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Chauhan M, Barot R, Yadav R, Joshi K, Mirza S, Chikhale R, Srivastava VK, Yadav MR, Murumkar PR. The Mycobacterium tuberculosis Cell Wall: An Alluring Drug Target for Developing Newer Anti-TB Drugs-A Perspective. Chem Biol Drug Des 2024; 104:e14612. [PMID: 39237482 DOI: 10.1111/cbdd.14612] [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: 11/16/2023] [Revised: 06/26/2024] [Accepted: 08/05/2024] [Indexed: 09/07/2024]
Abstract
The Mycobacterium cell wall is a capsule-like structure comprising of various layers of biomolecules such as mycolic acid, peptidoglycans, and arabinogalactans, which provide the Mycobacteria a sort of cellular shield. Drugs like isoniazid, ethambutol, cycloserine, delamanid, and pretomanid inhibit cell wall synthesis by inhibiting one or the other enzymes involved in cell wall synthesis. Many enzymes present across these layers serve as potential targets for the design and development of newer anti-TB drugs. Some of these targets are currently being exploited as the most druggable targets like DprE1, InhA, and MmpL3. Many of the anti-TB agents present in clinical trials inhibit cell wall synthesis. The present article covers a systematic perspective of developing cell wall inhibitors targeting various enzymes involved in cell wall biosynthesis as potential drug candidates for treating Mtb infection.
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Affiliation(s)
- Monica Chauhan
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Rahul Barot
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Rasana Yadav
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Karan Joshi
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Sadaf Mirza
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Rupesh Chikhale
- The Cambridge Crystallography Data Center, Cambridge, UK
- School of Pharmacy, University College London, London, UK
| | | | - Mange Ram Yadav
- Centre of Research for Development, Parul University, Vadodara, Gujarat, India
| | - Prashant R Murumkar
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
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2
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Jiang Q, Hu R, Liu F, Huang F, Zhang L, Zhang H. Characterization of a Novel Oxidative Stress Responsive Transcription Regulator in Mycobacterium bovis. Biomedicines 2024; 12:1872. [PMID: 39200336 PMCID: PMC11351531 DOI: 10.3390/biomedicines12081872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 08/14/2024] [Indexed: 09/02/2024] Open
Abstract
The antioxidant defense is critical for the survival of intracellular pathogens such as Mycobacterium tuberculosis complex (MTBC) species, including Mycobacterium bovis, which are often exposed to an oxidative environment caused by reactive oxygen species (ROS) in hosts. However, the signaling pathway in mycobacteria for sensing and responding to oxidative stress remains largely unclear. In this study, we characterize a TetR-type transcription regulator BCG_3893c, designated AotM, as a novel redox sensor in Mycobacterium bovis that increases mycobacterial tolerance to oxidative stress. AotM is required for the growth of M. bovis in the presence of 1 mM hydrogen peroxide. Loss of the aotM gene leads to altered transcriptional profiles with 352 genes significantly up-regulated and 25 genes significantly down-regulated. AotM recognizes a 14-bp palindrome sequence motif and negatively regulates the expression of a FAD-dependent oxidoreductase encoded by bcg_3892c. Overexpression of BCG_3892c increases intracellular ROS production and reduces the growth of M. bovis. In summary, we propose that AotM enhances the mycobacterial resistance against oxidative stress probably by inhibiting intracellular ROS production. Our findings reveal a novel underlying regulatory mechanism behind mycobacterial oxidative stress adaptation.
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Affiliation(s)
- Qiang Jiang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.J.)
| | - Rong Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.J.)
| | - Feng Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.J.)
| | - Feng Huang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.J.)
| | - Lei Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Hua Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.J.)
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Agarwal M, Bhaskar A, Singha B, Mukhopadhyay S, Pahuja I, Singh A, Chaturvedi S, Agarwal N, Dwivedi VP, Nandicoori VK. Depletion of essential mycobacterial gene glmM reduces pathogen survival and induces host-protective immune responses against tuberculosis. Commun Biol 2024; 7:949. [PMID: 39107377 PMCID: PMC11303689 DOI: 10.1038/s42003-024-06620-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
The limitations of TB treatment are the long duration and immune-dampening effects of anti-tuberculosis therapy. The Cell wall plays a crucial role in survival and virulence; hence, enzymes involved in its biosynthesis are good therapeutic targets. Here, we identify Mycobacterium tuberculosis (Mtb) GlmM, (GlmMMtb) engaged in the UDP-GlcNAc synthesis pathway as an essential enzyme. We generated a conditional knockdown strain, Rv-glmMkD using the CRISPR interference-mediated gene silencing approach. Depletion of GlmMMtb affects the morphology and thickness of the cell wall. The Rv-glmMkD strain attenuated Mtb survival in vitro, in the host macrophages (ex vivo), and in a murine mice infection model (in vivo). Results suggest that the depletion of GlmMMtb induces M1 macrophage polarization, prompting a pro-inflammatory cytokine response, apparent from the upregulation of activation markers, including IFNɣ and IL-17 that resists the growth of Mtb. These observations provide a rationale for exploring GlmMMtb as a potential therapeutic target.
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Affiliation(s)
- Meetu Agarwal
- Signal Transduction Laboratory, National Institute of Immunology, New Delhi, India.
- Department of Molecular Medicine, Jamia Hamdard University, New Delhi, India.
| | - Ashima Bhaskar
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Biplab Singha
- Signal Transduction Laboratory, National Institute of Immunology, New Delhi, India
| | - Suparba Mukhopadhyay
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Isha Pahuja
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Archna Singh
- CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi, India
| | - Shivam Chaturvedi
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Ved Prakash Dwivedi
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Vinay Kumar Nandicoori
- Signal Transduction Laboratory, National Institute of Immunology, New Delhi, India.
- CSIR-Centre for Cellular and Molecular Biology, Habsiguda, Hyderabad, Telangana, India.
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Dash S, Rathi E, Kumar A, Chawla K, Joseph A, Kini SG. Structure-activity relationship mediated molecular insights of DprE1 inhibitors: A Comprehensive Review. J Biomol Struct Dyn 2024; 42:6472-6522. [PMID: 37395797 DOI: 10.1080/07391102.2023.2230312] [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: 04/03/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023]
Abstract
Emerging threats of multi-drug resistant (MDR), extensively drug-resistant (XDR), and totally drug-resistant (TDR) tuberculosis led to the discovery of a novel target which was entitled Decaprenylphosphoryl-β-D-ribose 2'-epimerase (DprE1) enzyme. DprE1 is composed of two isoforms, decaprenylphosphoryl-β-D-ribose oxidase (DprE1) and decaprenylphosphoryl-D-2-keto erythro pentose reductase (DprE2). The enzymes, DprE1 and DprE2, regulate the two-step epimerization process to form DPA (Decaprenylphosphoryl arabinose) from DPX (Decaprenylphosphoryl-D-ribose), which is the sole precursor in the cell wall synthesis of arabinogalactan (AG) and lipoarabinomannan (LAM). Target-based and whole-cell-based screening played an imperative role in the identification of the druggable target, DprE1, whereas the druggability of the DprE2 enzyme is not proved yet. To date, diverse scaffolds of heterocyclic and aromatic ring systems have been reported as DprE1 inhibitors based on their interaction mode, i.e. covalent, and non-covalent inhibitors. This review describes the structure-activity relationship (SAR) of reported covalent and non-covalent inhibitors to enlighten about the crucial pharmacophoric features required for DprE1 inhibition, along with in-silico studies which characterize the amino acid residues responsible for covalent and non-covalent interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Swagatika Dash
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ekta Rathi
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Avinash Kumar
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Suvarna G Kini
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
- Manipal Mc Gill Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, Karnataka, India
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Deshpande A, Likhar R, Khan T, Omri A. Decoding drug resistance in Mycobacterium tuberculosis complex: genetic insights and future challenges. Expert Rev Anti Infect Ther 2024; 22:511-527. [PMID: 39219506 DOI: 10.1080/14787210.2024.2400536] [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: 03/25/2024] [Revised: 06/02/2024] [Accepted: 08/31/2024] [Indexed: 09/04/2024]
Abstract
INTRODUCTION Tuberculosis (TB), particularly its drug-resistant forms (MDR-TB and XDR-TB), continues to pose a significant global health challenge. Despite advances in treatment and diagnosis, the evolving nature of drug resistance in Mycobacterium tuberculosis (MTB) complicates TB eradication efforts. This review delves into the complexities of anti-TB drug resistance, its mechanisms, and implications on healthcare strategies globally. AREAS COVERED We explore the genetic underpinnings of resistance to both first-line and second-line anti-TB drugs, highlighting the role of mutations in key genes. The discussion extends to advanced diagnostic techniques, such as Whole-Genome Sequencing (WGS), CRISPR-based diagnostics and their impact on identifying and managing drug-resistant TB. Additionally, we discuss artificial intelligence applications, current treatment strategies, challenges in managing MDR-TB and XDR-TB, and the global disparities in TB treatment and control, translating to different therapeutic outcomes and have the potential to revolutionize our understanding and management of drug-resistant tuberculosis. EXPERT OPINION The current landscape of anti-TB drug resistance demands an integrated approach combining advanced diagnostics, novel therapeutic strategies, and global collaborative efforts. Future research should focus on understanding polygenic resistance and developing personalized medicine approaches. Policymakers must prioritize equitable access to diagnosis and treatment, enhancing TB control strategies, and support ongoing research and augmented government funding to address this critical public health issue effectively.
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Affiliation(s)
- Amey Deshpande
- Department of Pharmaceutical Chemistry, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth's College of Pharmacy, Navi Mumbai, India
| | - Rupali Likhar
- Department of Pharmaceutical Chemistry, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India
- Department of Pharmaceutical Chemistry, LSHGCT's Gahlot Institute of Pharmacy, Navi Mumbai, India
| | - Tabassum Khan
- Department of Pharmaceutical Chemistry, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India
| | - Abdelwahab Omri
- The Novel Drug & Vaccine Delivery Systems Facility, Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
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Chikhale RV, Choudhary R, Malhotra J, Eldesoky GE, Mangal P, Patil PC. Identification of novel hit molecules targeting M. tuberculosis polyketide synthase 13 by combining generative AI and physics-based methods. Comput Biol Med 2024; 176:108573. [PMID: 38723396 DOI: 10.1016/j.compbiomed.2024.108573] [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: 02/21/2024] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024]
Abstract
In this work we investigated the Pks13-TE domain, which plays a critical role in the viability of the mycobacteria. In this report, we have used a series of AI and Physics-based tools to identify Pks13-TE inhibitors. The Reinvent 4, pKCSM, KDeep, and SwissADME are AI-ML-based tools. AutoDock Vina, PLANTS, MDS, and MM-GBSA are physics-based methods. A combination of these methods yields powerful support in the drug discovery cycle. Known inhibitors of Pks13-TE were collected, curated, and used as input for the AI-based tools, and Mol2Mol molecular optimisation methods generated novel inhibitors. These ligands were filtered based on physics-based methods like molecular docking and molecular dynamics using multiple tools for consensus generation. Rigorous analysis was performed on the selected compounds to reduce the chemical space while retaining the most promising compounds. The molecule interactions, stability of the protein-ligand complexes and the comparable binding energies with the native ligand were essential factors for narrowing the ligands set. The filtered ligands from docking, MDS, and binding energy colocations were further tested for their ADMET properties since they are among the essential criteria for this series of molecules. It was found that ligands Mt1 to Mt6 have excellent predicted pharmacokinetic, pharmacodynamic and toxicity profiles and good synthesisability.
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Affiliation(s)
- Rupesh V Chikhale
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, UK.
| | - Rinku Choudhary
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 5600413, India; Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed to Be University, Pune-Satara Road, Pune, India
| | - Jagriti Malhotra
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 5600413, India; Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed to Be University, Pune-Satara Road, Pune, India
| | - Gaber E Eldesoky
- Chemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Parth Mangal
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 5600413, India; Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed to Be University, Pune-Satara Road, Pune, India
| | - Pritee Chunarkar Patil
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed to Be University, Pune-Satara Road, Pune, India
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Khairullah AR, Moses IB, Kusala MKJ, Tyasningsih W, Ayuti SR, Rantam FA, Fauziah I, Silaen OSM, Puspitasari Y, Aryaloka S, Raharjo HM, Hasib A, Yanestria SM, Nurhidayah N. Unveiling insights into bovine tuberculosis: A comprehensive review. Open Vet J 2024; 14:1330-1344. [PMID: 39055751 PMCID: PMC11268907 DOI: 10.5455/ovj.2024.v14.i6.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/17/2024] [Indexed: 07/27/2024] Open
Abstract
The frequent zoonotic disease known as "bovine tuberculosis" is brought on by the Mycobacterium bovis bacteria, which can infect both people and animals. The aim of this review article is to provide an explanation of the etiology, history, epidemiology, pathogenesis, clinical symptoms, diagnosis, transmission, risk factors, public health importance, economic impact, treatment, and control of bovine tuberculosis. Primarily, bovine tuberculosis affects cattle, but other animals may also be affected. Bovine tuberculosis is present throughout the world, with the exception of Antarctica. Cattle that contract bovine tuberculosis might suffer from a persistent, crippling illness. In the early stages of the disease, there are no symptoms. The tuberculin test is the primary method for detecting bovine tuberculosis in cows. Depending on its localized site in the infected animal, M. bovis can be found in respiratory secretions, milk, urine, feces, vaginal secretions, semen, feces, and exudates from lesions (such as lymph node drainage and some skin lesions). This illness generally lowers cattle productivity and could have a negative financial impact on the livestock business, particularly the dairy industry. The most effective first-line anti-tuberculosis chemotherapy consists of isoniazid, ethambutol, rifampin, and streptomycin. Second-line drugs used against bovine tuberculosis include ethionamide, capreomycin, thioacetazone, and cycloserine. To successfully control and eradicate bovine tuberculosis, developed nations have implemented routine testing and culling of infected animals under national mandatory programs.
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Affiliation(s)
- Aswin Rafif Khairullah
- Research Center for Veterinary Science, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Ikechukwu Benjamin Moses
- Department of Applied Microbiology, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | | | - Wiwiek Tyasningsih
- Division of Veterinary Microbiology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Siti Rani Ayuti
- Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Fedik Abdul Rantam
- Division of Veterinary Microbiology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Ima Fauziah
- Research Center for Veterinary Science, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Otto Sahat Martua Silaen
- Doctoral Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Yulianna Puspitasari
- Division of Veterinary Microbiology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Suhita Aryaloka
- Master Program of Veterinary Agribusiness, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Hartanto Mulyo Raharjo
- Division of Veterinary Microbiology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Abdullah Hasib
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, Australia
| | | | - Nanis Nurhidayah
- Research Center for Veterinary Science, National Research and Innovation Agency (BRIN), Bogor, Indonesia
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Nyazema KB, Shey BA, Sei CJ, Peters RP, Maningi NE, Fischer GW, Bernard Fourie P. In vitro evaluation of the binding activity of novel mouse IgG1 opsonic monoclonal antibodies to Mycobacterium tuberculosis and other selected mycobacterial species. J Clin Tuberc Other Mycobact Dis 2024; 35:100435. [PMID: 38601919 PMCID: PMC11004620 DOI: 10.1016/j.jctube.2024.100435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024] Open
Abstract
Antimicrobial resistance alongside other challenges in tuberculosis (TB) therapeutics have stirred renewed interest in host-directed interventions, including the role of antibodies as adjunct therapeutic agents. This study assessed the binding efficacy of two novel IgG1 opsonic monoclonal antibodies (MABs; GG9 & JG7) at 5, 10, and 25 µg/mL to live cultures of Mycobacterium tuberculosis, M. avium, M. bovis, M. fortuitum, M. intracellulare, and M. smegmatis American Type Culture Collection laboratory reference strains, as well as clinical susceptible, multi-drug resistant, and extensively drug resistant M. tuberculosis strains using indirect enzyme-linked immunosorbent assays. These three MAB concentrations were selected from a range of concentrations used in previous optimization (binding and functional) assays. Both MABs bound to all mycobacterial species and sub-types tested, albeit to varying degrees. Statistically significant differences in MAB binding activity were observed when comparing the highest and lowest MAB concentrations (p < 0.05) for both MABs GG9 and JG7, irrespective of the M. tuberculosis resistance profile. Binding affinity increased with an increase in MAB concentration, and optimal binding was observed at 25 µg/mL. JG7 showed better binding activity than GG9. Both MABs also bound to five MOTT species, albeit at varied levels. This non-selective binding to different mycobacterial species suggests a potential role for GG9 and JG7 as adjunctive agents in anti-TB chemotherapy with the aim to enhance bacterial killing.
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Affiliation(s)
- Kudzai B. Nyazema
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Bong-Akee Shey
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Clara J. Sei
- Vaccine and Antibody Development, Longhorn Vaccines and Diagnostics, Gaithersburg, MD, USA
| | - Remco P.H. Peters
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, South Africa
- Foundation for Professional Development, Research Unit, East London, South Africa
| | - Nontuthuko E. Maningi
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, South Africa
- Department of Microbiology, School of Life Sciences, University of KwaZulu-Natal, South Africa
| | - Gerald W. Fischer
- Vaccine and Antibody Development, Longhorn Vaccines and Diagnostics, Gaithersburg, MD, USA
| | - P. Bernard Fourie
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, South Africa
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Shaku MT, Um PK, Ocius KL, Apostolos AJ, Pires MM, Bishai WR, Kana BD. A modified BCG with depletion of enzymes associated with peptidoglycan amidation induces enhanced protection against tuberculosis in mice. eLife 2024; 13:e89157. [PMID: 38639995 PMCID: PMC11132681 DOI: 10.7554/elife.89157] [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: 05/08/2023] [Accepted: 04/17/2024] [Indexed: 04/20/2024] Open
Abstract
Mechanisms by which Mycobacterium tuberculosis (Mtb) evades pathogen recognition receptor activation during infection may offer insights for the development of improved tuberculosis (TB) vaccines. Whilst Mtb elicits NOD-2 activation through host recognition of its peptidoglycan-derived muramyl dipeptide (MDP), it masks the endogenous NOD-1 ligand through amidation of glutamate at the second position in peptidoglycan side-chains. As the current BCG vaccine is derived from pathogenic mycobacteria, a similar situation prevails. To alleviate this masking ability and to potentially improve efficacy of the BCG vaccine, we used CRISPRi to inhibit expression of the essential enzyme pair, MurT-GatD, implicated in amidation of peptidoglycan side-chains. We demonstrate that depletion of these enzymes results in reduced growth, cell wall defects, increased susceptibility to antibiotics, altered spatial localization of new peptidoglycan and increased NOD-1 expression in macrophages. In cell culture experiments, training of a human monocyte cell line with this recombinant BCG yielded improved control of Mtb growth. In the murine model of TB infection, we demonstrate that depletion of MurT-GatD in BCG, which is expected to unmask the D-glutamate diaminopimelate (iE-DAP) NOD-1 ligand, yields superior prevention of TB disease compared to the standard BCG vaccine. In vitro and in vivo experiments in this study demonstrate the feasibility of gene regulation platforms such as CRISPRi to alter antigen presentation in BCG in a bespoke manner that tunes immunity towards more effective protection against TB disease.
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Affiliation(s)
- Moagi Tube Shaku
- DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, University of the Witwatersrand, National Health Laboratory ServiceJohannesburgSouth Africa
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Peter K Um
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Karl L Ocius
- Department of Chemistry, University of VirginiaCharlottesvilleUnited States
| | - Alexis J Apostolos
- Department of Chemistry, University of VirginiaCharlottesvilleUnited States
| | - Marcos M Pires
- Department of Chemistry, University of VirginiaCharlottesvilleUnited States
| | - William R Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Bavesh D Kana
- DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, University of the Witwatersrand, National Health Laboratory ServiceJohannesburgSouth Africa
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Hsu TW, Fang JM. Advances and prospects of analytic methods for bacterial transglycosylation and inhibitor discovery. Analyst 2024; 149:2204-2222. [PMID: 38517346 DOI: 10.1039/d3an01968c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
The cell wall is essential for bacteria to maintain structural rigidity and withstand external osmotic pressure. In bacteria, the cell wall is composed of peptidoglycan. Lipid II is the basic unit for constructing highly cross-linked peptidoglycan scaffolds. Transglycosylase (TGase) is the initiating enzyme in peptidoglycan synthesis that catalyzes the ligation of lipid II moieties into repeating GlcNAc-MurNAc polysaccharides, followed by transpeptidation to generate cross-linked structures. In addition to the transglycosylases in the class-A penicillin-binding proteins (aPBPs), SEDS (shape, elongation, division and sporulation) proteins are also present in most bacteria and play vital roles in cell wall renewal, elongation, and division. In this review, we focus on the latest analytical methods including the use of radioactive labeling, gel electrophoresis, mass spectrometry, fluorescence labeling, probing undecaprenyl pyrophosphate, fluorescence anisotropy, ligand-binding-induced tryptophan fluorescence quenching, and surface plasmon resonance to evaluate TGase activity in cell wall formation. This review also covers the discovery of TGase inhibitors as potential antibacterial agents. We hope that this review will give readers a better understanding of the chemistry and basic research for the development of novel antibiotics.
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Affiliation(s)
- Tse-Wei Hsu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
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11
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Hu T, Yang X, Zhu Y, Liu F, Yang X, Xiong Z, Liang J, Lin Z, Ran Y, Guddat LW, Rao Z, Zhang B. Molecular basis for substrate transport of Mycobacterium tuberculosis ABC importer DppABCD. SCIENCE ADVANCES 2024; 10:eadk8521. [PMID: 38507491 PMCID: PMC10954201 DOI: 10.1126/sciadv.adk8521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
The type I adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter DppABCD is believed to be responsible for the import of exogenous heme as an iron source into the cytoplasm of the human pathogen Mycobacterium tuberculosis (Mtb). Additionally, this system is also known to be involved in the acquisition of tri- or tetra-peptides. Here, we report the cryo-electron microscopy structures of the dual-function Mtb DppABCD transporter in three forms, namely, the apo, substrate-bound, and ATP-bound states. The apo structure reveals an unexpected and previously uncharacterized assembly mode for ABC importers, where the lipoprotein DppA, a cluster C substrate-binding protein (SBP), stands upright on the translocator DppBCD primarily through its hinge region and N-lobe. These structural data, along with biochemical studies, reveal the assembly of DppABCD complex and the detailed mechanism of DppABCD-mediated transport. Together, these findings provide a molecular roadmap for understanding the transport mechanism of a cluster C SBP and its translocator.
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Affiliation(s)
- Tianyu Hu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaolin Yang
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Yuanchen Zhu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fengjiang Liu
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Zhiqi Xiong
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Jingxi Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China
| | - Zhenli Lin
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuting Ran
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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12
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Desire IA, Luqman M, Puspitasari Y, Tyasningsih W, Wardhana DK, Meles DK, Dhamayanti Y, Permatasari DA, Witaningrum AM, Perwitasari ADS, Raharjo HM, Ayuti SR, Kurniawan SC, Kamaruzaman INA, Silaen OSM. First detection of bovine tuberculosis by Ziehl-Neelsen staining and polymerase chain reaction at dairy farms in the Lekok Sub-District, Pasuruan Regency, and Surabaya region, Indonesia. Vet World 2024; 17:577-584. [PMID: 38680137 PMCID: PMC11045540 DOI: 10.14202/vetworld.2024.577-584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/16/2024] [Indexed: 05/01/2024] Open
Abstract
Background and Aim Bovine tuberculosis (TB) is a zoonotic disease of great public health importance, particularly in Indonesia, where control measures are limited or are not implemented. This study aimed to detect the presence of Mycobacterium pathogens in milk samples from dairy cattle in Pasuruan regency and Surabaya City, East Java, using Ziehl-Neelsen acid-fast staining and polymerase chain reaction (PCR). Materials and Methods Milk samples were aseptically collected from 50 cattle in the Lekok Subdistrict, Pasuruan Regency, and 44 from dairy farms in the Lakarsantri Subdistrict, Wonocolo Subdistrict, Mulyorejo Subdistrict, and Kenjeran Subdistrict, Surabaya, East Java. To detect Mycobacteria at the species level, each sample was assessed by Ziehl-Neelsen staining and PCR using the RD1 and RD4 genes. Results The results of PCR assay from 50 samples in Lekok Subdistrict, Pasuruan Regency showed that 30 samples (60%) were positive for Mycobacterium tuberculosis and two samples (4%) were positive for Mycobacterium bovis, although Ziehl-Neelsen staining did not show the presence of Mycobacterium spp. In the Surabaya region, 31 samples (70.45%) were positive for M. tuberculosis and three samples (6.8%) were positive for M. bovis. Six samples (13.63%) from all PCR-positive samples could be detected microscopically with Ziehl-Neelsen. Conclusion The presence of bovine TB in this study supports the importance of using a molecular tool alongside routine surveillance for a better understanding of the epidemiology of bovine TB in East Java.
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Affiliation(s)
- Itfetania Aemilly Desire
- Bachelor Program of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Muhammad Luqman
- Bachelor Program of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Yulianna Puspitasari
- Division of Veterinary Microbiology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Wiwiek Tyasningsih
- Division of Veterinary Microbiology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Dhandy Koesoemo Wardhana
- Division of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Dewa Ketut Meles
- Division of Basic Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Yeni Dhamayanti
- Division of Veterinary Anatomy, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Dian Ayu Permatasari
- Division of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Adiana Mutamsari Witaningrum
- Division of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Agnes Dwi Sis Perwitasari
- Department of Tuberculosis, Institute Tropical Disease, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Hartanto Mulyo Raharjo
- Division of Veterinary Microbiology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Siti Rani Ayuti
- Biochemistry Laboratory, Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, Indonesia
| | - Shendy Canadya Kurniawan
- Master Program of Animal Sciences, Department of Animal Sciences, Specialisation in Molecule, Cell and Organ Functioning, Wageningen University and Research, Wageningen, Netherlands
| | - Intan Noor Aina Kamaruzaman
- Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kelantan, Malaysia
| | - Otto Sahat Martua Silaen
- Doctoral Program of Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
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13
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Nair G, Jain V. An intramolecular cross-talk in D29 mycobacteriophage endolysin governs the lytic cycle and phage-host population dynamics. SCIENCE ADVANCES 2024; 10:eadh9812. [PMID: 38335296 PMCID: PMC10857449 DOI: 10.1126/sciadv.adh9812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
D29 mycobacteriophage encodes LysA endolysin, which mediates mycobacterial host cell lysis by targeting its peptidoglycan layer, thus projecting itself as a potential therapeutic. However, the regulatory mechanism of LysA during the phage lytic cycle remains ill defined. Here, we show that during D29 lytic cycle, structural and functional regulation of LysA not only orchestrates host cell lysis but also is critical for maintaining phage-host population dynamics by governing various phases of lytic cycle. We report that LysA exists in two conformations, of which only one is active, and the protein undergoes a host peptidoglycan-dependent conformational switch to become active for carrying out endogenous host cell lysis. D29 maintains a pool of inactive LysA, allowing complete assembly of phage progeny, thus helping avoid premature host lysis. In addition, we show that the switch reverses after lysis, thus preventing exogenous targeting of bystanders, which otherwise negatively affects phage propagation in the environment.
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Affiliation(s)
- Gokul Nair
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, Madhya Pradesh, India
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14
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Andrés Libreros-Zúñiga G, Pavão E Pavão D, de Morais Barroso V, Cristina de Moraes Roso Mesquita N, Fehelberg Pinto Braga S, Oliva G, Salgado Ferreira R, Ishida K, Vinicius Bertacine Dias M. Integration of biophysical and biological approaches to validate fragment-like compounds targeting l,d-transpeptidases from Mycobacterium tuberculosis. Bioorg Chem 2024; 142:106960. [PMID: 37944368 DOI: 10.1016/j.bioorg.2023.106960] [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: 09/16/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Tuberculosis is one of the major causes of death worldwide; more than a million people die every year because of this infection. The constant emergency of Mycobacterium tuberculosis resistant strains against the most used treatments also contributes to the burden caused by this disease. Consequently, the development of new alternative therapies against this disease is constantly required. In recent years, only a few molecules have reached the market as new antituberculosis agents. The mycobacterial cell wall biosynthesis is for a longstanding considered an important target for drug development. Particularly, in M. tuberculosis, the peptidoglycan cross-links are predominantly formed by nonclassical bridges between the third residues of adjacent tetrapeptides. The responsible enzymes for these reactions are ld-transpeptidases (Ldts), for which M. tuberculosis has five paralogues. Although these enzymes are distinct from the penicillin-binding proteins (PBPs), they can also be inactivated by β-lactam antibiotics, but since M. tuberculosis has a chromosomal β-lactamase, most of the antibiotics of these classes can be degraded. Thus, to identify alternative scaffolds for the development of new antimicrobials against tuberculosis, we have integrated several fragment-based drug discovery techniques. Based on that, we identified and validated a number of small molecules that could be the starting point in the synthesis of more potent inhibitors against at least two Ldts from M. tuberculosis, LdtMt2 and LdtMt3. Eight identified molecules inhibited the Ldts activity in at least 20%, and three of them have antimycobacterial activity. The cell ultrastructural analysis suggested that one of the best compounds induced severe effects on the septum and cell wall morphologies, which corroborates our target-based approach to identifying new Ldts hits.
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Affiliation(s)
- Gerardo Andrés Libreros-Zúñiga
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil; IBILCE, São Paulo State University, Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo 15054-000, Brazil; Department of Microbiology, Faculty of Health, University of Valle, Calle 4B # 36-00, 760043, Cali, Valle del Cauca, Colombia.
| | - Danilo Pavão E Pavão
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil
| | - Vinicius de Morais Barroso
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil
| | | | - Saulo Fehelberg Pinto Braga
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais. Av. Antônio Carlos, 6627 - Belo Horizonte, 31270-901 Minas Gerais, Brazil
| | - Glaucius Oliva
- Institute of Physics of São Carlos, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, Brazil
| | - Rafaela Salgado Ferreira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais. Av. Antônio Carlos, 6627 - Belo Horizonte, 31270-901 Minas Gerais, Brazil
| | - Kelly Ishida
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil
| | - Marcio Vinicius Bertacine Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil; IBILCE, São Paulo State University, Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo 15054-000, Brazil; Department of Chemistry, University of Warwick, Coventry CV4 7AL, England.
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15
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Wynn EA, Dide-Agossou C, Reichlen M, Rossmassler K, Al Mubarak R, Reid JJ, Tabor ST, Born SEM, Ransom MR, Davidson RM, Walton KN, Benoit JB, Hoppers A, Loy DE, Bauman AA, Massoudi LM, Dolganov G, Strong M, Nahid P, Voskuil MI, Robertson GT, Moore CM, Walter ND. Transcriptional adaptation of Mycobacterium tuberculosis that survives prolonged multi-drug treatment in mice. mBio 2023; 14:e0236323. [PMID: 37905920 PMCID: PMC10746229 DOI: 10.1128/mbio.02363-23] [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: 09/13/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE A major reason that curing tuberculosis requires prolonged treatment is that drug exposure changes bacterial phenotypes. The physiologic adaptations of Mycobacterium tuberculosis that survive drug exposure in vivo have been obscure due to low sensitivity of existing methods in drug-treated animals. Using the novel SEARCH-TB RNA-seq platform, we elucidated Mycobacterium tuberculosis phenotypes in mice treated for with the global standard 4-drug regimen and compared them with the effect of the same regimen in vitro. This first view of the transcriptome of the minority Mycobacterium tuberculosis population that withstands treatment in vivo reveals adaptation of a broad range of cellular processes, including a shift in metabolism and cell wall modification. Surprisingly, the change in gene expression induced by treatment in vivo and in vitro was largely similar. This apparent "portability" from in vitro to the mouse provides important new context for in vitro transcriptional analyses that may support early preclinical drug evaluation.
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Affiliation(s)
- Elizabeth A. Wynn
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
| | - Christian Dide-Agossou
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Matthew Reichlen
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Karen Rossmassler
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Reem Al Mubarak
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Justin J. Reid
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Samuel T. Tabor
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sarah E. M. Born
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Monica R. Ransom
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Rebecca M. Davidson
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Kendra N. Walton
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Jeanne B. Benoit
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Amanda Hoppers
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Dorothy E. Loy
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Allison A. Bauman
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Lisa M. Massoudi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Gregory Dolganov
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Palo Alto, California, USA
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Payam Nahid
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, USA
- UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, California, USA
| | - Martin I. Voskuil
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Gregory T. Robertson
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Camille M. Moore
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Nicholas D. Walter
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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16
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Hervin V, Roy V, Agrofoglio LA. Antibiotics and Antibiotic Resistance-Mur Ligases as an Antibacterial Target. Molecules 2023; 28:8076. [PMID: 38138566 PMCID: PMC10745416 DOI: 10.3390/molecules28248076] [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: 07/29/2023] [Revised: 11/09/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The emergence of Multidrug Resistance (MDR) strains of bacteria has accelerated the search for new antibacterials. The specific bacterial peptidoglycan biosynthetic pathway represents opportunities for the development of novel antibacterial agents. Among the enzymes involved, Mur ligases, described herein, and especially the amide ligases MurC-F are key targets for the discovery of multi-inhibitors, as they share common active sites and structural features.
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Affiliation(s)
| | - Vincent Roy
- ICOA UMR CNRS 7311, Université d’Orléans et CNRS, Rue de Chartres, 45067 Orléans, France;
| | - Luigi A. Agrofoglio
- ICOA UMR CNRS 7311, Université d’Orléans et CNRS, Rue de Chartres, 45067 Orléans, France;
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17
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Verma A, Naik B, Kumar V, Mishra S, Choudhary M, Khan JM, Gupta AK, Pandey P, Rustagi S, Kakati B, Gupta S. Revolutionizing Tuberculosis Treatment: Uncovering New Drugs and Breakthrough Inhibitors to Combat Drug-Resistant Mycobacterium tuberculosis. ACS Infect Dis 2023; 9:2369-2385. [PMID: 37944023 DOI: 10.1021/acsinfecdis.3c00436] [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] [Indexed: 11/12/2023]
Abstract
Tuberculosis (TB) is a global health threat that causes significant mortality. This review explores chemotherapeutics that target essential processes in Mycobacterium tuberculosis, such as DNA replication, protein synthesis, cell wall formation, energy metabolism, and proteolysis. We emphasize the need for new drugs to treat drug-resistant strains and shorten the treatment duration. Emerging targets and promising inhibitors were identified by examining the intricate biology of TB. This review provides an overview of recent developments in the search for anti-TB drugs with a focus on newly validated targets and inhibitors. We aimed to contribute to efforts to combat TB and improve therapeutic outcomes.
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Affiliation(s)
- Ankit Verma
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Bindu Naik
- Department of Food Science and Technology, Graphic Era Deemed to be University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Vijay Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Sadhna Mishra
- Faculty of Agricultural Sciences, GLA University, Mathura 281406, UP, India
| | - Megha Choudhary
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Arun Kumar Gupta
- Department of Food Science and Technology, Graphic Era Deemed to be University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchur 788011, Assam, India
| | - Sarvesh Rustagi
- Department of Food Technology, UCALS, Uttaranchal University, Dehradun 248007, Uttarakhand, India
| | - Barnali Kakati
- Department of Microbiology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, U.K., India
| | - Sanjay Gupta
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
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18
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Panda AP, Pandey SD, Jain D, Ghosh AS. The MSMEG_1586 of M. smegmatis Is a Penicillin-Interactive Enzyme That Can Potentially Hydrolyse Aztreonam and Cephalosporins. Curr Microbiol 2023; 81:26. [PMID: 38041782 DOI: 10.1007/s00284-023-03545-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/30/2023] [Indexed: 12/03/2023]
Abstract
Mycobacteria are intrinsically resistant to beta-lactams as they possess several putative penicillin-interactive enzymes (PIEs), some of those are with dual-activity, namely DD-carboxypeptidase and beta-lactamase. Here, with help of molecular approaches, we elucidated the nature of one such putative PIE, MSMEG_1586, in Mycobacterium smegmatis. The in vivo expression of the membrane-bound form of MSMEG_1586 enhanced the beta-lactam resistance of a beta-lactamase deleted host E. coli strain (AM1OC), particularly for aztreonam (eight-fold) and cephalosporins (8-16 fold). To understand the reason for such elevation of resistance, soluble-form of MSMEG_1586 (sMSMEG_1586) was created by removing signal peptides and partially eliminating the amphipathic helix, and finally, expressed and purified. The purified sMSMEG_1586 was active and manifested a strong penicillin-binding affinity as shown by its ability to bind to fluorescent penicillin (Bocillin-FL). Interestingly, the steady-state kinetics apparently confirmed the hydrolytic ability of sMSMEG_1586 towards cefotaxime and aztreonam where hydrolysing aztreonam is a unique and rare behaviour among the beta-lactamases. However, sMSMEG_1586 was devoid of exerting DD-carboxypeptidase like activity. Finally, in silico analysis of MSMEG_1586 revealed a special folding that resembles class C beta-lactamase, except for the absence of a characteristic R2 loop. Overall, MSMEG_1586 could be categorized as a cephalosporinase with the ability to hydrolyse aztreonam.
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Affiliation(s)
- Aditya Prasad Panda
- Department of Biosciences and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Satya Deo Pandey
- Department of Biosciences and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, 40202, USA
| | - Diamond Jain
- Department of Biosciences and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Anindya S Ghosh
- Department of Biosciences and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
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19
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Liu X, Brčić J, Cassell GH, Cegelski L. CPMAS NMR platform for direct compositional analysis of mycobacterial cell-wall complexes and whole cells. JOURNAL OF MAGNETIC RESONANCE OPEN 2023; 16-17:100127. [PMID: 38125335 PMCID: PMC10732466 DOI: 10.1016/j.jmro.2023.100127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Tuberculosis and non-tuberculosis mycobacterial infections are rising each year and often result in chronic incurable disease. Important antibiotics target cell-wall biosynthesis, yet some mycobacteria are alarmingly resistant or tolerant to currently available antibiotics. This resistance is often attributed to assumed differences in composition of the complex cell wall of different mycobacterial strains and species. However, due to the highly crosslinked and insoluble nature of mycobacterial cell walls, direct comparative determinations of cell-wall composition pose a challenge to analysis through conventional biochemical analyses. We introduce an approach to directly observe the chemical composition of mycobacterial cell walls using solid-state NMR spectroscopy. 13C CPMAS spectra are provided of individual components (peptidoglycan, arabinogalactan, and mycolic acids) and of in situ cell-wall complexes. We assigned the spectroscopic contributions of each component in the cell-wall spectrum. We uncovered a higher arabinogalactan-to-peptidoglycan ratio in the cell wall of M. abscessus, an organism noted for its antibiotic resistance, relative to M. smegmatis. Furthermore, differentiating influences of different types of cell-wall targeting antibiotics were observed in spectra of antibiotic-treated whole cells. This platform will be of value in evaluating cell-wall composition and antibiotic activity among different mycobacteria and in considering the most effective combination treatment regimens.
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Affiliation(s)
- Xinyu Liu
- Department of Chemistry, Stanford University, CA 94305, United States
| | - Jasna Brčić
- Department of Chemistry, Stanford University, CA 94305, United States
| | - Gail H. Cassell
- PAI Life Sciences Inc, Seattle WA 98102, United States
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA 02115, United States
| | - Lynette Cegelski
- Department of Chemistry, Stanford University, CA 94305, United States
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20
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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21
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Li F, Li X, Jiang M, Wang C, Liu G, Yang Z, Wu Y. Research progress into the application of Mycobacterium phlei in veterinary medicine. Vet Med Sci 2023; 9:2617-2624. [PMID: 37723902 PMCID: PMC10650220 DOI: 10.1002/vms3.1262] [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: 04/04/2023] [Revised: 08/21/2023] [Accepted: 09/03/2023] [Indexed: 09/20/2023] Open
Abstract
Mycobacterium phlei is a gram-positive acid-fast mycobacterium from the family Mycobacteriaceae. It is a valuable resource for both natural drugs and microecological preparations. It has been widely used in the field of human medicine; however, in the field of animal husbandry and veterinary medicine, the research and application of M. phlei is still in the preliminary exploration stage. This study aims to summarize the research progress of M. phlei in the field of veterinary medicine and provide a valuable reference for future research. Key words, such as 'M. phlei', 'veterinary field', 'immune balancer', 'genome' and other relevant words to this study, were used to search through PubMed, Web of Science, SciELO, Science Direct and Google Scholar databases. The results showed that the culture conditions of M. phlei were relatively simple, but its bacterial composition and genome sequence were relatively complex, and various components in the cell wall may have immunoregulatory effects. Therefore, the inactivated preparation made from M. phlei can have various applications in the veterinary field, such as growth regulation, immune regulation, antitumour, anti-parasite and asthma treatment. The literature review indicates that M. phlei preparation is an efficient and convenient immune system balance agent. Despite the challenges associated with the use of M. phlei preparations, it has a strong potential for application in veterinary medicine.
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Affiliation(s)
- Fan Li
- College of Veterinary MedicineHunan Agricultural UniversityChangshaHunanChina
| | - Xiang Li
- Hunan Canzoho Biological Technology Co., Ltd.LiuyangHunanChina
| | - Meng‐Lin Jiang
- College of Veterinary MedicineHunan Agricultural UniversityChangshaHunanChina
| | - Chun‐Hua Wang
- College of Veterinary MedicineHunan Agricultural UniversityChangshaHunanChina
| | - Gao‐Feng Liu
- Hunan Canzoho Biological Technology Co., Ltd.LiuyangHunanChina
| | - Zi Yang
- Academician WorkstationChangsha Medical UniversityChangshaHunanChina
| | - Yong Wu
- College of Veterinary MedicineHunan Agricultural UniversityChangshaHunanChina
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22
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Williams JT, Baker JJ, Zheng H, Dechow SJ, Fallon J, Murto M, Albrecht VJ, Gilliland HN, Olive AJ, Abramovitch RB. A genetic selection for Mycobacterium smegmatis mutants tolerant to killing by sodium citrate defines a combined role for cation homeostasis and osmotic stress in cell death. mSphere 2023; 8:e0035823. [PMID: 37681985 PMCID: PMC10597346 DOI: 10.1128/msphere.00358-23] [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: 07/19/2023] [Accepted: 07/23/2023] [Indexed: 09/09/2023] Open
Abstract
Mycobacteria can colonize environments where the availability of metal ions is limited. Biological or inorganic chelators play an important role in limiting metal availability, and we developed a model to examine Mycobacterium smegmatis survival in the presence of the chelator sodium citrate. We observed that instead of restricting M. smegmatis growth, concentrated sodium citrate killed M. smegmatis. RNAseq analysis during sodium citrate treatment revealed transcriptional signatures of metal starvation and hyperosmotic stress. Notably, metal starvation and hyperosmotic stress, individually, do not kill M. smegmatis under these conditions. A forward genetic transposon selection was conducted to examine why sodium citrate was lethal, and several sodium-citrate-tolerant mutants were isolated. Based on the identity of three tolerant mutants, mgtE, treZ, and fadD6, we propose a dual stress model of killing by sodium citrate, where sodium citrate chelate metals from the cell envelope and then osmotic stress in combination with a weakened cell envelope causes cell lysis. This sodium citrate tolerance screen identified mutants in several other genes with no known function, with most conserved in the pathogen M. tuberculosis. Therefore, this model will serve as a basis to define their functions, potentially in maintaining cell wall integrity, cation homeostasis, or osmotolerance. IMPORTANCE Bacteria require mechanisms to adapt to environments with differing metal availability. When Mycobacterium smegmatis is treated with high concentrations of the metal chelator sodium citrate, the bacteria are killed. To define the mechanisms underlying killing by sodium citrate, we conducted a genetic selection and observed tolerance to killing in mutants of the mgtE magnesium transporter. Further characterization studies support a model where killing by sodium citrate is driven by a weakened cell wall and osmotic stress, that in combination cause cell lysis.
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Affiliation(s)
- John T. Williams
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Jacob J. Baker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Huiqing Zheng
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Shelby J. Dechow
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Jared Fallon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Megan Murto
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Veronica J. Albrecht
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Haleigh N. Gilliland
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Andrew J. Olive
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Robert B. Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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23
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Allué-Guardia A, Garcia-Vilanova A, Schami AM, Olmo-Fontánez AM, Hicks A, Peters J, Maselli DJ, Wewers MD, Wang Y, Torrelles JB. Exposure of Mycobacterium tuberculosis to human alveolar lining fluid shows temporal and strain-specific adaptation to the lung environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559381. [PMID: 37808780 PMCID: PMC10557635 DOI: 10.1101/2023.09.27.559381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Upon infection, Mycobacterium tuberculosis ( M.tb ) reaches the alveolar space and comes in close contact with human alveolar lining fluid (ALF) for an uncertain period of time prior to its encounter with alveolar cells. We showed that homeostatic ALF hydrolytic enzymes modify the M.tb cell envelope, driving M.tb -host cell interactions. Still, the contribution of ALF during M.tb infection is poorly understood. Here, we exposed 4 M.tb strains with different levels of virulence, transmissibility, and drug resistance (DR) to physiological concentrations of human ALF for 15-min and 12-h, and performed RNA sequencing. Gene expression analysis showed a temporal and strain-specific adaptation to human ALF. Differential expression (DE) of ALF-exposed vs. unexposed M.tb revealed a total of 397 DE genes associated with lipid metabolism, cell envelope and processes, intermediary metabolism and respiration, and regulatory proteins, among others. Most DE genes were detected at 12-h post-ALF exposure, with DR- M.tb strain W-7642 having the highest number of DE genes. Interestingly, genes from the KstR2 regulon, which controls the degradation of cholesterol C and D rings, were significantly upregulated in all strains post-ALF exposure. These results indicate that M.tb -ALF contact drives initial metabolic and physiologic changes in M.tb , with potential implications in infection outcome. IMPORTANCE Tuberculosis, caused by airborne pathogen Mycobacterium tuberculosis ( M.tb ), is one of the leading causes of mortality worldwide. Upon infection, M.tb reaches the alveoli and gets in contact with human alveolar lining fluid (ALF), where ALF hydrolases modify the M.tb cell envelope driving subsequent M.tb -host cell interactions. Still, the contributions of ALF during infection are poorly understood. We exposed 4 M.tb strains to ALF for 15-min and 12-h and performed RNA sequencing, demonstrating a temporal and strain-specific adaptation of M.tb to ALF. Interestingly, genes associated with cholesterol degradation were highly upregulated in all strains. This study shows for the first time that ALF drives global metabolic changes in M.tb during the initial stages of the infection, with potential implications in disease outcome. Biologically relevant networks and common and strain-specific bacterial determinants derived from this study could be further investigated as potential therapeutic candidates.
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24
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Sachan RK, Mistry V, Dholaria M, Rana A, Devgon I, Ali I, Iqbal J, Eldin SM, Mohammad Said Al-Tawaha AR, Bawazeer S, Dutta J, Karnwal A. Overcoming Mycobacterium tuberculosis Drug Resistance: Novel Medications and Repositioning Strategies. ACS OMEGA 2023; 8:32244-32257. [PMID: 37720746 PMCID: PMC10500578 DOI: 10.1021/acsomega.3c02563] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023]
Abstract
Mycobacterium tuberculosis, the bacterium responsible for tuberculosis, is a global health concern, affecting millions worldwide. This bacterium has earned a reputation as a formidable adversary due to its multidrug-resistant nature, allowing it to withstand many antibiotics. The development of this drug resistance in Mycobacterium tuberculosis is attributed to innate and acquired mechanisms. In the past, rifampin was considered a potent medication for treating tuberculosis infections. However, the rapid development of resistance to this drug by the bacterium underscores the pressing need for new therapeutic agents. Fortunately, several other medications previously overlooked for tuberculosis treatment are already available in the market. Moreover, several innovative drugs are under clinical investigation, offering hope for more effective treatments. To enhance the effectiveness of these drugs, it is recommended that researchers concentrate on identifying unique target sites within the bacterium during the drug development process. This strategy could potentially circumvent the issues presented by Mycobacterium drug resistance. This review primarily focuses on the characteristics of novel drug resistance mechanisms in Mycobacterium tuberculosis. It also discusses potential medications being repositioned or sourced from novel origins. The ultimate objective of this review is to discover efficacious treatments for tuberculosis that can successfully tackle the hurdles posed by Mycobacterium drug resistance.
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Affiliation(s)
| | - Vyoma Mistry
- C.
G. Bhakta Institute of Biotechnology, Uka
Tarsadia University, Bardoli 394350, Surat, India
| | - Mayuri Dholaria
- Naran
Lala College of Professional and Applied Sciences, Navsari 396450, Gujarat, India
| | - Abhishek Rana
- Jindal
Global Law School, OP Jindal Global University, Sonepat 131001, Haryana, India
| | - Inderpal Devgon
- Lovely
Professional University, Phagwara 144411, Punjab, India
| | - Iftikhar Ali
- Center
for Plant Science and Biodiversity, University
of Swat, Charbagh 19120, Pakistan
- Department
of Genetics and Development, Columbia University
Irving Medical Center, New York, New York 10032, United States
| | - Javed Iqbal
- Department
of Botany, Bacha Khan University, Charsadda, 24420 Khyber Pakhtunkhwa, Pakistan
| | - Sayed M. Eldin
- Center
of Research, Faculty of Engineering, Future
University in Egypt, New Cairo 11835, Egypt
| | | | - Sami Bawazeer
- Faculty
of Pharmacy, Department of Pharmacognosy, Umm Al-Qura University, Makkah 4041-4152, Kingdom of Saudi Arabia
| | - Joydeep Dutta
- Lovely
Professional University, Phagwara 144411, Punjab, India
| | - Arun Karnwal
- Lovely
Professional University, Phagwara 144411, Punjab, India
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25
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Shaku MT, Ocius KL, Apostolos AJ, Pires MM, VanNieuwenhze MS, Dhar N, Kana BD. Amidation of glutamate residues in mycobacterial peptidoglycan is essential for cell wall cross-linking. Front Cell Infect Microbiol 2023; 13:1205829. [PMID: 37692163 PMCID: PMC10484409 DOI: 10.3389/fcimb.2023.1205829] [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: 04/14/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023] Open
Abstract
Introduction Mycobacteria assemble a complex cell wall with cross-linked peptidoglycan (PG) which plays an essential role in maintenance of cell wall integrity and tolerance to osmotic pressure. We previously demonstrated that various hydrolytic enzymes are required to remodel PG during essential processes such as cell elongation and septal hydrolysis. Here, we explore the chemistry associated with PG cross-linking, specifically the requirement for amidation of the D-glutamate residue found in PG precursors. Methods Synthetic fluorescent probes were used to assess PG remodelling dynamics in live bacteria. Fluorescence microscopy was used to assess protein localization in live bacteria and CRISPR-interference was used to construct targeted gene knockdown strains. Time-lapse microscopy was used to assess bacterial growth. Western blotting was used to assess protein phosphorylation. Results and discussion In Mycobacterium smegmatis, we confirmed the essentiality for D-glutamate amidation in PG biosynthesis by labelling cells with synthetic fluorescent PG probes carrying amidation modifications. We also used CRISPRi targeted knockdown of genes encoding the MurT-GatD complex, previously implicated in D-glutamate amidation, and demonstrated that these genes are essential for mycobacterial growth. We show that MurT-rseGFP co-localizes with mRFP-GatD at the cell poles and septum, which are the sites of cell wall synthesis in mycobacteria. Furthermore, time-lapse microscopic analysis of MurT-rseGFP localization, in fluorescent D-amino acid (FDAA)-labelled mycobacterial cells during growth, demonstrated co-localization with maturing PG, suggestive of a role for PG amidation during PG remodelling and repair. Depletion of MurT and GatD caused reduced PG cross-linking and increased sensitivity to lysozyme and β-lactam antibiotics. Cell growth inhibition was found to be the result of a shutdown of PG biosynthesis mediated by the serine/threonine protein kinase B (PknB) which senses uncross-linked PG. Collectively, these data demonstrate the essentiality of D-glutamate amidation in mycobacterial PG precursors and highlight the MurT-GatD complex as a novel drug target.
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Affiliation(s)
- Moagi T. Shaku
- DSI/NRF Centre of Excellence for Biomedical Tuberculosis (TB) Research, Faculty of Health Sciences, University of the Witwatersrand, National Health Laboratory Service, Johannesburg, South Africa
| | - Karl L. Ocius
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Alexis J. Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | | | - Neeraj Dhar
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Bavesh D. Kana
- DSI/NRF Centre of Excellence for Biomedical Tuberculosis (TB) Research, Faculty of Health Sciences, University of the Witwatersrand, National Health Laboratory Service, Johannesburg, South Africa
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26
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Ma H, Xing F, Zhou Y, Yu P, Luo R, Xu J, Xiang Z, Rommens PM, Duan X, Ritz U. Design and fabrication of intracellular therapeutic cargo delivery systems based on nanomaterials: current status and future perspectives. J Mater Chem B 2023; 11:7873-7912. [PMID: 37551112 DOI: 10.1039/d3tb01008b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Intracellular cargo delivery, the introduction of small molecules, proteins, and nucleic acids into a specific targeted site in a biological system, is an important strategy for deciphering cell function, directing cell fate, and reprogramming cell behavior. With the advancement of nanotechnology, many researchers use nanoparticles (NPs) to break through biological barriers to achieving efficient targeted delivery in biological systems, bringing a new way to realize efficient targeted drug delivery in biological systems. With a similar size to many biomolecules, NPs possess excellent physical and chemical properties and a certain targeting ability after functional modification on the surface of NPs. Currently, intracellular cargo delivery based on NPs has emerged as an important strategy for genome editing regimens and cell therapy. Although researchers can successfully deliver NPs into biological systems, many of them are delivered very inefficiently and are not specifically targeted. Hence, the development of efficient, target-capable, and safe nanoscale drug delivery systems to deliver therapeutic substances to cells or organs is a major challenge today. In this review, on the basis of describing the research overview and classification of NPs, we focused on the current research status of intracellular cargo delivery based on NPs in biological systems, and discuss the current problems and challenges in the delivery process of NPs in biological systems.
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Affiliation(s)
- Hong Ma
- Department of Orthopedic Surgery, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, China.
| | - Fei Xing
- Department of Orthopedic Surgery, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, China.
| | - Yuxi Zhou
- Department of Periodontology, Justus-Liebig-University of Giessen, Ludwigstraße 23, 35392 Giessen, Germany
| | - Peiyun Yu
- LIMES Institute, Department of Molecular Brain Physiology and Behavior, University of Bonn, Carl-Troll-Str. 31, 53115 Bonn, Germany
| | - Rong Luo
- Department of Orthopedic Surgery, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, China.
| | - Jiawei Xu
- Department of Orthopedic Surgery, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, China.
| | - Zhou Xiang
- Department of Orthopedic Surgery, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, China.
| | - Pol Maria Rommens
- Department of Orthopaedics and Traumatology, Biomatics Group, University Medical Center of the Johannes Gutenberg University, Langenbeckstr. 1, 55131 Mainz, Germany.
| | - Xin Duan
- Department of Orthopedic Surgery, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, China.
- Department of Orthopedic Surgery, The Fifth People's Hospital of Sichuan Province, Chengdu, China
| | - Ulrike Ritz
- Department of Orthopaedics and Traumatology, Biomatics Group, University Medical Center of the Johannes Gutenberg University, Langenbeckstr. 1, 55131 Mainz, Germany.
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27
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Verma A, Kumar V, Naik B, Masood Khan J, Singh P, Erik Joakim Saris P, Gupta S. Screening and molecular dynamics simulation of compounds inhibiting MurB enzyme of drug-resistant Mycobacterium tuberculosis: An in-silico approach. Saudi J Biol Sci 2023; 30:103730. [PMID: 37483837 PMCID: PMC10362793 DOI: 10.1016/j.sjbs.2023.103730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/25/2023] Open
Abstract
Mycobacterium tuberculosis (MTB) is becoming more and more resistant to drugs and it is a common problem, making current antimicrobials ineffective and highlighting the need for new TB drugs. One of the promising targets for treating MTB is MurB enzymes. This study aimed to identify potential inhibitors of MurB enzymes in M. tuberculosis, as drug resistance among MTB is a significant problem. Attempts are being made to conduct a virtual screening of 30,417 compounds, and thirty-two compounds were chosen for further analysis based on their binding conformations. The selected compounds were assessed for their drug-likeness, pharmacokinetics, and physiochemical characteristics, and seven compounds with binding energy lower than flavin (FAD) were identified. Further, molecular dynamics simulation analysis of these seven compounds found that four of them, namely DB12983, DB15688, ZINC084726167, and ZINC254071113 formed stable complexes with the MurB binding site, exhibiting promising inhibitory activity. These compounds have not been mentioned in any other study, indicating their novelty. The study suggests that these four compounds could be promising candidates for treating MTB, but their effectiveness needs to be validated through in vitro and in vivo experiments. Overall, the findings of this study provide new insight into potential drug targets and candidates for combating drug-resistant MTB.
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Affiliation(s)
- Ankit Verma
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India 248140
| | - Vijay Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India 248140
| | - Bindu Naik
- Department of Food Science and Technology, Graphic Era (Deemed to be University), Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Pallavi Singh
- Department of Biotechnology, Graphic Era (Deemed to be University), Bell Road, Clement town, 248002 Dehradun, Uttarakhand, India
| | - Per Erik Joakim Saris
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Finland
| | - Sanjay Gupta
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India 248140
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28
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Nayak T, Kakkar A, Singh RK, Jaiswal LK, Singh AK, Temple L, Gupta A. Isolation and characterization of a novel mycobacteriophage Kashi-VT1 infecting Mycobacterium species. Front Cell Infect Microbiol 2023; 13:1173894. [PMID: 37545854 PMCID: PMC10400892 DOI: 10.3389/fcimb.2023.1173894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Mycobacteriophages are viruses that infect members of genus Mycobacterium. Because of the rise in antibiotic resistance in mycobacterial diseases such as tuberculosis, mycobacteriophages have received renewed attention as alternative therapeutic agents. Mycobacteriophages are highly diverse, and, on the basis of their genome sequences, they are grouped into 30 clusters and 10 singletons. In this article, we have described the isolation and characterization of a novel mycobacteriophage Kashi-VT1 (KVT1) infecting Mycobacterium >smegmatis mc2 155 (M. smegmatis) and Mycobacterium fortuitum isolated from Varanasi, India. KVT1 is a cluster K1 temperate phage that belongs to Siphoviridae family as visualized in transmission electron microscopy. The phage genome is 61,010 base pairs with 66.5% Guanine/Cytosine (GC) content, encoding 101 putative open reading frames. The KVT1 genome encodes an immunity repressor, a tyrosine integrase, and an excise protein, which are the characteristics of temperate phages. It also contains genes encoding holin, lysin A, and lysin B involved in host cell lysis. The one-step growth curve demonstrated that KVT1 has a latency time of 90 min and an average burst size of 101 phage particles per infected cell. It can withstand a temperature of up to 45°C and has a maximum viability between pH 8 and 9. Some mycobacteriophages from cluster K are known to infect the pathogenic Mycobacterium tuberculosis (M. tuberculosis); hence, KVT1 holds potential for the phage therapy against tuberculosis, and it can also be engineered to convert into an exclusively lytic phage.
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Affiliation(s)
- Tanmayee Nayak
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anuja Kakkar
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rakesh Kumar Singh
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Lav Kumar Jaiswal
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anand Kumar Singh
- Interdisciplinary School of Life Sciences, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Louise Temple
- School of Integrated Sciences, James Madison University, Harrisonburg, VA, United States
| | - Ankush Gupta
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
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29
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Mahajan PS, Girigosavi P, Chauware V, Mokashi ND, Nema V. Issues with the current drugs for Mycobacterium tuberculosis cure and potential of cell envelope proteins for new drug discovery. Indian J Tuberc 2023; 70:286-296. [PMID: 37562902 DOI: 10.1016/j.ijtb.2023.03.015] [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: 06/10/2022] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 08/12/2023]
Abstract
Mycobacterium tuberculosis has been the smartest pathogen ever and a challenge to drug development. Its replicative machinery is unique, so targeting the same for killing the pathogen remains a challenge. Our body typically throws out the drugs before they see the bacterium multiply. The pathogen has also learned how to remove drugs from its internal chambers and not allow them to reach their targets. Another strategy for Mtb is the mutation of the targets to reject drug binding and bypass the drug's inhibitory actions. In this review, we tried to explore possible targets on the outer side of the bacterial cell. We have also explored if those targets are promising enough and if there are drugs or inhibitors available. We also discuss the essential proteins and why they remain to be a good target. We concluded that the cell envelope has got a few proteins that can be targeted in isolation or maybe along with other machinery while making the outer environment more conducive for penetration of current drugs or newly proposed drugs.
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Affiliation(s)
- Pratik S Mahajan
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India
| | - Payal Girigosavi
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India
| | - Vijay Chauware
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India
| | - Nitin D Mokashi
- Postgraduate Institute, Yashwantrao Chavan Memorial Hospital, Pune, 411018, India
| | - Vijay Nema
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India.
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30
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Soni V, Rosenn EH, Venkataraman R. Insights into the central role of N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU) in peptidoglycan metabolism and its potential as a therapeutic target. Biochem J 2023; 480:1147-1164. [PMID: 37498748 DOI: 10.1042/bcj20230173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Several decades after the discovery of the first antibiotic (penicillin) microbes have evolved novel mechanisms of resistance; endangering not only our abilities to combat future bacterial pandemics but many other clinical challenges such as acquired infections during surgeries. Antimicrobial resistance (AMR) is attributed to the mismanagement and overuse of these medications and is complicated by a slower rate of the discovery of novel drugs and targets. Bacterial peptidoglycan (PG), a three-dimensional mesh of glycan units, is the foundation of the cell wall that protects bacteria against environmental insults. A significant percentage of drugs target PG, however, these have been rendered ineffective due to growing drug resistance. Identifying novel druggable targets is, therefore, imperative. Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) is one of the key building blocks in PG production, biosynthesized by the bifunctional enzyme N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU). UDP-GlcNAc metabolism has been studied in many organisms, but it holds some distinctive features in bacteria, especially regarding the bacterial GlmU enzyme. In this review, we provide an overview of different steps in PG biogenesis, discuss the biochemistry of GlmU, and summarize the characteristic structural elements of bacterial GlmU vital to its catalytic function. Finally, we will discuss various studies on the development of GlmU inhibitors and their significance in aiding future drug discoveries.
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Affiliation(s)
- Vijay Soni
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
| | - Eric H Rosenn
- Tel Aviv University School of Medicine, Tel Aviv 6997801, Israel
| | - Ramya Venkataraman
- Laboratory of Innate Immunity, National Institute of Immunology, New Delhi 110067, India
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Irfan A, Faisal S, Zahoor AF, Noreen R, Al-Hussain SA, Tuzun B, Javaid R, Elhenawy AA, Zaki MEA, Ahmad S, Abdellattif MH. In Silico Development of Novel Benzofuran-1,3,4-Oxadiazoles as Lead Inhibitors of M. tuberculosis Polyketide Synthase 13. Pharmaceuticals (Basel) 2023; 16:829. [PMID: 37375776 DOI: 10.3390/ph16060829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Benzofuran and 1,3,4-oxadiazole are privileged and versatile heterocyclic pharmacophores which display a broad spectrum of biological and pharmacological therapeutic potential against a wide variety of diseases. This article reports in silico CADD (computer-aided drug design) and molecular hybridization approaches for the evaluation of the chemotherapeutic efficacy of 16 S-linked N-phenyl acetamide moiety containing benzofuran-1,3,4-oxadiazole scaffolds BF1-BF16. This virtual screening was carried out to discover and assess the chemotherapeutic efficacy of BF1-BF16 structural motifs as Mycobacterium tuberculosis polyketide synthase 13 (Mtb Pks13) enzyme inhibitors. The CADD study results revealed that the benzofuran clubbed oxadiazole derivatives BF3, BF4, and BF8 showed excellent and remarkably significant binding energies against the Mtb Pks13 enzyme comparable with the standard benzofuran-based TAM-16 inhibitor. The best binding affinity scores were displayed by 1,3,4-oxadiazoles-based benzofuran scaffolds BF3 (-14.23 kcal/mol), BF4 (-14.82 kcal/mol), and BF8 (-14.11 kcal/mol), in comparison to the binding affinity score of the standard reference TAM-16 drug (-14.61 kcal/mol). 2,5-Dimethoxy moiety-based bromobenzofuran-oxadiazole derivative BF4 demonstrated the highest binding affinity score amongst the screened compounds, and was higher than the reference Pks13 inhibitor TAM-16 drug. The bindings of these three leads BF3, BF4, and BF8 were further confirmed by the MM-PBSA investigations in which they also exhibited strong bindings with the Pks13 of Mtb. Moreover, the stability analysis of these benzofuran-1,3,4-oxadiazoles in the active sites of the Pks13 enzyme was achieved through molecular dynamic (MD) simulations at 250 ns virtual simulation time, which indicated that these three in silico predicted bio-potent benzofuran tethered oxadiazole molecules BF3, BF4, and BF8 demonstrated stability with the active site of the Pks13 enzyme.
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Affiliation(s)
- Ali Irfan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Razia Noreen
- Department of Biochemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Sami A Al-Hussain
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13623, Saudi Arabia
| | - Burak Tuzun
- Plant and Animal Production Department, Technical Sciences Vocational School of Sivas, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Rakshanda Javaid
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Ahmed A Elhenawy
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
- Chemistry Department, Faculty of Science and Art, AlBaha University, Mukhwah, Al Bahah 65731, Saudi Arabia
| | - Magdi E A Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13623, Saudi Arabia
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Magda H Abdellattif
- Department of Chemistry, College of Science, Taif University, Taif 21944, Saudi Arabia
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Sreelatha S, Nagarajan U, Natarajan S. Protein targets in Mycobacterium tuberculosis and their inhibitors for therapeutic implications: A narrative review. Int J Biol Macromol 2023:125022. [PMID: 37244342 DOI: 10.1016/j.ijbiomac.2023.125022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
Advancement in the area of anti-tubercular drug development has been full-fledged, yet, a very less number of drug molecules have reached phase II clinical trials, and therefore "End-TB" is still a global challenge. Inhibitors to specific metabolic pathways of Mycobacterium tuberculosis (Mtb) gain importance in strategizing anti-tuberculosis drug discovery. The lead compounds that target DNA replication, protein synthesis, cell wall biosynthesis, bacterial virulence and energy metabolism are emerging as potential chemotherapeutic options against Mtb growth and survival within the host. In recent times, the in silico approaches have become most promising tools in the identification of suitable inhibitors for specific protein targets of Mtb. An update in the fundamental understanding of these inhibitors and the mechanism of interaction may bring hope to future perspectives in novel drug development and delivery approaches. This review provides a collective impression of the small molecules with potential antimycobacterial activities and their target pathways in Mtb such as cell wall biosynthesis, DNA replication, transcription and translation, efflux pumps, antivirulence pathways and general metabolism. The mechanism of interaction of specific inhibitor with their respective protein targets has been discussed. The comprehensive knowledge of such an impactful area of research would essentially reflect in the discovery of novel drug molecules and effective delivery approaches. This narrative review encompasses the knowledge of emerging targets and promising n that could potentially translate in to the anti-TB-drug discovery.
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Affiliation(s)
- Souparnika Sreelatha
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India
| | - Usharani Nagarajan
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India
| | - Saravanan Natarajan
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India.
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Jacobo-Delgado YM, Rodríguez-Carlos A, Serrano CJ, Rivas-Santiago B. Mycobacterium tuberculosis cell-wall and antimicrobial peptides: a mission impossible? Front Immunol 2023; 14:1194923. [PMID: 37266428 PMCID: PMC10230078 DOI: 10.3389/fimmu.2023.1194923] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 06/03/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is one of the most important infectious agents worldwide and causes more than 1.5 million deaths annually. To make matters worse, the drug resistance among Mtb strains has risen substantially in the last few decades. Nowadays, it is not uncommon to find patients infected with Mtb strains that are virtually resistant to all antibiotics, which has led to the urgent search for new molecules and therapies. Over previous decades, several studies have demonstrated the efficiency of antimicrobial peptides to eliminate even multidrug-resistant bacteria, making them outstanding candidates to counterattack this growing health problem. Nevertheless, the complexity of the Mtb cell wall makes us wonder whether antimicrobial peptides can effectively kill this persistent Mycobacterium. In the present review, we explore the complexity of the Mtb cell wall and analyze the effectiveness of antimicrobial peptides to eliminate the bacilli.
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Kristensen SS, Diep DB, Kjos M, Mathiesen G. The role of site-2-proteases in bacteria: a review on physiology, virulence, and therapeutic potential. MICROLIFE 2023; 4:uqad025. [PMID: 37223736 PMCID: PMC10202637 DOI: 10.1093/femsml/uqad025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/25/2023]
Abstract
Site-2-proteases are a class of intramembrane proteases involved in regulated intramembrane proteolysis. Regulated intramembrane proteolysis is a highly conserved signaling mechanism that commonly involves sequential digestion of an anti-sigma factor by a site-1- and site-2-protease in response to external stimuli, resulting in an adaptive transcriptional response. Variation of this signaling cascade continues to emerge as the role of site-2-proteases in bacteria continues to be explored. Site-2-proteases are highly conserved among bacteria and play a key role in multiple processes, including iron uptake, stress response, and pheromone production. Additionally, an increasing number of site-2-proteases have been found to play a pivotal role in the virulence properties of multiple human pathogens, such as alginate production in Pseudomonas aeruginosa, toxin production in Vibrio cholerae, resistance to lysozyme in enterococci and antimicrobials in several Bacillus spp, and cell-envelope lipid composition in Mycobacterium tuberculosis. The prominent role of site-2-proteases in bacterial pathogenicity highlights the potential of site-2-proteases as novel targets for therapeutic intervention. In this review, we summarize the role of site-2-proteases in bacterial physiology and virulence, as well as evaluate the therapeutic potential of site-2-proteases.
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Affiliation(s)
- Sofie S Kristensen
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), 1433 Ås, Norway
| | | | - Morten Kjos
- Corresponding author. NMBU, P.O. Box 5003, 1433 Ås, Norway. E-mail:
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Shaku MT, Um P, Ocius KL, Apostolos AJ, Pires MM, Bishai WR, Kana BD. A modified BCG with depletion of enzymes associated with peptidoglycan amidation induces enhanced protection against tuberculosis in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539199. [PMID: 37205421 PMCID: PMC10187164 DOI: 10.1101/2023.05.03.539199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mechanisms by which Mycobacterium tuberculosis (Mtb) evades pathogen recognition receptor activation during infection may offer insights for the development of improved tuberculosis (TB) vaccines. Whilst Mtb elicits NOD-2 activation through host recognition of its peptidoglycan-derived muramyl dipeptide (MDP), it masks the endogenous NOD-1 ligand through amidation of glutamate at the second position in peptidoglycan sidechains. As the current BCG vaccine is derived from pathogenic mycobacteria, a similar situation prevails. To alleviate this masking ability and to potentially improve efficacy of the BCG vaccine, we used CRISPRi to inhibit expression of the essential enzyme pair, MurT-GatD, implicated in amidation of peptidoglycan sidechains. We demonstrate that depletion of these enzymes results in reduced growth, cell wall defects, increased susceptibility to antibiotics and altered spatial localization of new peptidoglycan. In cell culture experiments, training of monocytes with this recombinant BCG yielded improved control of Mtb growth. In the murine model of TB infection, we demonstrate that depletion of MurT-GatD in BCG, resulting in unmasking of the D-glutamate diaminopimelate (iE-DAP) NOD-1 ligand, yields superior prevention of TB disease compared to the standard BCG vaccine. This work demonstrates the feasibility of gene regulation platforms such as CRISPRi to alter antigen presentation in BCG in a bespoke manner that tunes immunity towards more effective protection against TB disease.
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Gong Y, Wang J, Li F, Zhu B. Polysaccharides and glycolipids of Mycobacterium tuberculosis and their induced immune responses. Scand J Immunol 2023; 97:e13261. [PMID: 39008002 DOI: 10.1111/sji.13261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 02/05/2023] [Accepted: 02/16/2023] [Indexed: 07/16/2024]
Abstract
Tuberculosis (TB) is a chronic infectious disease mainly caused by Mycobacterium tuberculosis (M. tuberculosis). The structures of polysaccharides and glycolipids at M. tuberculosis cell wall vary among different strains, which affect the physiology and pathogenesis of mycobacteria by activating or inhibiting innate and acquired immunity. Among them, some components such as lipomannan (LM) and lipoarabinomannan (LAM) activate innate immunity by recognizing some kinds of pattern recognition receptors (PRRs) like Toll-like receptors, while other components like mannose-capped lipoarabinomannan (ManLAM) could prevent innate immune responses by inhibiting the secretion of pro-inflammatory cytokines and maturation of phagosomes. In addition, many glycolipids can activate natural killer T (NKT) cells and CD1-restricted T cells to produce interferon-γ (IFN-γ). Furthermore, humoral immunity against cell wall components, such as antibodies against LAM, plays a role in immunity against M. tuberculosis infection. Cell wall polysaccharides and glycolipids of M. tuberculosis have potential applications as antigens and adjuvants for novel TB subunit vaccines.
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Affiliation(s)
- Yang Gong
- Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation & Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Juan Wang
- Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation & Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Fei Li
- Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation & Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Bingdong Zhu
- Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation & Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou, China
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Silveiro C, Marques M, Olivença F, Pires D, Mortinho D, Nunes A, Pimentel M, Anes E, Catalão MJ. CRISPRi-mediated characterization of novel anti-tuberculosis targets: Mycobacterial peptidoglycan modifications promote beta-lactam resistance and intracellular survival. Front Cell Infect Microbiol 2023; 13:1089911. [PMID: 37009497 PMCID: PMC10050696 DOI: 10.3389/fcimb.2023.1089911] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/03/2023] [Indexed: 03/17/2023] Open
Abstract
The lack of effective therapeutics against emerging multi-drug resistant strains of Mycobacterium tuberculosis (Mtb) prompts the identification of novel anti-tuberculosis targets. The essential nature of the peptidoglycan (PG) layer of the mycobacterial cell wall, which features several distinctive modifications, such as the N-glycolylation of muramic acid and the amidation of D-iso-glutamate, makes it a target of particular interest. To understand their role in susceptibility to beta-lactams and in the modulation of host-pathogen interactions, the genes encoding the enzymes responsible for these PG modifications (namH and murT/gatD, respectively) were silenced in the model organism Mycobacterium smegmatis using CRISPR interference (CRISPRi). Although beta-lactams are not included in TB-therapy, their combination with beta-lactamase inhibitors is a prospective strategy to treat MDR-TB. To uncover synergistic effects between the action of beta-lactams and the depletion of these PG modifications, knockdown mutants were also constructed in strains lacking the major beta-lactamase of M. smegmatis BlaS, PM965 (M. smegmatis ΔblaS1) and PM979 (M. smegmatis ΔblaS1 ΔnamH). The phenotyping assays affirmed the essentiality of the amidation of D-iso-glutamate to the survival of mycobacteria, as opposed to the N-glycolylation of muramic acid. The qRT-PCR assays confirmed the successful repression of the target genes, along with few polar effects and differential knockdown level depending on PAM strength and target site. Both PG modifications were found to contribute to beta-lactam resistance. While the amidation of D-iso-glutamate impacted cefotaxime and isoniazid resistance, the N-glycolylation of muramic acid substantially promoted resistance to the tested beta-lactams. Their simultaneous depletion provoked synergistic reductions in beta-lactam MICs. Moreover, the depletion of these PG modifications promoted a significantly faster bacilli killing by J774 macrophages. Whole-genome sequencing revealed that these PG modifications are highly conserved in a set of 172 clinical strains of Mtb, demonstrating their potential as therapeutic targets against TB. Our results support the development of new therapeutic agents targeting these distinctive mycobacterial PG modifications.
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Affiliation(s)
- Cátia Silveiro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Mariana Marques
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Francisco Olivença
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - David Pires
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
- Universidade Católica Portuguesa, Católica Medical School, Centre for Interdisciplinary Research in Health, Lisbon, Portugal
| | - Diana Mortinho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Alexandra Nunes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
- Faculty of Veterinary Medicine, Universidade Lusófona, Lisbon, Portugal
| | - Madalena Pimentel
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Elsa Anes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Maria João Catalão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
- *Correspondence: Maria João Catalão,
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Wynn EA, Dide-Agossou C, Reichlen M, Rossmassler K, Al Mubarak R, Reid JJ, Tabor ST, Born SEM, Ransom MR, Davidson RM, Walton KN, Benoit JB, Hoppers A, Bauman AA, Massoudi LM, Dolganov G, Nahid P, Voskuil MI, Robertson GT, Moore CM, Walter ND. Transcriptional adaptation of drug-tolerant Mycobacterium tuberculosis in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531356. [PMID: 36945388 PMCID: PMC10028792 DOI: 10.1101/2023.03.06.531356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Transcriptome evaluation of Mycobacterium tuberculosis in the lungs of laboratory animals during long-term treatment has been limited by extremely low abundance of bacterial mRNA relative to eukaryotic RNA. Here we report a targeted amplification RNA sequencing method called SEARCH-TB. After confirming that SEARCH-TB recapitulates conventional RNA-seq in vitro, we applied SEARCH-TB to Mycobacterium tuberculosis-infected BALB/c mice treated for up to 28 days with the global standard isoniazid, rifampin, pyrazinamide, and ethambutol regimen. We compared results in mice with 8-day exposure to the same regimen in vitro. After treatment of mice for 28 days, SEARCH-TB suggested broad suppression of genes associated with bacterial growth, transcription, translation, synthesis of rRNA proteins and immunogenic secretory peptides. Adaptation of drug-stressed Mycobacterium tuberculosis appeared to include a metabolic transition from ATP-maximizing respiration towards lower-efficiency pathways, modification and recycling of cell wall components, large-scale regulatory reprogramming, and reconfiguration of efflux pumps expression. Despite markedly different expression at pre-treatment baseline, murine and in vitro samples had broadly similar transcriptional change during treatment. The differences observed likely indicate the importance of immunity and pharmacokinetics in the mouse. By elucidating the long-term effect of tuberculosis treatment on bacterial cellular processes in vivo, SEARCH-TB represents a highly granular pharmacodynamic monitoring tool with potential to enhance evaluation of new regimens and thereby accelerate progress towards a new generation of more effective tuberculosis treatment.
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Affiliation(s)
- Elizabeth A Wynn
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Department of Biostatistics and Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
| | - Christian Dide-Agossou
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew Reichlen
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Karen Rossmassler
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Reem Al Mubarak
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Justin J Reid
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Samuel T Tabor
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sarah E M Born
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Monica R Ransom
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Rebecca M Davidson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Kendra N Walton
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Jeanne B Benoit
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Amanda Hoppers
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Allison A Bauman
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Lisa M Massoudi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Gregory Dolganov
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Palo Alto, CA, USA
| | - Payam Nahid
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, CA, USA
- UCSF Center for Tuberculosis, University of California, San Francisco, CA, USA
| | - Martin I Voskuil
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Gregory T Robertson
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Camille M Moore
- Department of Biostatistics and Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Nicholas D Walter
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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G K, Vasudevan K, Dey H, Kausar T, Udhaya Kumar S, Thirumal Kumar D, Zayed H, George Priya Doss C. Elucidating the mechanism of antimicrobial resistance in Mycobacterium tuberculosis using gene interaction networks. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 134:53-74. [PMID: 36858742 DOI: 10.1016/bs.apcsb.2022.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antimicrobial resistance (AMR) in microorganisms is an urgent global health threat. AMR of Mycobacterium tuberculosis is associated with significant morbidity and mortality. It is of great importance to underpin the resistance pathways involved in the mechanisms of AMR and identify the genes that are directly involved in AMR. The focus of the current study was the bacteria M. tuberculosis, which carries AMR genes that give resistance that lead to multidrug resistance. We, therefore, built a network of 43 genes and examined for potential gene-gene interactions. Then we performed a clustering analysis and identified three closely related clusters that could be involved in multidrug resistance mechanisms. Through the bioinformatics pipeline, we consistently identified six-hub genes (dnaN, polA, ftsZ, alr, ftsQ, and murC) that demonstrated the highest number of interactions within the clustering analysis. This study sheds light on the multidrug resistance of MTB and provides a protocol for discovering genes that might be involved in multidrug resistance, which will improve the treatment of resistant strains of TB.
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Affiliation(s)
- Keerthana G
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, India; Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India; Faculty of Allied Health Sciences, Meenakshi Academy of Higher Education and Research (Deemed to be University), Chennai, India; Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, India.
| | - Hrituraj Dey
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, India
| | - Tasmia Kausar
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - D Thirumal Kumar
- Faculty of Allied Health Sciences, Meenakshi Academy of Higher Education and Research (Deemed to be University), Chennai, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
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Qu M, Liang Z, Chen Y, Wang Y, Wang H, Liu Z, Liu Y, Dong Y, Ge X, Li H, Zhou X. Antibodies Targeting the Cell Wall Induce Protection against Virulent Mycobacterium bovis Infection. Microbiol Spectr 2023; 11:e0343122. [PMID: 36847491 PMCID: PMC10100962 DOI: 10.1128/spectrum.03431-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/11/2022] [Indexed: 03/01/2023] Open
Abstract
Accumulating evidence indicates that antibodies can protect against some intracellular pathogens. Mycobacterium bovis is an intracellular bacterium, and its cell wall (CW) is essential for its virulence and survival. However, the questions of whether antibodies play a protective role in immunity against M. bovis infection and what effects antibodies specific to the CW of M. bovis have still remain unclear. Here, we report that antibodies targeting the CW of an isolated pathogenic M. bovis strain and that of an attenuated bacillus Calmette-Guérin (BCG) strain could induce protection against virulent M. bovis infection in vitro and in vivo. Further research found that the antibody-induced protection was mainly achieved by promoting Fc gamma receptor (FcγR)-mediated phagocytosis, inhibiting bacterial intracellular growth, and enhancing the fusion of phagosomes and lysosomes, and it also depended on T cells for its efficacy. Additionally, we analyzed and characterized the B-cell receptor (BCR) repertoires of CW-immunized mice via next-generation sequencing. CW immunization stimulated BCR changes in the complementarity determining region 3 (CDR3) isotype distribution, gene usage, and somatic hypermutation. Overall, our study validates the idea that antibodies targeting the CW induce protection against virulent M. bovis infection. This study highlights the importance of antibodies targeting the CW in the defense against tuberculosis. IMPORTANCE M. bovis is the causative agent of animal tuberculosis (TB) and human TB. Research on M. bovis is of great public health significance. Currently, TB vaccines are mainly aimed at eliciting protection by enhancement of cell-mediated immunity, and there are few studies on protective antibodies. This is the first report of protective antibodies against M. bovis infection, and the antibodies had both preventive and even therapeutic effects in an M. bovis infection mouse model. Additionally, we reveal the relationship between CDR3 gene diversity and the immune characteristics of the antibodies. These results will provide valuable advice for the rational development of TB vaccines.
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Affiliation(s)
- Mengjin Qu
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhengmin Liang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yulan Chen
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yuanzhi Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Haoran Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ziyi Liu
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yiduo Liu
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yuhui Dong
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xin Ge
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hao Li
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiangmei Zhou
- College of Veterinary Medicine, China Agricultural University, Beijing, China
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Kaur K, Sharma S, Abhishek S, Kaur P, Saini UC, Dhillon MS, Karakousis PC, Verma I. Metabolic switching and cell wall remodelling of Mycobacterium tuberculosis during bone tuberculosis. J Infect 2023; 86:134-146. [PMID: 36549425 DOI: 10.1016/j.jinf.2022.12.014] [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: 04/13/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Bone tuberculosis (TB) is the third most common types of extrapulmonary tuberculosis. It is critical to understand mycobacterial adaptive strategies within bone lesions to identify mycobacterial factors that may have role in disease pathogenesis. METHODS Whole genome microarray was used to characterize the in-vivo transcriptome of Mycobacterium tuberculosis (M.tb) within bone TB specimens. Mycobacterial virulent proteins were identified by bioinformatic software. An in vitro osteoblast cell line model was used to study the role of these proteins in bone TB pathogenesis. RESULTS 914 mycobacterial genes were significantly overexpressed and 1688 were repressed in bone TB specimens. Pathway analysis of differentially expressed genes demonstrated a non-replicative and hypometabolic state of M.tb, reinforcement of the mycobacterial cell wall and induction of DNA damage repair responses, suggesting possible survival strategies of M.tb within bone. Bioinformatics mining of microarray data led to identification of five virulence proteins. The genes encoding these proteins were also upregulated in the in vitro MC3T3 osteoblast cell line model of bone TB. Further, exposure of osteoblast cells to two of these virulence proteins (Rv1046c and Rv3663c) significantly inhibited osteoblast differentiation. CONCLUSION M.tb alters its transcriptome to establish infection in bone by upregulating certain virulence genes which play a key role in disturbing bone homeostasis.
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Affiliation(s)
- Khushpreet Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sumedha Sharma
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sudhanshu Abhishek
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Prabhdeep Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Uttam Chand Saini
- Department of Orthopaedics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Mandeep Singh Dhillon
- Department of Orthopaedics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Petros C Karakousis
- Centers for Tuberculosis Research and Systems Approaches for Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Indu Verma
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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Kumari M, Singh R, Subbarao N. Exploring the interaction mechanism between potential inhibitor and multi-target Mur enzymes of mycobacterium tuberculosis using molecular docking, molecular dynamics simulation, principal component analysis, free energy landscape, dynamic cross-correlation matrices, vector movements, and binding free energy calculation. J Biomol Struct Dyn 2022; 40:13497-13526. [PMID: 34662260 DOI: 10.1080/07391102.2021.1989040] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Multi-targeting enzyme approaches are considered to be the most significant in suppressing pathogen growth and disease control for MDR and XDR-resistant Mycobacterium tuberculosis. The multiple Mur enzymes involved in peptidoglycan biosynthesis play a key role in a cell's growth. Firstly, homology modeling was employed to construct the 3 D structure of the Mur enzymes. The computational approaches, including molecular docking and molecular dynamics simulations and MM-PBSA methods, were performed to explore the detailed interaction mechanism to evaluate the inhibitory activity against targeted proteins. The computational calculations revealed that the best-docked phytochemical compound (gallomyricitrin) inhibits the selected targets: Mur enzymes by forming stable hydrogen bonds. The analysis of RMSD, RMSF, Rg, PCA, DCCM, cross-correlation network, FEL, H-bond, and vector movement reveal that the docked complex of MurA, MurI, MurG, MurC, and MurE is more stable compared to MurB, MurF, MurD, and MurX docked complexes during MD simulations. Moreover, FEL exposed that gallomyricitrin stabilized to the minimum global energy of Mur Enzymes. The PCA, DCCM, and vector movements and binding free energy results provided further evidence for the stability of gallomyricitrin's interactions inside the binding sites by forming hydrogen bonds. The cross-correlation analysis reveals that Mur enzymes exhibit a positive and negative correlated motion between residues in different protein domains. The computational results contribute in several ways to our understanding of inhibition activity and provide a basic insight into the binding activity of gallomyricitrin as a multi-target drug for tuberculosis. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhulata Kumari
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ruhar Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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43
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Zeynali kelishomi F, Khanjani S, Fardsanei F, Saghi Sarabi H, Nikkhahi F, Dehghani B. Bacteriophages of Mycobacterium tuberculosis, their diversity, and potential therapeutic uses: a review. BMC Infect Dis 2022; 22:957. [PMID: 36550444 PMCID: PMC9773572 DOI: 10.1186/s12879-022-07944-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tuberculosis) is a highly infectious disease and worldwide health problem. Based on the WHO TB report, 9 million active TB cases are emerging, leading to 2 million deaths each year. The recent emergence of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) strains emphasizes the necessity to improve novel therapeutic plans. Among the various developing antibacterial approaches, phage therapy is thought to be a precise hopeful resolution. Mycobacteriophages are viruses that infect bacteria such as Mycobacterium spp., containing the M. tuberculosis complex. Phages and phage-derived proteins can act as promising antimicrobial agents. Also, phage cocktails can broaden the spectrum of lysis activity against bacteria. Recent researches have also shown the effective combination of antibiotics and phages to defeat the infective bacteria. There are limitations and concerns about phage therapy. For example, human immune response to phage therapy, transferring antibiotic resistance genes, emerging resistance to phages, and safety issues. So, in the present study, we introduced mycobacteriophages, their use as therapeutic agents, and their advantages and limitations as therapeutic applications.
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Affiliation(s)
- Fatemeh Zeynali kelishomi
- grid.412606.70000 0004 0405 433XMedical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Susan Khanjani
- grid.412606.70000 0004 0405 433XMedical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Fatemeh Fardsanei
- grid.412606.70000 0004 0405 433XMedical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Hediyeh Saghi Sarabi
- grid.412606.70000 0004 0405 433XMedical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Farhad Nikkhahi
- grid.412606.70000 0004 0405 433XMedical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Behzad Dehghani
- grid.412571.40000 0000 8819 4698Department of Bacteriology-Virology, Shiraz University of Medical Sciences, Shiraz, Iran
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Eshraghisamani R, Mirto AJ, Wang J, Behr MA, Barkema HW, De Buck J. Identification of essential genes in Mycobacterium avium subsp. paratuberculosis genome for persistence in dairy calves. Front Microbiol 2022; 13:994421. [PMID: 36338087 PMCID: PMC9631821 DOI: 10.3389/fmicb.2022.994421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/05/2022] [Indexed: 11/02/2023] Open
Abstract
To cause disease Mycobacterium avium subsp. paratuberculosis needs to enter mammalian cells, arrest phagosomal maturation and manipulate the host immune system. The genetic basis of the bacterial capacity to achieve these outcomes remains largely unknown. Identifying these genes would allow us to gain a deeper understanding of MAP's pathogenesis and potentially develop a live attenuated Johne's disease vaccine by knocking out these genes. MAP genes demonstrated to be essential for colonization in the natural host, ruminants, are unknown. Genome-wide transposon mutagenesis and high-throughput sequencing were combined to evaluate the essentiality of each coding region in the bacterial genome to survive in dairy calves. A saturated library of 3,852 MAP Tn mutants, with insertions in 56% of TA sites, interrupting 88% of genes, was created using a MycoMarT7 phagemid containing a mariner transposon. Six calves were inoculated with a high dose of a library of MAP mutants, 1011 CFUs, (input) at 2 weeks of age. Following 2 months of incubation, MAP cells were isolated from the ileum, jejunum, and their associated lymph nodes of calves, resulting in approximately 100,000 colonies grown on solid media across 6 animals (output). Targeted next-generation sequencing was used to identify the disrupted genes in all the mutants in the input pool and the output pool recovered from the tissues to identify in vivo essential genes. Statistical analysis for the determination of essential genes was performed by a Hidden Markov Model (HMM), categorizing genes into essential genes that are devoid of insertions and growth-defect genes whose disruption impairs the growth of the organism. Sequence analysis identified 430 in vivo essential and 260 in vivo growth-defect genes. Gene ontology enrichment analysis of the in vivo essential and growth-defect genes with the highest reduction in the tissues revealed a high representation of genes involved in metabolism and respiration, cell wall and cell processing, virulence, and information pathway processes. This study has systematically identified essential genes for the growth and persistence of MAP in the natural host body.
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Affiliation(s)
- Razieh Eshraghisamani
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Amanda J. Mirto
- Environmental Health and Safety, University of Wisconsin-Madison, Madison, WI, United States
| | - Joyce Wang
- Department of Medicine, Faculty of Medicine, Health Centre, McGill University, Montréal, QC, Canada
| | - Marcel A. Behr
- Department of Medicine, Faculty of Medicine, Health Centre, McGill University, Montréal, QC, Canada
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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45
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Iron–Sulfur Clusters toward Stresses: Implication for Understanding and Fighting Tuberculosis. INORGANICS 2022. [DOI: 10.3390/inorganics10100174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) remains the leading cause of death due to a single pathogen, accounting for 1.5 million deaths annually on the global level. Mycobacterium tuberculosis, the causative agent of TB, is persistently exposed to stresses such as reactive oxygen species (ROS), reactive nitrogen species (RNS), acidic conditions, starvation, and hypoxic conditions, all contributing toward inhibiting bacterial proliferation and survival. Iron–sulfur (Fe-S) clusters, which are among the most ancient protein prosthetic groups, are good targets for ROS and RNS, and are susceptible to Fe starvation. Mtb holds Fe-S containing proteins involved in essential biological process for Mtb. Fe-S cluster assembly is achieved via complex protein machineries. Many organisms contain several Fe-S assembly systems, while the SUF system is the only one in some pathogens such as Mtb. The essentiality of the SUF machinery and its functionality under the stress conditions encountered by Mtb underlines how it constitutes an attractive target for the development of novel anti-TB.
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46
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Fathiah Mohamed Zuki, Pourzolfaghar H, Edyvean RGJ, Hernandez JE. Interpretation of Initial Adhesion of Pseudomonas putida on Hematite and Quartz Using Surface Thermodynamics, DLVO, and XDLVO Theories. SURFACE ENGINEERING AND APPLIED ELECTROCHEMISTRY 2022. [DOI: 10.3103/s1068375522050131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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47
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Boopathi S, Ramasamy S, Haridevamuthu B, Murugan R, Veerabadhran M, Jia AQ, Arockiaraj J. Intercellular communication and social behaviors in mycobacteria. Front Microbiol 2022; 13:943278. [PMID: 36177463 PMCID: PMC9514802 DOI: 10.3389/fmicb.2022.943278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-to-cell communication is a fundamental process of bacteria to exert communal behaviors. Sputum samples of patients with cystic fibrosis have often been observed with extensive mycobacterial genetic diversity. The emergence of heterogenic mycobacterial populations is observed due to subtle changes in their morphology, gene expression level, and distributive conjugal transfer (DCT). Since each subgroup of mycobacteria has different hetero-resistance, they are refractory against several antibiotics. Such genetically diverse mycobacteria have to communicate with each other to subvert the host immune system. However, it is still a mystery how such heterogeneous strains exhibit synchronous behaviors for the production of quorum sensing (QS) traits, such as biofilms, siderophores, and virulence proteins. Mycobacteria are characterized by division of labor, where distinct sub-clonal populations contribute to the production of QS traits while exchanging complimentary products at the community level. Thus, active mycobacterial cells ensure the persistence of other heterogenic clonal populations through cooperative behaviors. Additionally, mycobacteria are likely to establish communication with neighboring cells in a contact-independent manner through QS signals. Hence, this review is intended to discuss our current knowledge of mycobacterial communication. Understanding mycobacterial communication could provide a promising opportunity to develop drugs to target key pathways of mycobacteria.
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Affiliation(s)
- Seenivasan Boopathi
- Key Laboratory of Tropical Biological Resources of Ministry Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Subbiah Ramasamy
- Department of Biochemistry, Cardiac Metabolic Disease Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - B. Haridevamuthu
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Raghul Murugan
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Maruthanayagam Veerabadhran
- Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, Tamil Nadu, India
| | - Ai-Qun Jia
- Key Laboratory of Tropical Biological Resources of Ministry Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- *Correspondence: Ai-Qun Jia
| | - Jesu Arockiaraj
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
- Jesu Arockiaraj ;
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48
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Thomson M, Liu Y, Nunta K, Cheyne A, Fernandes N, Williams R, Garza-Garcia A, Larrouy-Maumus G. Expression of a novel mycobacterial phosphodiesterase successfully lowers cAMP levels resulting in reduced tolerance to cell wall-targeting antimicrobials. J Biol Chem 2022; 298:102151. [PMID: 35718063 PMCID: PMC9293780 DOI: 10.1016/j.jbc.2022.102151] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 02/09/2023] Open
Abstract
cAMP and antimicrobial susceptibility in mycobacteriaAntimicrobial tolerance, the ability to survive exposure to antimicrobials via transient nonspecific means, promotes the development of antimicrobial resistance (AMR). The study of the molecular mechanisms that result in antimicrobial tolerance is therefore essential for the understanding of AMR. In gram-negative bacteria, the second messenger molecule 3'',5''-cAMP has been previously shown to be involved in AMR. In mycobacteria, however, the role of cAMP in antimicrobial tolerance has been difficult to probe due to its particular complexity. In order to address this difficulty, here, through unbiased biochemical approaches consisting in the fractionation of clear protein lysate from a mycobacterial strain deleted for the known cAMP phosphodiesterase (Rv0805c) combined with mass spectrometry techniques, we identified a novel cyclic nucleotide-degrading phosphodiesterase enzyme (Rv1339) and developed a system to significantly decrease intracellular cAMP levels through plasmid expression of Rv1339 using the constitutive expression system, pVV16. In Mycobacterium smegmatis mc2155, we demonstrate that recombinant expression of Rv1339 reduced cAMP levels threefold and resulted in altered gene expression, impaired bioenergetics, and a disruption in peptidoglycan biosynthesis leading to decreased tolerance to antimicrobials that target cell wall synthesis such as ethambutol, D-cycloserine, and vancomycin. This work increases our understanding of the role of cAMP in mycobacterial antimicrobial tolerance, and our observations suggest that nucleotide signaling may represent a new target for the development of antimicrobial therapies.
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Affiliation(s)
- Michael Thomson
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Yi Liu
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Kanokkan Nunta
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Ashleigh Cheyne
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Nadia Fernandes
- Imperial BRC Genomics Facility, Imperial College London, London, United Kingdom
| | - Richard Williams
- Imperial BRC Genomics Facility, Imperial College London, London, United Kingdom
| | | | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom.
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49
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Bongaerts N, Edoo Z, Abukar AA, Song X, Sosa-Carrillo S, Haggenmueller S, Savigny J, Gontier S, Lindner AB, Wintermute EH. Low-cost anti-mycobacterial drug discovery using engineered E. coli. Nat Commun 2022; 13:3905. [PMID: 35798732 PMCID: PMC9262897 DOI: 10.1038/s41467-022-31570-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 06/23/2022] [Indexed: 12/29/2022] Open
Abstract
Whole-cell screening for Mycobacterium tuberculosis (Mtb) inhibitors is complicated by the pathogen's slow growth and biocontainment requirements. Here we present a synthetic biology framework for assaying Mtb drug targets in engineered E. coli. We construct Target Essential Surrogate E. coli (TESEC) in which an essential metabolic enzyme is deleted and replaced with an Mtb-derived functional analog, linking bacterial growth to the activity of the target enzyme. High throughput screening of a TESEC model for Mtb alanine racemase (Alr) revealed benazepril as a targeted inhibitor, a result validated in whole-cell Mtb. In vitro biochemical assays indicated a noncompetitive mechanism unlike that of clinical Alr inhibitors. We establish the scalability of TESEC for drug discovery by characterizing TESEC strains for four additional targets.
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Affiliation(s)
- Nadine Bongaerts
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Zainab Edoo
- Sorbonne Université, Université Paris Cité, Inserm, Centre de Recherche des Cordeliers (CRC), Paris, France
| | - Ayan A Abukar
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Xiaohu Song
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Sebastián Sosa-Carrillo
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- Institut Pasteur, Inria de Paris, Université Paris Cité, InBio, Paris, France
| | - Sarah Haggenmueller
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Juline Savigny
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Sophie Gontier
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Ariel B Lindner
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France.
- CRI, Paris, France.
| | - Edwin H Wintermute
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France.
- CRI, Paris, France.
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50
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Rimal B, Senzani S, Ealand C, Lamichhane G, Kana B, Kim SJ. Peptidoglycan compositional analysis of Mycobacterium smegmatis using high-resolution LC-MS. Sci Rep 2022; 12:11061. [PMID: 35773428 PMCID: PMC9247062 DOI: 10.1038/s41598-022-15324-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/22/2022] [Indexed: 11/21/2022] Open
Abstract
Peptidoglycan (PG) is the exoskeleton of bacterial cells and is required for their viability, growth, and cell division. Unlike most bacteria, mycobacteria possess an atypical PG characterized by a high degree of unique linkages and chemical modifications which most likely serve as important determinants of virulence and pathogenesis in mycobacterial diseases. Despite this important role, the chemical composition and molecular architecture of mycobacterial PG have yet to be fully determined. Here we determined the chemical composition of PG from Mycobacterium smegmatis using high-resolution liquid chromatography-mass spectrometry. Purified cell walls from the stationary phase were digested with mutanolysin and compositional analysis was performed on 130 muropeptide ions that were identified using an in silico PG library. The relative abundance for each muropeptide ion was measured by integrating the extracted-ion chromatogram. The percentage of crosslink per PG subunit was measured at 45%. While both 3→3 and 4→3 transpeptide cross-linkages were found in PG dimers, a high abundance of 3→3 linkages was found associated with the trimers. Approximately 43% of disaccharides in the PG of M. smegmatis showed modifications by acetylation or deacetylation. A significant number of PG trimers are found with a loss of 41.00 amu that is consistent with N-deacetylation, whereas the dimers show a gain of 42.01 amu corresponding to O-acetylation of the PG disaccharides. This suggests a possible role of PG acetylation in the regulation of cell wall homeostasis in M. smegmatis. Collectively, these data report important novel insights into the ultrastructure of mycobacterial PG.
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Affiliation(s)
- Binayak Rimal
- Institute of Biomedical Studies, Baylor University, Waco, TX, 76798, USA.,Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Sibusiso Senzani
- National Health Laboratory Service, Faculty of Health Sciences, DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand, Johannesburg, 2001, South Africa
| | - Christopher Ealand
- National Health Laboratory Service, Faculty of Health Sciences, DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand, Johannesburg, 2001, South Africa
| | - Gyanu Lamichhane
- Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Bavesh Kana
- National Health Laboratory Service, Faculty of Health Sciences, DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand, Johannesburg, 2001, South Africa.
| | - Sung Joon Kim
- Department of Chemistry, Howard University, Chemistry Building, 525 College Street, Washington, DC, 20059, USA.
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