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Kachi K, Sato T, Nagasawa M, Cann I, Atomi H. The Lreu_1276 protein from Limosilactobacillus reuteri represents a third family of dihydroneopterin triphosphate pyrophosphohydrolases in bacteria. Appl Environ Microbiol 2024; 90:e0081424. [PMID: 38888337 PMCID: PMC11267939 DOI: 10.1128/aem.00814-24] [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: 04/25/2024] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
Tetrahydrofolate is a cofactor involved in C1 metabolism including biosynthesis pathways for adenine and serine. In the classical tetrahydrofolate biosynthesis pathway, the steps removing three phosphate groups from the precursor 7,8-dihydroneopterin triphosphate (DHNTP) remain unclear in many bacteria. DHNTP pyrophosphohydrolase hydrolyzes pyrophosphate from DHNTP and produces 7,8-dihydroneopterin monophosphate. Although two structurally distinct DHNTP pyrophosphohydrolases have been identified in the intestinal bacteria Lactococcus lactis and Escherichia coli, the distribution of their homologs is limited. Here, we aimed to identify a third DHNTP pyrophosphohydrolase gene in the intestinal lactic acid bacterium Limosilactobacillus reuteri. In a gene operon including genes involved in dihydrofolate biosynthesis, we focused on the lreu_1276 gene, annotated as Ham1 family protein or XTP/dITP diphosphohydrolase, as a candidate encoding DHNTP pyrophosphohydrolase. The Lreu_1276 recombinant protein was prepared using E. coli and purified. Biochemical analyses of the reaction product revealed that the Lreu_1276 protein displays significant pyrophosphohydrolase activity toward DHNTP. The optimal reaction temperature and pH were 35°C and around 7, respectively. Substrate specificity was relatively strict among 17 tested compounds. Although previously characterized DHNTP pyrophosphohydrolases prefer Mg2+, the Lreu_1276 protein exhibited maximum activity in the presence of Mn2+, with a specific activity of 28.2 ± 2.0 µmol min-1 mg-1 in the presence of 1 mM Mn2+. The three DHNTP pyrophosphohydrolases do not share structural similarity to one another, and the distribution of their homologs does not overlap, implying that the Lreu_1276 protein represents a third structurally novel DHNTP pyrophosphohydrolase in bacteria. IMPORTANCE The identification of a structurally novel DHNTP pyrophosphohydrolase in L. reuteri provides valuable information in understanding tetrahydrofolate biosynthesis in bacteria that possess lreu_1276 homologs. Interestingly, however, even with the identification of a third family of DHNTP pyrophosphohydrolases, there are still a number of bacteria that do not harbor homologs for any of the three genes while possessing other genes involved in the biosynthesis of the pterin ring structure. This suggests the presence of an unrecognized DHNTP pyrophosphohydrolase gene in bacteria. As humans do not harbor DHNTP pyrophosphohydrolase, the high structural diversity of enzymes responsible for a reaction in tetrahydrofolate biosynthesis may provide an advantage in designing inhibitors targeting a specific group of bacteria in the intestinal microbiota.
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Affiliation(s)
- Kaede Kachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Takaaki Sato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Integrated Research Center for Carbon Negative Science, Kyoto University, Kyoto, Japan
| | - Maina Nagasawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Isaac Cann
- Department of Animal Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Integrated Research Center for Carbon Negative Science, Kyoto University, Kyoto, Japan
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2
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Aragaw WW, Negatu DA, Bungard CJ, Dartois VA, Marrouni AE, Nickbarg EB, Olsen DB, Warrass R, Dick T. Pharmacological validation of dihydrofolate reductase as a drug target in Mycobacterium abscessus. Antimicrob Agents Chemother 2024; 68:e0071723. [PMID: 38018963 PMCID: PMC10777855 DOI: 10.1128/aac.00717-23] [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: 05/30/2023] [Accepted: 10/13/2023] [Indexed: 11/30/2023] Open
Abstract
The Mycobacterium abscessus drug development pipeline is poorly populated, with particularly few validated target-lead couples to initiate de novo drug discovery. Trimethoprim, an inhibitor of dihydrofolate reductase (DHFR) used for the treatment of a range of bacterial infections, is not active against M. abscessus. Thus, evidence that M. abscessus DHFR is vulnerable to pharmacological intervention with a small molecule inhibitor is lacking. Here, we show that the pyrrolo-quinazoline PQD-1, previously identified as a DHFR inhibitor active against Mycobacterium tuberculosis, exerts whole cell activity against M. abscessus. Enzyme inhibition studies showed that PQD-1, in contrast to trimethoprim, is a potent inhibitor of M. abscessus DHFR and over-expression of DHFR causes resistance to PQD-1, providing biochemical and genetic evidence that DHFR is a vulnerable target and mediates PQD-1's growth inhibitory activity in M. abscessus. As observed in M. tuberculosis, PQD-1 resistant mutations mapped to the folate pathway enzyme thymidylate synthase (TYMS) ThyA. Like trimethoprim in other bacteria, PQD-1 synergizes with the dihydropteroate synthase (DHPS) inhibitor sulfamethoxazole (SMX), offering an opportunity to exploit the successful dual inhibition of the folate pathway and develop similarly potent combinations against M. abscessus. PQD-1 is active against subspecies of M. abscessus and a panel of clinical isolates, providing epidemiological validation of the target-lead couple. Leveraging a series of PQD-1 analogs, we have demonstrated a dynamic structure-activity relationship (SAR). Collectively, the results identify M. abscessus DHFR as an attractive target and PQD-1 as a chemical starting point for the discovery of novel drugs and drug combinations that target the folate pathway in M. abscessus.
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Affiliation(s)
- Wassihun Wedajo Aragaw
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Dereje A. Negatu
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | | | - Véronique A. Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | | | | | | | - Ralf Warrass
- MSD Animal Health Innovation GmbH, Zur Propstei, Schwabenheim, Germany
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
- Department of Microbiology and Immunology, Georgetown University, Washington, USA
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3
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Zhu Z, Chen C, Zhang J, Lai F, Feng J, Wu G, Xia J, Zhang W, Han Z, Zhang C, Yang Q, Wang Y, Liu B, Li T, Wu S. Exploration and Biological Evaluation of 1,3-Diamino-7 H-pyrrol[3,2- f]quinazoline Derivatives as Dihydrofolate Reductase Inhibitors. J Med Chem 2023; 66:13946-13967. [PMID: 37698518 DOI: 10.1021/acs.jmedchem.3c00891] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Dihydrofolate reductase (DHFR), a core enzyme of folate metabolism, plays a crucial role in the biosynthesis of purines and thymidylate for cell proliferation and growth in both prokaryotic and eukaryotic cells. However, the development of new DHFR inhibitors is challenging due to the limited number of scaffolds available for drug development. Hence, we designed and synthesized a new class of DHFR inhibitors with a 1,3-diamino-7H-pyrrol[3,2-f]quinazoline derivative (PQD) structure bearing condensed rings. Compound 6r exhibited therapeutic effects on mouse models of systemic infection and thigh infection caused by methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300. Moreover, methyl-modified PQD compound 8a showed a strong efficacy in a murine model of breast cancer, which was better than the effects of taxol. The findings showcased in this study highlight the promising capabilities of novel DHFR inhibitors in addressing bacterial infections as well as breast cancer.
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Affiliation(s)
- Zihao Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Cantong Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jie Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Fangfang Lai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jing Feng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guangxu Wu
- Department of Pharmacy, The People Hospital of Liupanshui City, Guizhou, Liupanshui 553000, China
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wenxuan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zunsheng Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Chi Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qingyun Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yuchen Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Bo Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Tianlei Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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4
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Gurushankar K, Rimac H, Nadezhda P, Grishina M. Exploring the potential and identifying Withania somnifera alkaloids as novel dihydrofolate reductase (DHFR) inhibitors by the AlteQ method. J Biomol Struct Dyn 2023; 41:13963-13976. [PMID: 36762693 DOI: 10.1080/07391102.2023.2175727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/29/2023] [Indexed: 02/11/2023]
Abstract
There is an urgent need to discover and develop novel drugs to combat Mycobacterium tuberculosis, the causative agent of tuberculosis (TB) in humans. Alkaloids have been shown to have wide-ranging therapeutic application and could be ideal candidates for drug development, and research is underway to develop new anti-tubercular drugs from natural sources. In this regard, the current research deals with finding novel lead compounds from the Withania somnifera (WS) plant. Broad health benefits of WS are due to the presence of diverse chemical constituents which include anaferine and anahygrine and which belong to the alkaloid family. In the present study, these two compounds have been theoretically studied to understand their electronic properties using the density functional theory (DFT) at the B3LYP/6-311 + G (d,p) level. HOMO and LUMO properties and molecular electrostatic potential (MEP) surface were calculated. Further, to understand the mechanism of action of these compounds and to identify their putative drug target, molecular docking and dynamics studies were employed against Mycobacterium tuberculosis dihydrofolate reductase (DHFR). It was determined that NADP+ affects stability of the complexes by reducing fluctuations of residues 14-23 and 117-126. It was also found that Ile5 and Gln28 play an important role in complexation. Electron density analysis (using the AlteQ method) of the intermolecular region, analyzing both the anaferin-NADP+ and anahygrin-NADP+ complexes showed that anaferin and anahygrin complexes are more stable in the presence of NADP+. It has been established that in most intermolecular contacts the contribution of the ligand to the electron density is greater than that of NADP+. The present study thus provides an excellent way to analyze the effect of anaferine and anahygrine in essential processes of M. tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Krishnamoorthy Gurushankar
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
- Department of Physics, Kalasalingam Academy of Research and Education, Krishnankoil, Tamilnadu, India
| | - Hrvoje Rimac
- Department of Medicinal Chemistry, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Palko Nadezhda
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
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Lu Q, Liu J, Yu Y, Liang HF, Zhang SQ, Li ZB, Chen JX, Xu QG, Li JC. ALB, HP, OAF and RBP4 as novel protein biomarkers for identifying cured patients with pulmonary tuberculosis by DIA. Clin Chim Acta 2022; 535:82-91. [PMID: 35964702 DOI: 10.1016/j.cca.2022.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/09/2022] [Accepted: 08/01/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Pulmonary tuberculosis (TB) is a serious infectious disease that lacks robust blood-based biomarkers to identify cured TB. Some discharged patients are not fully cured and may relapse or even develop multidrug-resistant TB. This study is committed to finding proteomic-based plasma biomarkers to support establishing laboratory standards for clinical TB cure. METHODS Data-independent acquisition (DIA) was used to obtain the plasma protein expression profiles of TB patients at different treatment stages compared with healthy controls. Multivariate statistical methods and bioinformatics were used to analyze the data. RESULTS Bioinformatic analysis suggests coagulation dysfunction and vitamin and lipid metabolism disturbances in TB. Albumin (ALB), haptoglobin (HP), out at first protein homolog (OAF), and retinol-binding protein 4 (RBP4) can be used to establish a diagnostic model for the efficacy evaluation of TB with an area under the curve of 0.963, which could effectively distinguish untreated TB patients from cured patients. CONCLUSIONS Our research demonstrated that ALB, HP, OAF and RBP4 can be potential biomarkers for evaluating the efficacy of TB. These findings may provide experimental data for establishing the laboratory indicators of clinical TB cure and providing clinicians with new targets for exploring the underlying mechanisms of TB pathogenesis.
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Affiliation(s)
- Qiqi Lu
- The Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Jun Liu
- The Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Yi Yu
- The Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China
| | - Hong-Feng Liang
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China
| | - Shan-Qiang Zhang
- The Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Zhi-Bin Li
- The Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jia-Xi Chen
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Taizhou 318050, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qiu-Gui Xu
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China
| | - Ji-Cheng Li
- The Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
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Li ZB, Shi LY, Han YS, Chen J, Zhang SQ, Chen JX, Liu J, Tu HH, Lu QQ, Yu Y, Jiang TT, Li JC. Pyridoxal phosphate, pyridoxamine phosphate, and folic acid based on ceRNA regulatory network as potential biomarkers for the diagnosis of pulmonary tuberculosis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105240. [PMID: 35150890 DOI: 10.1016/j.meegid.2022.105240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 10/27/2021] [Accepted: 02/06/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Pulmonary tuberculosis (TB) is a serious disease burden worldwide, and its effective early diagnosis is still facing challenges. Knowledge, acquired from multi-omics integration analysis about the association between different types of differentially expressed molecules in the plasma of TB patients and the disease traits, is anticipated to improve the accuracy of TB diagnosis through the "integrative pattern". METHODS In this study, the lncRNA-miRNA-mRNA interaction network was constructed based on the competing endogenous RNA (ceRNA) hypothesis by integrating our previous data sets of lncRNA, mRNA, miRNA, and metabolites. Moreover, the key regulatory axis was established by co-expression analysis and verified at the level of metabolites. RESULTS A ceRNA regulatory network consisting of 23 lncRNAs, 10 miRNAs, and 113 mRNAs was constructed. The analysis results suggested that lncRNA (OSBPL10-AS1), miRNA (has-miR-485-5p), and mRNA (SLC23A2) might be involved in the regulation of vitamin metabolism in patients with TB. Metabolite analysis showed that compared with the normal control group, TB patients had abnormal vitamin metabolism, and the expression levels of pyridoxal phosphate, pyridoxamine phosphate, and folic acid were significantly different between the two groups (p < 0.05). CONCLUSION Integrated multi-omics analysis showed that vitamin metabolism disorder may be one of the pathological characteristic of TB. OSBPL10-AS1, hsa-miR-485-5p, SLC23A2, pyridoxal phosphate, pyridoxamine phosphate, and folic acid may collectively constitute the "integrative pattern" of multiple biomarkers, which may provide an accurate diagnosis of TB.
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Affiliation(s)
- Zhi-Bin Li
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou 310058, China
| | - Yu-Shuai Han
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jing Chen
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shan-Qiang Zhang
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Jia-Xi Chen
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jun Liu
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Hui-Hui Tu
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qi-Qi Lu
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Yi Yu
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ting-Ting Jiang
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Ji-Cheng Li
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China.
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7
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Czeczot ADM, Roth CD, Ducati RG, Pissinate K, Rambo RS, Timmers LFSM, Abbadi BL, Macchi FS, Pestana VZ, Basso LA, Machado P, Bizarro CV. 8-Mercaptoguanine-based inhibitors of Mycobacterium tuberculosis dihydroneopterin aldolase: synthesis, in vitro inhibition and docking studies. J Enzyme Inhib Med Chem 2021; 36:847-855. [PMID: 33752554 PMCID: PMC7993393 DOI: 10.1080/14756366.2021.1900157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The dihydroneopterin aldolase (DHNA, EC 4.1.2.25) activity of FolB protein is required for the conversion of 7,8-dihydroneopterin (DHNP) to 6-hydroxymethyl-7,8-dihydropterin (HP) and glycolaldehyde (GA) in the folate pathway. FolB protein from Mycobacterium tuberculosis (MtFolB) is essential for bacilli survival and represents an important molecular target for drug development. S8-functionalized 8-mercaptoguanine derivatives were synthesised and evaluated for inhibitory activity against MtFolB. The compounds showed IC50 values in the submicromolar range. The inhibition mode and inhibition constants were determined for compounds that exhibited the strongest inhibition. Additionally, molecular docking analyses were performed to suggest enzyme-inhibitor interactions and ligand conformations. To the best of our knowledge, this study describes the first class of MtFolB inhibitors.
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Affiliation(s)
- Alexia de Matos Czeczot
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Candida Deves Roth
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rodrigo Gay Ducati
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biotecnologia, Universidade do Vale do Taquari, Lajeado, Brazil
| | - Kenia Pissinate
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Raoní Scheibler Rambo
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Bruno Lopes Abbadi
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda Souza Macchi
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Víctor Zajaczkowski Pestana
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiz Augusto Basso
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Pablo Machado
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Cristiano Valim Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
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8
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Potency boost of a Mycobacterium tuberculosis dihydrofolate reductase inhibitor by multienzyme F 420H 2-dependent reduction. Proc Natl Acad Sci U S A 2021; 118:2025172118. [PMID: 34161270 PMCID: PMC8237569 DOI: 10.1073/pnas.2025172118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial metabolism can cause intrinsic drug resistance but can also convert inactive parent drugs into bioactive derivatives, as is the case for several antimycobacterial prodrugs. Here, we show that the intrabacterial metabolism of a Mtb dihydrofolate reductase (DHFR) inhibitor with moderate affinity for its target boosts its on-target activity by two orders of magnitude. This is a “prodrug-like” antimycobacterial that possesses baseline activity in the absence of intracellular bioactivation. By elucidating the metabolic enhancement mechanism, we have provided the basis for the rational optimization of a class of DHFR inhibitors and uncovered an antibacterial drug discovery concept. Triaza-coumarin (TA-C) is a Mycobacterium tuberculosis (Mtb) dihydrofolate reductase (DHFR) inhibitor with an IC50 (half maximal inhibitory concentration) of ∼1 µM against the enzyme. Despite this moderate target inhibition, TA-C shows exquisite antimycobacterial activity (MIC50, concentration inhibiting growth by 50% = 10 to 20 nM). Here, we investigated the mechanism underlying this potency disconnect. To confirm that TA-C targets DHFR and investigate its unusual potency pattern, we focused on resistance mechanisms. In Mtb, resistance to DHFR inhibitors is frequently associated with mutations in thymidylate synthase thyA, which sensitizes Mtb to DHFR inhibition, rather than in DHFR itself. We observed thyA mutations, consistent with TA-C interfering with the folate pathway. A second resistance mechanism involved biosynthesis of the redox coenzyme F420. Thus, we hypothesized that TA-C may be metabolized by Mtb F420–dependent oxidoreductases (FDORs). By chemically blocking the putative site of FDOR-mediated reduction in TA-C, we reproduced the F420-dependent resistance phenotype, suggesting that F420H2-dependent reduction is required for TA-C to exert its potent antibacterial activity. Indeed, chemically synthesized TA-C-Acid, the putative product of TA-C reduction, displayed a 100-fold lower IC50 against DHFR. Screening seven recombinant Mtb FDORs revealed that at least two of these enzymes reduce TA-C. This redundancy in activation explains why no mutations in the activating enzymes were identified in the resistance screen. Analysis of the reaction products confirmed that FDORs reduce TA-C at the predicted site, yielding TA-C-Acid. This work demonstrates that intrabacterial metabolism converts TA-C, a moderately active “prodrug,” into a 100-fold-more-potent DHFR inhibitor, thus explaining the disconnect between enzymatic and whole-cell activity.
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9
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Minias A, Żukowska L, Lechowicz E, Gąsior F, Knast A, Podlewska S, Zygała D, Dziadek J. Early Drug Development and Evaluation of Putative Antitubercular Compounds in the -Omics Era. Front Microbiol 2021; 11:618168. [PMID: 33603720 PMCID: PMC7884339 DOI: 10.3389/fmicb.2020.618168] [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: 10/16/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, the disease is one of the top 10 causes of death of people worldwide. Mycobacterium tuberculosis is an intracellular pathogen with an unusually thick, waxy cell wall and a complex life cycle. These factors, combined with M. tuberculosis ability to enter prolonged periods of latency, make the bacterium very difficult to eradicate. The standard treatment of TB requires 6-20months, depending on the drug susceptibility of the infecting strain. The need to take cocktails of antibiotics to treat tuberculosis effectively and the emergence of drug-resistant strains prompts the need to search for new antitubercular compounds. This review provides a perspective on how modern -omic technologies facilitate the drug discovery process for tuberculosis treatment. We discuss how methods of DNA and RNA sequencing, proteomics, and genetic manipulation of organisms increase our understanding of mechanisms of action of antibiotics and allow the evaluation of drugs. We explore the utility of mathematical modeling and modern computational analysis for the drug discovery process. Finally, we summarize how -omic technologies contribute to our understanding of the emergence of drug resistance.
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Affiliation(s)
- Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Lidia Żukowska
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- BioMedChem Doctoral School of the University of Lodz and the Institutes of the Polish Academy of Sciences in Lodz, Lodz, Poland
| | - Ewelina Lechowicz
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Filip Gąsior
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- BioMedChem Doctoral School of the University of Lodz and the Institutes of the Polish Academy of Sciences in Lodz, Lodz, Poland
| | - Agnieszka Knast
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Sabina Podlewska
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Krakow, Poland
- Maj Institute of Pharmacology, Polish Academy of Sciences, Krakow, Poland
| | - Daria Zygała
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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10
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Riboldi GP, Zigweid R, Myler PJ, Mayclin SJ, Couñago RM, Staker BL. Identification of P218 as a potent inhibitor of Mycobacterium ulcerans DHFR. RSC Med Chem 2021; 12:103-109. [PMID: 34046602 PMCID: PMC8130613 DOI: 10.1039/d0md00303d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/07/2020] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium ulcerans is the causative agent of Buruli ulcer, a debilitating chronic disease that mainly affects the skin. Current treatments for Buruli ulcer are efficacious, but rely on the use of antibiotics with severe side effects. The enzyme dihydrofolate reductase (DHFR) plays a critical role in the de novo biosynthesis of folate species and is a validated target for several antimicrobials. Here we describe the biochemical and structural characterization of M. ulcerans DHFR and identified P218, a safe antifolate compound in clinical evaluation for malaria, as a potent inhibitor of this enzyme. We expect our results to advance M. ulcerans DHFR as a target for future structure-based drug discovery campaigns.
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Affiliation(s)
- Gustavo P Riboldi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP) Campinas SP 13083-875 Brazil
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP Campinas SP 13083-886 Brazil
| | - Rachael Zigweid
- Center for Infectious Disease Research, Seattle Children's Research Institute Seattle Washington 98109 USA
| | - Peter J Myler
- Center for Infectious Disease Research, Seattle Children's Research Institute Seattle Washington 98109 USA
- Department of Pediatrics, University of Washington Seattle Washington 91895 USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID) Seattle Washington 98109 USA
- UCB Bainbridge Island Washington 98110 USA
| | - Rafael M Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP) Campinas SP 13083-875 Brazil
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP Campinas SP 13083-886 Brazil
| | - Bart L Staker
- Center for Infectious Disease Research, Seattle Children's Research Institute Seattle Washington 98109 USA
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11
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Kordus SL, Baughn AD. Revitalizing antifolates through understanding mechanisms that govern susceptibility and resistance. MEDCHEMCOMM 2019; 10:880-895. [PMID: 31303985 PMCID: PMC6595967 DOI: 10.1039/c9md00078j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022]
Abstract
In prokaryotes and eukaryotes, folate (vitamin B9) is an essential metabolic cofactor required for all actively growing cells. Specifically, folate serves as a one-carbon carrier in the synthesis of amino acids (such as methionine, serine, and glycine), N-formylmethionyl-tRNA, coenzyme A, purines and thymidine. Many microbes are unable to acquire folates from their environment and rely on de novo folate biosynthesis. In contrast, mammals lack the de novo folate biosynthesis pathway and must obtain folate from commensal microbiota or the environment using proton-coupled folate transporters. The essentiality and dichotomy between mammalian and bacterial folate biosynthesis and utilization pathways make it an ideal drug target for the development of antimicrobial agents and cancer chemotherapeutics. In this minireview, we discuss general aspects of folate biosynthesis and the underlying mechanisms that govern susceptibility and resistance of organisms to antifolate drugs.
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Affiliation(s)
- Shannon Lynn Kordus
- Department of Microbiology and Immunology , University of Minnesota , Minneapolis , MN , USA .
| | - Anthony David Baughn
- Department of Microbiology and Immunology , University of Minnesota , Minneapolis , MN , USA .
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12
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Sharma K, Tanwar O, Deora GS, Ali S, Alam MM, Zaman MS, Krishna VS, Sriram D, Akhter M. Expansion of a novel lead targeting M. tuberculosis DHFR as antitubercular agents. Bioorg Med Chem 2019; 27:1421-1429. [PMID: 30827867 DOI: 10.1016/j.bmc.2019.02.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 01/26/2023]
Abstract
A series of 1-(1-benzyl-2-methyl-5-((1-phenyl-1H-1,2,3-triazol-4-yl)methoxy)-1H-indol-3-yl)ethanone and ethyl 1-benzyl-2-methyl-5-((1-phenyl-1H-1,2,3-triazol-4-yl)methoxy)-1H-indole-3-carboxylate derivatives were designed based on bioisosteric replacement of previously reported antitubercular agent (IND-07). Twenty ligands were successfully synthesized and some of them were found to have good in vitro activity (MIC < 10 μM) against the H37Rv strain of Mycobacterium tuberculosis. Among these compounds, KC-08 and KC-11 inhibited Mtb-DHFR with 4- and 18-fold selectivity for Mtb-DHFR over h-DHFR, respectively. Compound KC-11 display acceptable ADME, and better pharmacokinetic profiles than IND-07. Docking studies were performed to predict the binding mode of the compounds within the active site of Mtb-DHFR and h-DHFR. The results of our study suggest that compound KC-11 may serve as a valuable lead for the design and development of selective inhibitors of Mtb-DHFR with potential therapeutic application in tuberculosis.
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Affiliation(s)
- Kalicharan Sharma
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India
| | - Omprakash Tanwar
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India
| | - Girdhar Singh Deora
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - S Ali
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi 110062, India; Bioinformatics Infrastructure Facility Lab, Jamia Hamdard, New Delhi 110062, India
| | - M M Alam
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India
| | - M S Zaman
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India
| | - Vagolu Siva Krishna
- Department of Pharmacy, Birla Institute of Technology & Science, Pilani, Hyderabad 500078, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology & Science, Pilani, Hyderabad 500078, India
| | - Mymoona Akhter
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India; Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi 110062, India.
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13
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Hajian B, Scocchera E, Shoen C, Krucinska J, Viswanathan K, G-Dayanandan N, Erlandsen H, Estrada A, Mikušová K, Korduláková J, Cynamon M, Wright D. Drugging the Folate Pathway in Mycobacterium tuberculosis: The Role of Multi-targeting Agents. Cell Chem Biol 2019; 26:781-791.e6. [PMID: 30930162 DOI: 10.1016/j.chembiol.2019.02.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/22/2019] [Accepted: 02/24/2019] [Indexed: 01/19/2023]
Abstract
The folate biosynthetic pathway offers many druggable targets that have yet to be exploited in tuberculosis therapy. Herein, we have identified a series of small molecules that interrupt Mycobacterium tuberculosis (Mtb) folate metabolism by dual targeting of dihydrofolate reductase (DHFR), a key enzyme in the folate pathway, and its functional analog, Rv2671. We have also compared the antifolate activity of these compounds with that of para-aminosalicylic acid (PAS). We found that the bioactive metabolite of PAS, in addition to previously reported activity against DHFR, inhibits flavin-dependent thymidylate synthase in Mtb, suggesting a multi-targeted mechanism of action for this drug. Finally, we have shown that antifolate treatment in Mtb decreases the production of mycolic acids, most likely due to perturbation of the activated methyl cycle. We conclude that multi-targeting of the folate pathway in Mtb is associated with highly potent anti-mycobacterial activity.
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Affiliation(s)
- Behnoush Hajian
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Eric Scocchera
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | | | - Jolanta Krucinska
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Kishore Viswanathan
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | | | - Heidi Erlandsen
- Center for Open Research Resources and Equipment, University of Connecticut, Storrs, CT 06269, USA
| | - Alexavier Estrada
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina CH-1, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Jana Korduláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina CH-1, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | | | - Dennis Wright
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA.
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14
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Richter A, Strauch A, Chao J, Ko M, Av-Gay Y. Screening of Preselected Libraries Targeting Mycobacterium abscessus for Drug Discovery. Antimicrob Agents Chemother 2018; 62:e00828-18. [PMID: 30012760 PMCID: PMC6125491 DOI: 10.1128/aac.00828-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/08/2018] [Indexed: 12/23/2022] Open
Abstract
Mycobacterium abscessus is intrinsically resistant to many antimycobacterial antibiotics, which presents serious problems in therapy. Here, we describe the development of a novel phenotype-based microscopic and computerized imaging drug screening approach. A pilot screen of 568 compounds from two libraries identified 17 hits. Eleven of these compounds are described for the first time as active against M. abscessus The impact of growth media on the activity of these compounds was tested, revealing that cation-adjusted Mueller-Hinton broth (MHII) supports better growth of actively replicating M. abscessus and improves the activity of associated compounds.
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Affiliation(s)
- Adrian Richter
- Division of Infectious Diseases, Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Angelika Strauch
- Division of Infectious Diseases, Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joseph Chao
- Division of Infectious Diseases, Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mary Ko
- Division of Infectious Diseases, Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yossef Av-Gay
- Division of Infectious Diseases, Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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15
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Abstract
Coevolution of pathogens and host has led to many metabolic strategies employed by intracellular pathogens to deal with the immune response and the scarcity of food during infection. Simply put, bacterial pathogens are just looking for food. As a consequence, the host has developed strategies to limit nutrients for the bacterium by containment of the intruder in a pathogen-containing vacuole and/or by actively depleting nutrients from the intracellular space, a process called nutritional immunity. Since metabolism is a prerequisite for virulence, such pathways could potentially be good targets for antimicrobial therapies. In this chapter, we review the current knowledge about the in vivo diet of Mycobacterium tuberculosis, with a focus on amino acid and cofactors, discuss evidence for the bacilli's nutritionally independent lifestyle in the host, and evaluate strategies for new chemotherapeutic interventions.
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16
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1,3,5-triazaspiro[5.5]undeca-2,4-dienes as selective Mycobacterium tuberculosis dihydrofolate reductase inhibitors with potent whole cell activity. Eur J Med Chem 2017; 144:262-276. [PMID: 29274493 DOI: 10.1016/j.ejmech.2017.12.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/17/2017] [Accepted: 12/05/2017] [Indexed: 11/23/2022]
Abstract
The emergence of multi- and extensively-drug resistant tubercular (MDR- and XDR-TB) strains of mycobacteria has limited the use of existing therapies, therefore new drugs are needed. Dihydrofolate reductase (DHFR) has recently attracted much attention as a target for the development of anti-TB agents. This study aimed to develop selective M. tuberculosis DHFR inhibitors using rationale scaffolding design and synthesis, phenotype-oriented screening, enzymatic inhibitory study, whole cell on-target validation, molecular modeling, and in vitro DMPK determination to derive new anti-TB agents. 2,4-diamino-1-phenyl-1,3,5-triazaspiro[5.5]undeca-2,4-dienes 20b and 20c were identified as selective M. tuberculosis DHFR inhibitors, showing promising antimycobacterial activities (MIC50: 0.01 μM and MIC90: 0.025 μM on M. tuberculosis H37Rv). This study provided compelling evidence that compound 20b and 20c exerted whole cell antimycobacterial activity through DHFR inhibition. In addition, these two compounds exhibited low cytotoxicity and low hemolytic activity. The in vitro DMPK and physiochemical properties suggested their potential in vivo efficacy.
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17
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Santa Maria JP, Park Y, Yang L, Murgolo N, Altman MD, Zuck P, Adam G, Chamberlin C, Saradjian P, Dandliker P, Boshoff HIM, Barry CE, Garlisi C, Olsen DB, Young K, Glick M, Nickbarg E, Kutchukian PS. Linking High-Throughput Screens to Identify MoAs and Novel Inhibitors of Mycobacterium tuberculosis Dihydrofolate Reductase. ACS Chem Biol 2017; 12:2448-2456. [PMID: 28806050 DOI: 10.1021/acschembio.7b00468] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Though phenotypic and target-based high-throughput screening approaches have been employed to discover new antibiotics, the identification of promising therapeutic candidates remains challenging. Each approach provides different information, and understanding their results can provide hypotheses for a mechanism of action (MoA) and reveal actionable chemical matter. Here, we describe a framework for identifying efficacy targets of bioactive compounds. High throughput biophysical profiling against a broad range of targets coupled with machine learning was employed to identify chemical features with predicted efficacy targets for a given phenotypic screen. We validate the approach on data from a set of 55 000 compounds in 24 historical internal antibacterial phenotypic screens and 636 bacterial targets screened in high-throughput biophysical binding assays. Models were built to reveal the relationships between phenotype, target, and chemotype, which recapitulated mechanisms for known antibacterials. We also prospectively identified novel inhibitors of dihydrofolate reductase with nanomolar antibacterial efficacy against Mycobacterium tuberculosis. Molecular modeling provided structural insight into target-ligand interactions underlying selective killing activity toward mycobacteria over human cells.
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Affiliation(s)
- John P. Santa Maria
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Yumi Park
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Lihu Yang
- Department of Chemistry, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Nicholas Murgolo
- Department of Information & Analytics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Michael D. Altman
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Paul Zuck
- Research Science, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Greg Adam
- Department of Pharmacology, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Chad Chamberlin
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Saradjian
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Dandliker
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Helena I. M. Boshoff
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Clifton E. Barry
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Charles Garlisi
- Department of Pharmacology, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - David B. Olsen
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Katherine Young
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Meir Glick
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Elliott Nickbarg
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter S. Kutchukian
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
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18
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Hajian B, Scocchera E, Keshipeddy S, G-Dayanandan N, Shoen C, Krucinska J, Reeve S, Cynamon M, Anderson AC, Wright DL. Propargyl-Linked Antifolates Are Potent Inhibitors of Drug-Sensitive and Drug-Resistant Mycobacterium tuberculosis. PLoS One 2016; 11:e0161740. [PMID: 27580226 PMCID: PMC5006990 DOI: 10.1371/journal.pone.0161740] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/10/2016] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis continues to cause widespread, life-threatening disease. In the last decade, this threat has grown dramatically as multi- and extensively-drug resistant (MDR and XDR) bacteria have spread globally and the number of agents that effectively treat these infections is significantly reduced. We have been developing the propargyl-linked antifolates (PLAs) as potent inhibitors of the essential enzyme dihydrofolate reductase (DHFR) from bacteria and recently found that charged PLAs with partial zwitterionic character showed improved mycobacterial cell permeability. Building on a hypothesis that these PLAs may penetrate the outer membrane of M. tuberculosis and inhibit the essential cytoplasmic DHFR, we screened a group of PLAs for antitubercular activity. In this work, we identified several PLAs as potent inhibitors of the growth of M. tuberculosis with several of the compounds exhibiting minimum inhibition concentrations equal to or less than 1 μg/mL. Furthermore, two of the compounds were very potent inhibitors of MDR and XDR strains. A high resolution crystal structure of one PLA bound to DHFR from M. tuberculosis reveals the interactions of the ligands with the target enzyme.
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Affiliation(s)
- Behnoush Hajian
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Eric Scocchera
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Santosh Keshipeddy
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Narendran G-Dayanandan
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Carolyn Shoen
- Veterans Affairs Medical Center, Syracuse, New York, United States of America
| | - Jolanta Krucinska
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Stephanie Reeve
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Michael Cynamon
- Veterans Affairs Medical Center, Syracuse, New York, United States of America
| | - Amy C. Anderson
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail: (ACA); (DLW)
| | - Dennis L. Wright
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail: (ACA); (DLW)
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19
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Nyíri K, Vértessy BG. Perturbation of genome integrity to fight pathogenic microorganisms. Biochim Biophys Acta Gen Subj 2016; 1861:3593-3612. [PMID: 27217086 DOI: 10.1016/j.bbagen.2016.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Resistance against antibiotics is unfortunately still a major biomedical challenge for a wide range of pathogens responsible for potentially fatal diseases. SCOPE OF REVIEW In this study, we aim at providing a critical assessment of the recent advances in design and use of drugs targeting genome integrity by perturbation of thymidylate biosynthesis. MAJOR CONCLUSION We find that research efforts from several independent laboratories resulted in chemically highly distinct classes of inhibitors of key enzymes within the routes of thymidylate biosynthesis. The present article covers numerous studies describing perturbation of this metabolic pathway in some of the most challenging pathogens like Mycobacterium tuberculosis, Plasmodium falciparum, and Staphylococcus aureus. GENERAL SIGNIFICANCE Our comparative analysis allows a thorough summary of the current approaches to target thymidylate biosynthesis enzymes and also include an outlook suggesting novel ways of inhibitory strategies. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Kinga Nyíri
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
| | - Beáta G Vértessy
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
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