarboxylase PanD. ACS Infect Dis 2017; 3:807-819. [PMID: 28991455 DOI: 10.1021/acsinfecdis.7b00079] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Previously, we showed that a major in vitro and in vivo mechanism of resistance to pyrazinoic acid (POA), the bioactive component of the critical tuberculosis (TB) prodrug pyrazinamide (PZA), involves missense mutations in the aspartate decarboxylase PanD, an enzyme required for coenzyme A biosynthesis. What is the mechanism of action of POA? Upon demonstrating that treatment of M. bovis BCG with POA resulted in a depletion of intracellular coenzyme A and confirming that this POA-mediated depletion is prevented by either missense mutations in PanD or exogenous supplementation of pantothenate, we hypothesized that POA binds to PanD and that this binding blocks the biosynthetic pathway. Here, we confirm both hypotheses. First, metabolomic analyses showed that POA treatment resulted in a reduction of the concentrations of all coenzyme A precursors downstream of the PanD-mediated catalytic step. Second, using isothermal titration calorimetry, we established that POA, but not its prodrug PZA, binds to PanD. Binding was abolished for mutant PanD proteins. Taken together, these findings support a mechanism of action of POA in which the bioactive component of PZA inhibits coenzyme A biosynthesis via binding to aspartate decarboxylase PanD. Together with previous works, these results establish PanD as a genetically, metabolically, and biophysically validated target of PZA.
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Affiliation(s)
- Pooja Gopal
- Department of Microbiology
and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545
| | - Wilson Nartey
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798
| | - Jansy Sarathy
- Public
Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Firat Kaya
- Public
Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Michelle Yee
- Department of Microbiology
and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545
| | - Claudia Setzer
- Department of Microbiology
and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545
| | | | - Véronique Dartois
- Public
Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798
| | - Thomas Dick
- Department of Microbiology
and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545
- Public
Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, 225 Warren Street, Newark, New Jersey 07103, United States
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26
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Ngabonziza JCS, Diallo AB, Tagliani E, Diarra B, Kadanga AE, Togo ACG, Thiam A, de Rijk WB, Alagna R, Houeto S, Ba F, Dagnra AY, Ivan E, Affolabi D, Schwoebel V, Trebucq A, de Jong BC, Rigouts L, Daneau G. Half of rifampicin-resistant Mycobacterium tuberculosis complex isolated from tuberculosis patients in Sub-Saharan Africa have concomitant resistance to pyrazinamide. PLoS One 2017; 12:e0187211. [PMID: 29088294 PMCID: PMC5663438 DOI: 10.1371/journal.pone.0187211] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/16/2017] [Indexed: 11/18/2022] Open
Abstract
Background Besides inclusion in 1st line regimens against tuberculosis (TB), pyrazinamide (PZA) is used in 2nd line anti-TB regimens, including in the short regimen for multidrug-resistant TB (MDR-TB) patients. Guidelines and expert opinions are contradictory about inclusion of PZA in case of resistance. Moreover, drug susceptibility testing (DST) for PZA is not often applied in routine testing, and the prevalence of resistance is unknown in several regions, including in most African countries. Methods Six hundred and twenty-three culture isolates from rifampicin-resistant (RR) patients were collected in twelve Sub-Saharan African countries. Among those isolates, 71% were from patients included in the study on the Union short-course regimen for MDR-TB in Benin, Burkina Faso, Burundi, Cameroon, Central Africa Republic, the Democratic Republic of the Congo, Ivory Coast, Niger, and Rwanda PZA resistance, and the rest (29%) were consecutive isolates systematically stored from 2014–2015 in Mali, Rwanda, Senegal, and Togo. Besides national guidelines, the isolates were tested for PZA resistance through pncA gene sequencing. Results Over half of these RR-TB isolates (54%) showed a mutation in the pncA gene, with a significant heterogeneity between countries. Isolates with fluoroquinolone resistance (but not with injectable resistance or XDR) were more likely to have concurrent PZA resistance. The pattern of mutations in the pncA gene was quite diverse, although some isolates with an identical pattern of mutations in pncA and other drug-related genes were isolated from the same reference center, suggesting possible transmission of these strains. Conclusion Similar to findings in other regions, more than half of the patients having RR-TB in West and Central Africa present concomitant resistance to PZA. Further investigations are needed to understand the relation between resistance to PZA and resistance to fluoroquinolones, and whether continued use of PZA in the face of PZA resistance provides clinical benefit to the patients.
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Affiliation(s)
- Jean Claude Semuto Ngabonziza
- National Reference Laboratory Division, Biomedical Services Department, Rwanda Biomedical Centre, Kigali, Rwanda
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- * E-mail:
| | - Awa Ba Diallo
- Mycobacteriology Unit, Bacteriology- Virology Laboratory, CHNU Aristide le Dantec, Dakar, Senegal
| | - Elisa Tagliani
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bassirou Diarra
- SEREFO/UCRC Program, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | | | | | - Aliou Thiam
- Mycobacteriology Unit, Bacteriology- Virology Laboratory, CHNU Aristide le Dantec, Dakar, Senegal
| | - Willem Bram de Rijk
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Riccardo Alagna
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sabine Houeto
- Laboratoire de Référence des Mycobactéries, Cotonou, Benin
| | - Fatoumata Ba
- Laboratoire de Reference des Mycobactéries, Dakar, Senegal
| | | | - Emil Ivan
- National Reference Laboratory Division, Biomedical Services Department, Rwanda Biomedical Centre, Kigali, Rwanda
| | | | - Valérie Schwoebel
- International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Arnaud Trebucq
- International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Bouke Catherine de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Géraldine Daneau
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Biomedical section, Haute Ecole Francisco Ferrer, Brussels, Belgium
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27
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Dillon NA, Peterson ND, Feaga HA, Keiler KC, Baughn AD. Anti-tubercular Activity of Pyrazinamide is Independent of trans-Translation and RpsA. Sci Rep 2017; 7:6135. [PMID: 28733601 PMCID: PMC5522395 DOI: 10.1038/s41598-017-06415-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/24/2017] [Indexed: 12/22/2022] Open
Abstract
Pyrazinamide (PZA) is a first line anti-tubercular drug for which the mechanism of action remains unresolved. Recently, it was proposed that the active form of PZA, pyrazinoic acid (POA), disrupts the ribosome rescue process of trans-translation in Mycobacterium tuberculosis. This model suggested that POA binds within the carboxy-terminal domain of ribosomal protein S1 (RpsA) and inhibits trans-translation leading to accumulation of stalled ribosomes. Here, we demonstrate that M. tuberculosis RpsA interacts with single stranded RNA, but not with POA. Further, we show that an rpsA polymorphism previously identified in a PZA resistant strain does not confer PZA resistance when reconstructed in a laboratory strain. Finally, by utilizing an in vitro trans-translation assay with purified M. tuberculosis ribosomes we find that an interfering oligonucleotide can inhibit trans-translation, yet POA does not inhibit trans-translation. Based on these findings, we conclude that the action of PZA is entirely independent of RpsA and trans-translation in M. tuberculosis.
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Affiliation(s)
- Nicholas A Dillon
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Nicholas D Peterson
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Heather A Feaga
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Kenneth C Keiler
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Anthony D Baughn
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
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