1
|
Guida M, Tammaro C, Quaranta M, Salvucci B, Biava M, Poce G, Consalvi S. Amino Acid Biosynthesis Inhibitors in Tuberculosis Drug Discovery. Pharmaceutics 2024; 16:725. [PMID: 38931847 PMCID: PMC11206623 DOI: 10.3390/pharmaceutics16060725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/15/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
According to the latest World Health Organization (WHO) report, an estimated 10.6 million people were diagnosed with tuberculosis (TB) in 2022, and 1.30 million died. A major concern is the emergence of multi-drug-resistant (MDR) and extensively drug-resistant (XDR) strains, fueled by the length of anti-TB treatment and HIV comorbidity. Innovative anti-TB agents acting with new modes of action are the only solution to counteract the spread of resistant infections. To escape starvation and survive inside macrophages, Mtb has evolved to become independent of the host by synthesizing its own amino acids. Therefore, targeting amino acid biosynthesis could subvert the ability of the mycobacterium to evade the host immune system, providing innovative avenues for drug discovery. The aim of this review is to give an overview of the most recent progress in the discovery of amino acid biosynthesis inhibitors. Among the hits discovered over the past five years, tryptophan (Trp) inhibitors stand out as the most advanced and have significantly contributed to demonstrating the feasibility of this approach for future TB drug discovery. Future efforts should be directed at prioritizing the chemical optimization of these hits to enrich the TB drug pipeline with high-quality leads.
Collapse
Affiliation(s)
| | | | | | | | | | - Giovanna Poce
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, Piazzale A. Moro, 5, 00185 Rome, Italy; (M.G.); (C.T.); (M.Q.); (B.S.); (M.B.)
| | - Sara Consalvi
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, Piazzale A. Moro, 5, 00185 Rome, Italy; (M.G.); (C.T.); (M.Q.); (B.S.); (M.B.)
| |
Collapse
|
2
|
Lee MH, Kim HL, Seo H, Jung S, Kim BJ. A secreted form of chorismate mutase (Rv1885c) in Mycobacterium bovis BCG contributes to pathogenesis by inhibiting mitochondria-mediated apoptotic cell death of macrophages. J Biomed Sci 2023; 30:95. [PMID: 38110948 PMCID: PMC10729386 DOI: 10.1186/s12929-023-00988-2] [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: 08/30/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), and its pathogenicity is associated with its ability to evade the host defense system. The secretory form of the chorismate mutase of M. tuberculosis (TBCM, encoded by Rv1885c) is assumed to play a key role in the pathogenesis of TB; however, the mechanism remains unknown. METHODS A tbcm deletion mutant (B∆tbcm) was generated by targeted gene knockout in BCG to investigate the pathogenic role of TBCM in mice or macrophages. We compared the pathogenesis of B∆tbcm and wild-type BCG in vivo by measuring the bacterial clearance rate and the degree of apoptosis. Promotion of the intrinsic apoptotic pathway was evaluated in infected bone marrow-derived macrophages (BMDMs) by measuring apoptotic cell death, loss of mitochondrial membrane potential and translocation of pore-forming proteins. Immunocytochemistry, western blotting and real-time PCR were also performed to assess the related protein expression levels after infection. Furthermore, these findings were validated by complementation of tbcm in BCG. RESULTS Deletion of the tbcm gene in BCG leads to reduced pathogenesis in a mouse model, compared to wild type BCG, by promoting apoptotic cell death and bacterial clearance. Based on these findings, we found that intrinsic apoptosis and mitochondrial impairment were promoted in B∆tbcm-infected BMDMs. B∆tbcm down-regulates the expression of Bcl-2, which leads to mitochondrial outer membrane permeabilization (MOMP), culminating in cytochrome c release from mitochondria. Consistent with this, transcriptome profiling also indicated that B∆tbcm infection is more closely related to altered mitochondrial-related gene expression than wild-type BCG infection, suggesting an inhibitory role of TBCM in mitochondrial dysfunction. Moreover, genetic complementation of B∆tbcm (C∆tbcm) restored its capacity to inhibit mitochondria-mediated apoptotic cell death. CONCLUSIONS Our findings demonstrate the contribution of TBCM to bacterial survival, inhibiting intrinsic apoptotic cell death of macrophages as a virulence factor of M. tuberculosis complex (MTBC) strains, which could be a potential target for the development of TB therapy.
Collapse
Affiliation(s)
- Mi-Hyun Lee
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, 103 Daehak-Ro, Jongno-Gu, Seoul, 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Hye Lin Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, 103 Daehak-Ro, Jongno-Gu, Seoul, 03080, Republic of Korea
- Cancer Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Hyejun Seo
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, 103 Daehak-Ro, Jongno-Gu, Seoul, 03080, Republic of Korea
- Cancer Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- Seoul National University Medical Research Center (SNUMRC), Seoul, 03080, Republic of Korea
| | - Sangkwon Jung
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, 103 Daehak-Ro, Jongno-Gu, Seoul, 03080, Republic of Korea
- Cancer Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, 103 Daehak-Ro, Jongno-Gu, Seoul, 03080, Republic of Korea.
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
- Liver Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.
- Cancer Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.
- Seoul National University Medical Research Center (SNUMRC), Seoul, 03080, Republic of Korea.
| |
Collapse
|
3
|
Shukla S, Nishanth Rao R, Bhuktar H, Edwin RK, Jamma T, Medishetti R, Banerjee S, Giliyaru VB, Shenoy GG, Oruganti S, Misra P, Pal M. Wang resin catalysed sonochemical synthesis of pyrazolo[4,3-d]pyrimidinones and 2,3-dihydroquinazolin-4(1H)-ones: Identification of chorismate mutase inhibitors having effects on Mycobacterium tuberculosis cell viability. Bioorg Chem 2023; 134:106452. [PMID: 36889201 DOI: 10.1016/j.bioorg.2023.106452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/15/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023]
Abstract
The enzyme chorismate mutase (or CM that is vital for the survival of bacteria) is an interesting pharmacological target for the identification of new anti-tubercular agents. The 5,5-disibstituted pyrazolo[4,3-d]pyrimidinone derivatives containing the fragment based on 4-amino-1-methyl-3-propyl-1H-pyrazole-5-carboxamide were designed and explored as the potential inhibitors of chorismate mutase. Based on encouraging docking results of two representative molecules evaluated in silico against MtbCM (PDB: 2FP2) the Wang resin catalysed sonochemical synthesis of target N-heteroarenes were undertaken. The methodology involved the reaction of 4-amino-1-methyl-3-propyl-1H-pyrazole-5-carboxamide with the appropriate cyclic/acyclic ketones to afford the desired products in acceptable (51-94%) yields. The methodology was also extended successfully towards the synthesis of 2,2-disubstituted 2,3-dihydroquinazolin-4(1H)-ones in excellent (85-90%) yields. In vitro MTT assay against the RAW 264.7 cell line followed by enzymatic assay against MtbCM identified 3b and 3c as active compounds that showed two H-bonding via their NH (at position 6) and CO group with MtbCM in silico and encouraging (54-57%) inhibition at 30 µM in vitro. Notably, none of the 2,2-disubstituted 2,3-dihydroquinazolin-4(1H)-ones showed any significant inhibition of MtbCM suggesting the favourable role of the pyrazole moiety in case of pyrazolo[4,3-d]pyrimidinones. The favourable role of cyclopentyl ring attached to the pyrazolo[4,3-d]pyrimidinone moiety and that of two methyl groups in place of cyclopentyl ring was also indicated by the SAR study. Besides showing effects against MtbCM in the concentration response study, 3b and 3c showed little or no effects on mammalian cell viability up to 100 µM in an MTT assay but decreased the % Mtb cell viability at 10-30 µM with > 20% decrease at 30 µM in an Alamar Blue Assay. Moreover, no adverse effects were noted for these compounds when tested for teratogenicity and hepatotoxicity in zebrafish at various concentrations. Overall, being the only example of MtbCM inhibitors that showed effects on Mtb cell viability the compound 3b and 3c are of further interest form the view point of discovery and development of new anti-tubercular agents.
Collapse
Affiliation(s)
- Sharda Shukla
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - R Nishanth Rao
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India
| | - Harshavardhan Bhuktar
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Rebecca Kristina Edwin
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Trinath Jamma
- Department of Biological Sciences, B-225, BITS Pilani-Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, Hyderabad 500 078, Telangana, India
| | - Raghavender Medishetti
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Varadaraj Bhat Giliyaru
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Gautham G Shenoy
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Srinivas Oruganti
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Parimal Misra
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Manojit Pal
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India.
| |
Collapse
|
4
|
Addu N, Miriyala H, Kapavarapu R, Kolli SK, Pal M. Wang-OSO3H catalyzed one-pot sonochemical synthesis of 1,2,4-benzothiadiazine-1,1-dioxide derivatives: their in silico / in vitro assessments against MtbCM. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
|
5
|
Ramarao S, Pothireddy M, Venkateshwarlu R, Moturu KMVR, Siddaiah V, Kapavarapu R, Dandela R, Pal M. A rapid construction of 4(3H)-quinazolinone and related ring under ultrasound irradiation: In silico/in vitro studies of compounds synthesized. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
6
|
Proteomic Profiling Reveals Distinct Bacterial Extracellular Vesicle Subpopulations with Possibly Unique Functionality. Appl Environ Microbiol 2023; 89:e0168622. [PMID: 36533919 PMCID: PMC9888257 DOI: 10.1128/aem.01686-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial outer membrane vesicles (OMVs) are 20- to 200-nm secreted packages of lipids, small molecules, and proteins that contribute to diverse bacterial processes. In plant systems, OMVs from pathogenic and beneficial strains elicit plant immune responses that inhibit seedling growth and protect against future pathogen challenge. Previous studies of OMV-plant interactions suggest functionally important differences in the protein composition of Pseudomonas syringae and Pseudomonas fluorescens OMVs, and that their composition and activity differ as a result of medium culture conditions. Here, we show that plant apoplast-mimicking minimal medium conditions impact OMV protein content dramatically in P. syringae but not in P. fluorescens relative to complete medium conditions. Comparative, 2-way analysis of the four conditions reveals subsets of proteins that may contribute to OMV-mediated bacterial virulence and plant immune activation as well as those involved in bacterial stress tolerance or adaptation to a beneficial relationship with plants. Additional localization enrichment analysis of these subsets suggests the presence of outer-inner membrane vesicles (OIMVs). Collectively, these results reveal distinct differences in bacterial extracellular vesicle cargo and biogenesis routes from pathogenic and beneficial plant bacteria in different medium conditions and point to distinct populations of vesicles with diverse functional roles. IMPORTANCE Recent publications have shown that bacterial vesicles play important roles in interkingdom communication between bacteria and plants. Indeed, our recently published data reveal that bacterial vesicles from pathogenic and beneficial strains elicit immune responses in plants that protect against future pathogen challenge. However, the molecules underlying these striking phenomena remain unknown. Our recent work indicated that proteins packaged in vesicles are critically important for vesicle-mediated seedling growth inhibition, often considered an indirect measure of plant immune activation. In this study, we characterize the protein cargo of vesicles from Pseudomonas syringae pathovar tomato DC3000 and Pseudomonas fluorescens from two different medium conditions and show that distinct subpopulations of vesicles contribute to bacterial virulence and stress tolerance. Furthermore, we reveal differences in how beneficial and pathogenic bacterial species respond to harsh environmental conditions through vesicle packaging. Importantly, we find that protein cargo implicates outer-inner membrane vesicles in bacterial stress responses, while outer membrane vesicles are packaged for virulence.
Collapse
|
7
|
Krishnan SR, Bung N, Padhi S, Bulusu G, Misra P, Pal M, Oruganti S, Srinivasan R, Roy A. De novo design of anti-tuberculosis agents using a structure-based deep learning method. J Mol Graph Model 2023; 118:108361. [PMID: 36257148 DOI: 10.1016/j.jmgm.2022.108361] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/10/2022] [Accepted: 10/07/2022] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is a pathogen of major concern due to its ability to withstand both first- and second-line antibiotics, leading to drug resistance. Thus, there is a critical need for identification of novel anti-tuberculosis agents targeting Mtb-specific proteins. The ceaseless search for novel antimicrobial agents to combat drug-resistant bacteria can be accelerated by the development of advanced deep learning methods, to explore both existing and uncharted regions of the chemical space. The adaptation of deep learning methods to under-explored pathogens such as Mtb is a challenging aspect, as most of the existing methods rely on the availability of sufficient target-specific ligand data to design novel small molecules with optimized bioactivity. In this work, we report the design of novel anti-tuberculosis agents targeting the Mtb chorismate mutase protein using a structure-based drug design algorithm. The structure-based deep learning method relies on the knowledge of the target protein's binding site structure alone for conditional generation of novel small molecules. The method eliminates the need for curation of a high-quality target-specific small molecule dataset, which remains a challenge even for many druggable targets, including Mtb chorismate mutase. Novel molecules are proposed, that show high complementarity to the target binding site. The graph attention model could identify the probable key binding site residues, which influenced the conditional molecule generator to design new molecules with pharmacophoric features similar to the known inhibitors.
Collapse
Affiliation(s)
| | - Navneet Bung
- TCS Research (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India
| | - Siladitya Padhi
- TCS Research (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India
| | - Gopalakrishnan Bulusu
- TCS Research (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India; Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad, 500046, India
| | - Parimal Misra
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad, 500046, India
| | - Manojit Pal
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad, 500046, India
| | - Srinivas Oruganti
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad, 500046, India
| | - Rajgopal Srinivasan
- TCS Research (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India
| | - Arijit Roy
- TCS Research (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India.
| |
Collapse
|
8
|
Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
Collapse
Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| |
Collapse
|
9
|
Recent advances in transition metal-catalyzed reactions of chloroquinoxalines: Applications in bioorganic chemistry. Bioorg Chem 2022; 129:106195. [DOI: 10.1016/j.bioorg.2022.106195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 11/23/2022]
|
10
|
Bacteriomes in lesions of pulmonary tuberculosis and its association with status of Mycobacterium tuberculosis excretion. BMC Microbiol 2022; 22:280. [PMID: 36418957 PMCID: PMC9686068 DOI: 10.1186/s12866-022-02698-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Bacteria in lung play an important role in sustaining lung health. Understanding the characteristics of bacteriomes in lesions of pulmonary tuberculosis (TB) patients, who excrete Mycobacterium tuberculosis (MTB), is important for TB prevention and effective treatment. METHODS: In this study, bacteriomes in lesions from TB patients excreting bacteria (TB-E) and those from TB patients not excreting bacteria (TB-NE) with matched normal lung tissues (NT) were compared by 16S rRNA sequencing. Bacterial MetaCyc functions in TB lesions were also predicted by PICRUSt2 tool. RESULTS Alpha diversity of bacteria, including Chao 1 and Shannon indexes, for TB-E was significantly higher than those in TB-NE and NT; while for TB-NE group, Chao 1 index was higher than that in NT group. Predominant phyla in TB lesions and NT were Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, but analysis of similarity (ANOSIM, p < 0.001) revealed significantly different bacterial compositions among TB-E, TB-NE and NT samples. As for bacteriomes in TB lesions, a strong association (ANOSIM, p < 0.001) was observed with the status of MTB excretion. Indicator genera identified in TB-E and TB-NE demonstrated distinctive micro-ecological environments of TB lesions from patients with different clinical manifestations. Co-occurrence analysis revealed a densely-linked bacterial community in TB-NE compared to that in TB-E. MetaCyc functions responsible for menaquinone synthesis and chorismate metabolism that could potentially impact the persistent-state and nutrient metabolism of MTB were enriched in TB-E samples. While in TB-NE samples, enrichment of bacterial MetaCyc function responsible for heme b synthesis might contribute to TB pathology through ferroptosis. CONCLUSION Bacteriomes and their MetaCyc functions in TB lesions are elucidated, and they are associated with status of MTB excretion among pulmonary TB patients. These results serve as a basis for designing novel strategies for preventing and treating pulmonary TB disease.
Collapse
|
11
|
Anand P, Akhter Y. A review on enzyme complexes of electron transport chain from Mycobacterium tuberculosis as promising drug targets. Int J Biol Macromol 2022; 212:474-494. [PMID: 35613677 DOI: 10.1016/j.ijbiomac.2022.05.124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 12/20/2022]
Abstract
Energy metabolism is a universal process occurring in all life forms. In Mycobacterium tuberculosis (Mtb), energy production is carried out in two possible ways, oxidative phosphorylation (OxPhos) and substrate-level phosphorylation. Mtb is an obligate aerobic bacterium, making it dependent on OxPhos for ATP synthesis and growth. Mtb inhabits varied micro-niches during the infection cycle, outside and within the host cells, which alters its primary metabolic pathways during the pathogenesis. In this review, we discuss cellular respiration in the context of the mechanism and structural importance of the proteins and enzyme complexes involved. These protein-protein complexes have been proven to be essential for Mtb virulence as they aid the bacteria's survival during aerobic and hypoxic conditions. ATP synthase, a crucial component of the electron transport chain, has been in the limelight, as a prominent drug target against tuberculosis. Likewise, in this review, we have explored other protein-protein complexes of the OxPhos pathway, their functional essentiality, and their mechanism in Mtb's diverse lifecycle. The review summarises crucial target proteins and reported inhibitors of the electron transport chain pathway of Mtb.
Collapse
Affiliation(s)
- Pragya Anand
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India
| | - Yusuf Akhter
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India.
| |
Collapse
|
12
|
Frlan R. An Evolutionary Conservation and Druggability Analysis of Enzymes Belonging to the Bacterial Shikimate Pathway. Antibiotics (Basel) 2022; 11:antibiotics11050675. [PMID: 35625318 PMCID: PMC9137983 DOI: 10.3390/antibiotics11050675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022] Open
Abstract
Enzymes belonging to the shikimate pathway have long been considered promising targets for antibacterial drugs because they have no counterpart in mammals and are essential for bacterial growth and virulence. However, despite decades of research, there are currently no clinically relevant antibacterial drugs targeting any of these enzymes, and there are legitimate concerns about whether they are sufficiently druggable, i.e., whether they can be adequately modulated by small and potent drug-like molecules. In the present work, in silico analyses combining evolutionary conservation and druggability are performed to determine whether these enzymes are candidates for broad-spectrum antibacterial therapy. The results presented here indicate that the substrate-binding sites of most enzymes in this pathway are suitable drug targets because of their reasonable conservation and druggability scores. An exception was the substrate-binding site of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase, which was found to be undruggable because of its high content of charged residues and extremely high overall polarity. Although the presented study was designed from the perspective of broad-spectrum antibacterial drug development, this workflow can be readily applied to any antimicrobial target analysis, whether narrow- or broad-spectrum. Moreover, this research also contributes to a deeper understanding of these enzymes and provides valuable insights into their properties.
Collapse
Affiliation(s)
- Rok Frlan
- The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| |
Collapse
|
13
|
Yang Y, Xu Y, Yue Y, Wang H, Cui Y, Pan M, Zhang X, Zhang L, Li H, Xu M, Tang Y, Chen S. Investigate Natural Product Indolmycin and the Synthetically Improved Analogue Toward Antimycobacterial Agents. ACS Chem Biol 2022; 17:39-53. [PMID: 34908399 DOI: 10.1021/acschembio.1c00394] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Indolmycin (IND) is a microbial natural product that selectively inhibits bacterial tryptophanyl-tRNA synthetase (TrpRS). The tryptophan biosynthesis pathway was recently shown to be an important target for developing new antibacterial agents against Mycobacterium tuberculosis (Mtb). We investigated the antibacterial activity of IND against several mycobacterial model strains. A TrpRS biochemical assay was developed to analyze a library of synthetic IND analogues. The 4″-methylated IND compound, Y-13, showed improved anti-Mtb activity with a minimum inhibitory concentration (MIC) of 1.88 μM (∼0.5 μg/mL). The MIC increased significantly when overexpression of TrpRS was induced in the genetically engineered surrogate M. bovis BCG. The cocrystal structure of Mtb TrpRS complexed with IND and ATP has revealed that the amino acid pocket is in a state between the open form of apo protein and the closed complex with the reaction intermediate. In whole-cell-based experiments, we studied the combination effect of Y-13 paired with different antibacterial agents. We evaluated the killing kinetics, the frequency of resistance to INDs, and the mode of resistance of IND-resistant mycobacteria by genome sequencing. The synergistic interaction of Y-13 with the TrpE allosteric inhibitor, indole propionic acid, suggests that prospective IND analogues could shut down tryptophan biosynthesis and protein biosynthesis in pathogens, leading to a new class of antibiotics. Finally, we discuss a strategy to expand the genome mining of antibiotic-producing microbes specifically for antimycobacterial development.
Collapse
Affiliation(s)
- Yuhong Yang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yuanyuan Xu
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Yuan Yue
- Ministry of Education Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Heng Wang
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Yumeng Cui
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Miaomiao Pan
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Xi Zhang
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Lin Zhang
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Haitao Li
- Ministry of Education Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Min Xu
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Yefeng Tang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Shawn Chen
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| |
Collapse
|
14
|
Bajad NG, Singh SK, Singh SK, Singh TD, Singh M. Indole: A promising scaffold for the discovery and development of potential anti-tubercular agents. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2022; 3:100119. [PMID: 35992375 PMCID: PMC9389259 DOI: 10.1016/j.crphar.2022.100119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/13/2022] [Accepted: 07/05/2022] [Indexed: 11/08/2022] Open
Abstract
Indole-containing small molecules have been reported to have diverse pharmacological activities. The aromatic heterocyclic scaffold, which resembles various protein structures, has received attention from organic and medicinal chemists. Exploration of indole derivatives in drug discovery has rapidly yielded a vast array of biologically active compounds with broad therapeutic potential. Nature is the major source of indole scaffolds, but various classical and advanced synthesis methods for indoles have also been reported. One-pot synthesis is widely considered an efficient approach in synthetic organic chemistry and has been used to synthesize some indole compounds. The rapid emergence of drug-resistant tuberculosis is a major challenge to be addressed. Identifying novel targets and drug candidates for tuberculosis is therefore crucial. Researchers have extensively explored indole derivatives as potential anti-tubercular agents or drugs. Indole scaffolds containing the novel non-covalent (decaprenylphosphoryl-β-D-ribose2′-epimerase) DprE1 inhibitor 1,4-azaindole is currently in clinical trials to treat Mycobacterium tuberculosis. In addition, DG167 indazole sulfonamide with potent anti-tubercular activity is undergoing early-stage development in preclinical studies. Indole bearing cationic amphiphiles with high chemical diversity have been reported to depolarize and disrupt the mycobacterial membrane. Some indole-based compounds have potential inhibitory activities against distinct anti-tubercular targets, including the inhibition of cell wall synthesis, replication, transcription, and translation, as summarized in the graphical abstract. The success of computer-aided drug design in the fields of cancer and anti-viral drugs has accelerated in silico studies in antibacterial drug development. This review describes the sources of indole scaffolds, the potential for novel indole derivatives to serve as anti-tubercular agents, in silico findings, and proposed actions to facilitate the design of novel compounds with anti-tubercular activity. The Indole derivatives emerged as an efficient bioactive compoundes with wide range of therapeutic potential. Identifying novel drug candidates with indole derivatives can curtail the rapid emergence of drug-resistant tuberculosis. The current review highlights the sources of indole scaffolds, their derivatives, and in silico findings as anti-tubercular agents. Currently, DprE1 inhibitor 1,4-azaindole and DG167 indazole sulfonamide are in clinical trials to treat Mycobacterium tuberculosis.
Collapse
|
15
|
Reddy GS, Shukla S, Bhuktar H, Hossain KA, Edwin RK, Giliyaru VB, Misra P, Pal M. Pd/Cu-catalyzed access to novel 3-(benzofuran-2-ylmethyl) substituted (pyrazolo/benzo)triazinone derivatives: their in silico/ in vitro evaluation as inhibitors of chorismate mutase (CM). RSC Adv 2022; 12:26686-26695. [PMID: 36275143 PMCID: PMC9490447 DOI: 10.1039/d2ra05255e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/12/2022] [Indexed: 11/21/2022] Open
Abstract
In view of the reported chorismate mutase (CM or MtbCM) inhibitory activities of 3-indolylmethyl substituted (pyrazolo/benzo)triazinone derivatives the structurally similar 3-(benzofuran-2-ylmethyl) substituted (pyrazolo/benzo)triazinones were designed and evaluated in silico against CM. The docking of target molecules was performed at the interface site of MtbCM (PDB: 2FP2). All the best ranked molecules participated in a strong H-bonding with the ILE67 of the B chain at the backbone position in addition to several hydrophobic/van der Waals interactions with the hydrophobic residues. Based on encouraging docking results, the one-pot synthesis of newly designed benzofuran derivatives was carried out using tandem Pd/Cu-catalyzed Sonogashira cross-coupling followed by intramolecular cyclization of 2-iodophenols with appropriate terminal alkynes. A range of novel 3-(benzofuran-2-ylmethyl) substituted (pyrazolo/benzo)triazinone derivatives were prepared in high (>80%) yields. Three molecules i.e.3h, 3i and 3m that participated in good interaction with CM in silico showed encouraging (64–65%) inhibition at 30 μM in vitro. An SAR within this class of molecules suggested that the benzotriazinone series in general was better than the pyrazolotriazinone series. Based on molecular docking in silico, CM inhibition in vitro and computational ADME prediction the benzofuran derivatives 3i and 3m seemed to be of further medicinal interest in the context of discovery and development of new anti-tubercular agents. We report the Pd/Cu-catalyzed synthesis, in silico molecular docking, in vitro CM inhibition and computational ADME prediction of novel 3-(benzofuran-2-ylmethyl) substituted (pyrazolo/benzo)triazinone derivatives.![]()
Collapse
Affiliation(s)
- Gangireddy Sujeevan Reddy
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Sharda Shukla
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Harshavardhan Bhuktar
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Kazi Amirul Hossain
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Rebecca Kristina Edwin
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Varadaraj Bhat Giliyaru
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Parimal Misra
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Manojit Pal
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| |
Collapse
|
16
|
De novo transcriptome analysis of Justicia adhatoda reveals candidate genes involved in major biosynthetic pathway. Mol Biol Rep 2022; 49:10307-10314. [PMID: 36097107 PMCID: PMC9467423 DOI: 10.1007/s11033-022-07784-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Justicia adhatoda is an important medicinal plant traditionally used in the Indian system of medicine and the absence of molecular-level studies in this plant hinders its wide use, hence the study was aimed to analyse the genes involved in its various pathways. METHODS AND RESULTS The RNA isolated was subjected to Illumina sequencing. De novo assembly was performed using TRINITY software which produced 171,064 transcripts with 55,528 genes and N50 value of 2065 bp, followed by annotation of unigenes against NCBI, KEGG and Gene ontology databases resulted in 105,572 annotated unigenes and 40,288 non-annotated unigenes. A total of 5980 unigenes were mapped to 144 biochemical pathways, including the metabolism and biosynthesis pathways. The pathway analysis revealed the major transcripts involved in the tryptophan biosynthesis with TPM values of 6.0903, 33.6854, 11.527, 1.6959, and 8.1662 for Anthranilate synthase alpha, Anthranilate synthase beta, Arogenate/Prephenate dehydratase, Chorismate synthase and Chorismate mutase, respectively. The qRT-PCR validation of the key enzymes showed up-regulation in mid mature leaf when compared to root and young leaf tissue. A total of 16,154 SSRs were identified from the leaf transcriptome of J. Adhatoda ,which could be helpful in molecular breeding. CONCLUSIONS The study aimed at identifying transcripts involved in the tryptophan biosynthesis pathway for its medicinal properties, as it acts as a precursor to the acridone alkaloid biosynthesis with major key enzymes and their validation. This is the first study that reports transcriptome assembly and annotation of J. adhatoda plant.
Collapse
|
17
|
Sujeevan Reddy G, Sandeep Kumar J, Thirupataiah B, Amirul Hossain K, Babu Nallapati S, Bhat Giliyaru V, Chandrashekhar Hariharapura R, Gautham Shenoy G, Pal M. Propargylamines in Pd/Cu-catalyzed tandem coupling-cyclization-N-deprotection in a single pot: Construction of N-unsubstituted vs N-sulfonyl indole ring. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
18
|
Lee HA, Chu KB, Kim MJ, Quan FS, Kong HH, Moon EK. Chorismate mutase peptide antibody enables specific detection of Acanthamoeba. PLoS One 2021; 16:e0250342. [PMID: 33891646 PMCID: PMC8064552 DOI: 10.1371/journal.pone.0250342] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/05/2021] [Indexed: 11/19/2022] Open
Abstract
Accurate and rapid diagnosis of Acanthamoeba keratitis (AK) is difficult. Although the diagnostic procedure for AK has improved, further development and effective diagnostic tool utilization for AK need to continue. Chorismate mutase is a key regulatory enzyme involved in the shikimate pathway, a metabolic pathway absent in mammals but central for amino acid biosynthesis in bacteria, fungi, algae, and plants. In this study, we describe the identification and production of a polyclonal peptide antibody targeting chorismate mutase secreted by A. castellanii, which could be used for AK diagnosis. Western blot was performed using the protein lysates and conditioned media of the human corneal epithelial (HCE) cells, non-pathogenic Acanthamoeba, pathogenic Acanthamoeba, clinical isolate of Acanthamoeba spp., and other causes of keratitis such as Fusarium solani, Pseudomonas aeruginosa, and Staphylococcus aureus. Polyclonal antibodies raised against A. castellanii chorismate mutase specifically interacted with lysates of Acanthamoeba origin and their culture media, while such interactions were not observed from other samples. Acanthamoeba-specificity of chorismate mutase was also confirmed using immunocytochemistry after co-culturing Acanthamoeba with HCE cells. Specific binding of the chorismate mutase antibody to Acanthamoeba was observed, which were absent in the case of HCE cells. These results indicate that the chorismate mutase antibody of Acanthamoeba may serve as a method for rapid and differential Acanthamoeba identification.
Collapse
Affiliation(s)
- Hae-Ahm Lee
- Medical Research Center for Bioreaction to Reactive Oxygen Species and Biomedical Science Institute, School of Medicine, Graduate School, Kyung Hee University, Seoul, Korea
| | - Ki-Back Chu
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Min-Jeong Kim
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Fu-Shi Quan
- Medical Research Center for Bioreaction to Reactive Oxygen Species and Biomedical Science Institute, School of Medicine, Graduate School, Kyung Hee University, Seoul, Korea
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul, Korea
| | - Hyun-Hee Kong
- Department of Parasitology, Dong-A University College of Medicine, Busan, Korea
| | - Eun-Kyung Moon
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul, Korea
- * E-mail:
| |
Collapse
|
19
|
Diagnostic Potential of IgG and IgA Responses to Mycobacterium t uberculosis Antigens for Discrimination among Active Tuberculosis, Latent Tuberculosis Infection, and Non-Infected Individuals. Microorganisms 2020; 8:microorganisms8070979. [PMID: 32629849 PMCID: PMC7409123 DOI: 10.3390/microorganisms8070979] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis remains a major public health problem. Conventional tests are inadequate to distinguish between active tuberculosis (ATB) and latent tuberculosis infection (LTBI). We measured antibody responses to Mycobacterium tuberculosis antigens (Mycobacterium tuberculosis chorismate mutase (TBCM), antigen 85B (Ag85B), early secreted antigen-6 (ESAT-6), and culture filtrate protein-10 (CFP-10) in ATB, LTBI, and non-infected (NI) individuals. Serum immunoglobulin G (IgG) and immunoglobulin A (IgA) levels were measured and the QuantiFERON-TB Gold In-Tube assay was used to diagnose LTBI. IgG levels against TBCM were significantly higher in LTBI than NI subjects. IgG and IgA levels against Ag85B and IgG levels against CFP-10 were significantly higher in ATB, followed by LTBI, and then NI. When the ATB group was subdivided, IgG levels against Ag85B and CFP-10 were significantly higher in each subgroup compared with those in LTBI and NI groups. Positive correlation trends between interferon-gamma and IgG levels against Ag85B, TBCM, and CFP-10 and IgA levels against Ag85B in LTBI and NI subjects were observed. Age- and sex-adjusted models showed that IgG against TBCM and CFP-10 was independently related to LTBI diagnosis, and IgG against Ag85B was independently related to the diagnosis of ATB and could distinguish between LTBI and ATB. Overall, IgG antibody responses to TBCM, Ag85B, and CFP-10 can discriminate among ATB, LTBI, and NI groups.
Collapse
|
20
|
Dhananjaya G, Rao AD, Hossain KA, Anna VR, Pal M. In silico studies and β-cyclodextrin mediated neutral synthesis of 4-oxo-4,5,6,7-tetrahydroindoles of potential biological interest. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
21
|
Reddy GS, Hossain KA, Kumar JS, Thirupataiah B, Edwin RK, Giliyaru VB, Chandrashekhar Hariharapura R, Shenoy GG, Misra P, Pal M. Novel isatin–indole derivatives as potential inhibitors of chorismate mutase (CM): their synthesis along with unexpected formation of 2-indolylmethylamino benzoate ester under Pd–Cu catalysis. RSC Adv 2020; 10:289-297. [PMID: 35492515 PMCID: PMC9047634 DOI: 10.1039/c9ra09236f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/18/2019] [Indexed: 11/29/2022] Open
Abstract
A series of novel isatin–indole derivatives has been designed as potential inhibitors of chorismate mutase (CM) that is known to be present in bacteria, fungi and higher plants but not in human. The design was supported by in silico docking studies that predicted strong interactions of these molecules with CM. The target compounds were synthesized via the one-pot coupling/cyclization method involving the reaction of an isatin based terminal alkyne with 2-iodosulfanilides under Pd–Cu catalysis. A number of isatin–indole derivatives were prepared using this method. A side product e.g. 2-indolylmethylamino benzoate ester derivative was obtained as a result of isatin ring opening (ethanolysis) of products in certain cases. Additionally, regioselective reduction of selected compounds afforded the corresponding C-3 hydroxy derivatives. All isatin–indole derivatives showed good to high inhibition of CM in vitro among which two compounds (3e and 3f) showed inhibition at nanomolar concentration. Design, synthesis and evaluation of isatin–indole derivatives were undertaken to identify potent inhibitors of chorismate mutase.![]()
Collapse
Affiliation(s)
- Gangireddy Sujeevan Reddy
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
- Manipal College of Pharmaceutical Sciences
| | - Kazi Amirul Hossain
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
| | - Jetta Sandeep Kumar
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
- Manipal College of Pharmaceutical Sciences
| | - B. Thirupataiah
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
- Manipal College of Pharmaceutical Sciences
| | - Rebecca Kristina Edwin
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
| | | | | | - G. Gautham Shenoy
- Manipal College of Pharmaceutical Sciences
- Manipal Academy of Higher Education
- Manipal
- India
| | - Parimal Misra
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
| | - Manojit Pal
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
| |
Collapse
|
22
|
Kim M, Lee J, Heo L, Han SW. Putative Bifunctional Chorismate Mutase/Prephenate Dehydratase Contributes to the Virulence of Acidovorax citrulli. FRONTIERS IN PLANT SCIENCE 2020; 11:569552. [PMID: 33101336 PMCID: PMC7546022 DOI: 10.3389/fpls.2020.569552] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/09/2020] [Indexed: 05/21/2023]
Abstract
Acidovorax citrulli (Ac) is a plant pathogenic bacterium that causes bacterial fruit blotch (BFB) in cucurbit crops. Despite its importance in the cucurbit industry, resistant cultivars/lines against BFB have not yet been identified. Therefore, there is a need to characterize the virulence factors/mechanisms in Ac to control the disease. Chorismate mutase, a key enzyme in the shikimate pathway, produces aromatic amino acids. Here, we report the functions of putative bifunctional chorismate mutase/prephenate dehydratase in Ac (CmpAc) determined by proteomic analysis and phenotypic assays. Ac strain lacking CmpAc, AcΔcmpAc(EV), were significantly less virulent on watermelon in the germinated-seed inoculation and leaf infiltration assays. Sequence analysis revealed that CmpAc possesses two distinct domains: chorismate mutase and prephenate dehydratase, indicating that CmpAc is a bifunctional protein. Auxotrophic assays demonstrated that CmpAc is required for the biosynthesis of phenylalanine, but not tyrosine. The comparative proteomic analysis revealed that CmpAc is mostly involved in cell wall/membrane/envelop biogenesis. Furthermore, AcΔcmpAc(EV) showed reduced twitching halo production and enhanced biofilm formation. In addition, AcΔcmpAc(EV) was less tolerant to osmotic stress but more tolerant to antibiotics (polymyxin B). Thus, our study provides new insights into the functions of a putative bifunctional protein related to virulence in Ac.
Collapse
Affiliation(s)
- Minyoung Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Jongchan Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Lynn Heo
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Sang-Wook Han
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| |
Collapse
|
23
|
Reddy GS, Snehalatha AV, Edwin RK, Hossain KA, Giliyaru VB, Hariharapura RC, Gautham Shenoy G, Misra P, Pal M. Synthesis of 3-indolylmethyl substituted (pyrazolo/benzo)triazinone derivatives under Pd/Cu-catalysis: Identification of potent inhibitors of chorismate mutase (CM). Bioorg Chem 2019; 91:103155. [PMID: 31400552 DOI: 10.1016/j.bioorg.2019.103155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/04/2019] [Accepted: 07/24/2019] [Indexed: 11/17/2022]
Abstract
The chorismate mutase (CM) is considered as an attractive target for the identification of potential antitubercular agents due to its absence in animals but not in bacteria. A series of 3-indolylmethyl substituted pyrazolotriazinone derivatives were designed and docked into CM in silico as potential inhibitors. These compounds were efficiently synthesized using the Pd/Cu-catalyzed coupling-cyclization in a single pot involving the construction of indole ring. The methodology was later extended to the preparation of corresponding benzo analogs of pyrazolotriazinones i.e. 3-indolylmethyl substituted benzotriazinone derivatives. Several of these novel compounds showed significant inhibition of CM when tested in vitro at 30 µM. The SAR (Structure-Activity-Relationship) studies suggested that benzotriazinone moiety was more favorable over the pyrazolotriazinone ring. The two best active compounds showed IC50 ∼ 0.4-0.9 µM (better than the reference/known compounds used) and no toxicity till 30 µM in vitro.
Collapse
Affiliation(s)
- Gangireddy Sujeevan Reddy
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Ampalam Venkata Snehalatha
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Rebecca Kristina Edwin
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Kazi Amirul Hossain
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Varadaraj Bhat Giliyaru
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | | | - G Gautham Shenoy
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Parimal Misra
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Manojit Pal
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India.
| |
Collapse
|
24
|
Gut Microbiota Metabolite Indole Propionic Acid Targets Tryptophan Biosynthesis in Mycobacterium tuberculosis. mBio 2019; 10:mBio.02781-18. [PMID: 30914514 PMCID: PMC6437058 DOI: 10.1128/mbio.02781-18] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
New drugs against tuberculosis are urgently needed. The tryptophan (Trp) analog indole propionic acid (IPA) is the first antitubercular metabolite produced by human gut bacteria. Here, we show that this antibiotic blocks Trp synthesis, an in vivo essential biosynthetic pathway in M. tuberculosis. Intriguingly, IPA acts by decoupling a bacterial feedback regulatory mechanism: it mimics Trp as allosteric inhibitor of anthranilate synthase, thereby switching off Trp synthesis regardless of intracellular Trp levels. The identification of IPA’s target paves the way for the discovery of more potent TrpE ligands employing rational, target-based lead optimization. Indole propionic acid (IPA), produced by the gut microbiota, is active against Mycobacterium tuberculosisin vitro and in vivo. However, its mechanism of action is unknown. IPA is the deamination product of tryptophan (Trp) and thus a close structural analog of this essential aromatic amino acid. De novo Trp biosynthesis in M. tuberculosis is regulated through feedback inhibition: Trp acts as an allosteric inhibitor of anthranilate synthase TrpE, which catalyzes the first committed step in the Trp biosynthesis pathway. Hence, we hypothesized that IPA may mimic Trp as an allosteric inhibitor of TrpE and exert its antimicrobial effect by blocking synthesis of Trp at the TrpE catalytic step. To test our hypothesis, we carried out metabolic, chemical rescue, genetic, and biochemical analyses. Treatment of mycobacteria with IPA inhibited growth and reduced the intracellular level of Trp, an effect abrogated upon supplementation of Trp in the medium. Missense mutations at the allosteric Trp binding site of TrpE eliminated Trp inhibition and caused IPA resistance. In conclusion, we have shown that IPA blocks Trp biosynthesis in M. tuberculosis via inhibition of TrpE by mimicking the physiological allosteric inhibitor of this enzyme.
Collapse
|
25
|
Luo XW, Zhang DY, Zhu TH, Zhou XG, Peng J, Zhang SB, Liu Y. Adaptation mechanism and tolerance of Rhodopseudomonas palustris PSB-S under pyrazosulfuron-ethyl stress. BMC Microbiol 2018; 18:207. [PMID: 30526497 PMCID: PMC6286529 DOI: 10.1186/s12866-018-1361-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 11/29/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pyrazosulfuron-ethyl is a long lasting herbicide in the agro-ecosystem and its residue is toxic to crops and other non-target organisms. A better understanding of molecular basis in pyrazosulfuron-ethyl tolerant organisms will shed light on the adaptive mechanisms to this herbicide. RESULTS Pyrazosulfuron-ethyl inhibited biomass production in Rhodopseudomonas palustris PSB-S, altered cell morphology, suppressed flagella formation, and reduced pigment biosynthesis through significant suppression of carotenoids biosynthesis. A total of 1127 protein spots were detected in the two-dimensional gel electrophoresis. Among them, 72 spots representing 56 different proteins were found to be differently expressed using MALDI-TOF/TOF-MS, including 26 up- and 30 down-regulated proteins in the pyrazosulfuron-ethyl-treated PSB-S cells. The up-regulated proteins were involved predominantly in oxidative stress or energy generation pathways, while most of the down-regulated proteins were involved in the biomass biosynthesis pathway. The protein expression profiles suggested that the elongation factor G, cell division protein FtsZ, and proteins associated with the ABC transporters were crucial for R. palustris PSB-S tolerance against pyrazosulfuron-ethyl. CONCLUSION Up-regulated proteins, including elongation factor G, cell division FtsZ, ATP synthase, and superoxide dismutase, and down-regulated proteins, including ALS III and ABC transporters, as well as some unknown proteins might play roles in R. palustris PSB-S adaptation to pyrazosulfuron-ethyl induced stresses. Functional validations of these candidate proteins should help to develope transgenic crops resistant to pyrazosulfuron-ethyl.
Collapse
Affiliation(s)
- Xiang-Wen Luo
- Key laboratory of pest management of horticultural crop of Hunan province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, No 726 Second Yuanda Road, Furong District, Changsha, 410125, Hunan province, People's Republic of China.,Plant Protection College, Hunan Agricultural University, Changsha, 410128, China
| | - De-Yang Zhang
- Key laboratory of pest management of horticultural crop of Hunan province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, No 726 Second Yuanda Road, Furong District, Changsha, 410125, Hunan province, People's Republic of China.,Plant Protection College, Hunan Agricultural University, Changsha, 410128, China
| | - Teng-Hui Zhu
- Plant Protection College, Hunan Agricultural University, Changsha, 410128, China
| | - Xu-Guo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA
| | - Jing Peng
- Key laboratory of pest management of horticultural crop of Hunan province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, No 726 Second Yuanda Road, Furong District, Changsha, 410125, Hunan province, People's Republic of China.,Plant Protection College, Hunan Agricultural University, Changsha, 410128, China
| | - Song-Bai Zhang
- Key laboratory of pest management of horticultural crop of Hunan province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, No 726 Second Yuanda Road, Furong District, Changsha, 410125, Hunan province, People's Republic of China.
| | - Yong Liu
- Key laboratory of pest management of horticultural crop of Hunan province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, No 726 Second Yuanda Road, Furong District, Changsha, 410125, Hunan province, People's Republic of China. .,Plant Protection College, Hunan Agricultural University, Changsha, 410128, China.
| |
Collapse
|
26
|
Sujeevan Reddy G, Babu Nallapati S, Sri Saranya P, Sridhar B, Bhat Giliyaru V, Chandrashekhar Hariharapura R, Gautham Shenoy G, Pal M. Propargylamine (secondary) as a building block in indole synthesis involving ultrasound assisted Pd/Cu-catalyzed coupling-cyclization method: Unexpected formation of (pyrazole)imine derivatives. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.11.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
27
|
1,2,3-Triazole fused with pyridine/pyrimidine as new template for antimicrobial agents: Regioselective synthesis and identification of potent N-heteroarenes. Bioorg Med Chem Lett 2018; 28:3302-3306. [PMID: 30243590 DOI: 10.1016/j.bmcl.2018.09.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/08/2018] [Accepted: 09/16/2018] [Indexed: 01/11/2023]
Abstract
The 1,2,3-triazole ring fused with pyridine/pyrimidine was explored as new template for the identification of potential antimicrobial agents. The regioselective synthesis of these pre-designed N-heteroarenes was achieved via exploring the application of Buchwald's strategy (i.e. C-N bond formation/reduction/diazotization/cyclization sequence) to the N-heteroarene system. Two of them showed promising antibacterial (comparable to streptomycin) and several showed potent antifungal (comparable to mancozeb) activities.
Collapse
|
28
|
Asojo OA, Subramanian S, Abendroth J, Exley I, Lorimer DD, Edwards TE, Myler PJ. Crystal structure of chorismate mutase from Burkholderia phymatum. Acta Crystallogr F Struct Biol Commun 2018; 74:187-192. [PMID: 29633965 PMCID: PMC5894103 DOI: 10.1107/s2053230x18002868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/18/2018] [Indexed: 11/10/2022] Open
Abstract
The bacterium Burkholderia phymatum is a promiscuous symbiotic nitrogen-fixating bacterium that belongs to one of the largest groups of Betaproteobacteria. Other Burkholderia species are known to cause disease in plants and animals, and some are potential agents for biological warfare. Structural genomics efforts include characterizing the structures of enzymes from pathways that can be targeted for drug development. As part of these efforts, chorismate mutase from B. phymatum was produced and crystallized, and a 1.95 Å resolution structure is reported. This enzyme shares less than 33% sequence identity with other homologs of known structure. There are two classes of chorismate mutase: AroQ and AroH. The bacterial subclass AroQγ has reported roles in virulence. Chorismate mutase from B. phymatum has the prototypical AroQγ topology and retains the characteristic chorismate mutase active site. This suggests that substrate-based chorismate mutase inhibitors will not be specific and are likely to affect beneficial bacteria such as B. phymatum.
Collapse
Affiliation(s)
- Oluwatoyin A. Asojo
- National School of Tropical Medicine, Baylor College of Medicine, 1102 Bates Avenue Suite 550, Mail Stop BCM320, Houston, TX 77030-3411, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Ilyssa Exley
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| |
Collapse
|
29
|
Sunke R, Nallapati SB, Kumar JS, Shiva Kumar K, Pal M. Use of AlCl3 in Friedel Crafts arylation type reactions and beyond: an overview on the development of unique methodologies leading to N-heteroarenes. Org Biomol Chem 2017; 15:4042-4057. [DOI: 10.1039/c7ob00468k] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
An overview on the development of unique methodologies that highlight the use of AlCl3 in reactions leading to new N-heteroarenes of biological significance is presented.
Collapse
Affiliation(s)
- Rajnikanth Sunke
- Dr Reddy's Institute of Life Sciences
- Hyderabad Central University
- Hyderabad-500 046
- India
| | - Suresh Babu Nallapati
- Dr Reddy's Institute of Life Sciences
- Hyderabad Central University
- Hyderabad-500 046
- India
| | - Jetta Sandeep Kumar
- Dr Reddy's Institute of Life Sciences
- Hyderabad Central University
- Hyderabad-500 046
- India
| | - K. Shiva Kumar
- Department of Chemistry
- Osmania University
- Hyderabad-500 007
- India
| | - Manojit Pal
- Dr Reddy's Institute of Life Sciences
- Hyderabad Central University
- Hyderabad-500 046
- India
| |
Collapse
|