1
|
Guyeux C, Senelle G, Le Meur A, Supply P, Gaudin C, Phelan JE, Clark TG, Rigouts L, de Jong B, Sola C, Refrégier G. Newly Identified Mycobacterium africanum Lineage 10, Central Africa. Emerg Infect Dis 2024; 30:560-563. [PMID: 38407162 PMCID: PMC10902520 DOI: 10.3201/eid3003.231466] [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: 02/27/2024] Open
Abstract
Analysis of genome sequencing data from >100,000 genomes of Mycobacterium tuberculosis complex using TB-Annotator software revealed a previously unknown lineage, proposed name L10, in central Africa. Phylogenetic reconstruction suggests L10 could represent a missing link in the evolutionary and geographic migration histories of M. africanum.
Collapse
|
2
|
Jones BS, Pareek V, Hu DD, Weaver SD, Syska C, Galfano G, Champion MM, Champion PA. N - acetyl-transferases required for iron uptake and aminoglycoside resistance promote virulence lipid production in M. marinum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602253. [PMID: 39005365 PMCID: PMC11245092 DOI: 10.1101/2024.07.05.602253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Phagosomal lysis is a key aspect of mycobacterial infection of host macrophages. Acetylation is a protein modification mediated enzymatically by N-acetyltransferases (NATs) that impacts bacterial pathogenesis and physiology. To identify NATs required for lytic activity, we leveraged Mycobacterium marinum, a nontubercular pathogen and an established model for M. tuberculosis. M. marinum hemolysis is a proxy for phagolytic activity. We generated M. marinum strains with deletions in conserved NAT genes and screened for hemolytic activity. Several conserved lysine acetyltransferases (KATs) contributed to hemolysis. Hemolysis is mediated by the ESX-1 secretion system and by phthiocerol dimycocerosate (PDIM), a virulence lipid. For several strains, the hemolytic activity was restored by the addition of second copy of the ESX-1 locus. Using thin-layer chromatography (TLC), we found a single NAT required for PDIM and phenolic glycolipid (PGL) production. MbtK is a conserved KAT required for mycobactin siderophore synthesis and virulence. Mycobactin J exogenously complemented PDIM/PGL production in the Δ mbtK strain. The Δ mbtK M. marinum strain was attenuated in macrophage and Galleria mellonella infection models. Constitutive expression of either eis or papA5, which encode a KAT required for aminoglycoside resistance and a PDIM/PGL biosynthetic enzyme, rescued PDIM/PGL production and virulence of the Δ mbtK strain. Eis N-terminally acetylated PapA5 in vitro , supporting a mechanism for restored lipid production. Overall, our study establishes connections between the MbtK and Eis NATs, and between iron uptake and PDIM and PGL synthesis in M. marinum . Our findings underscore the multifunctional nature of mycobacterial NATs and their connection to key virulence pathways. Significance Statement Acetylation is a modification of protein N-termini, lysine residues, antibiotics and lipids. Many of the enzymes that promote acetylation belong to the GNAT family of proteins. M. marinum is a well-established as a model to understand how M. tuberculosis causes tuberculosis. In this study we sought to identify conserved GNAT proteins required for early stages of mycobacterial infection. Using M. marinum, we determined that several GNAT proteins are required for the lytic activity of M. marinum. We uncovered previously unknown connections between acetyl-transferases required for iron uptake and antimicrobial resistance, and the production of the unique mycobacterial lipids, PDIM and PGLOur data support that acetyl-transferases from the GNAT family are interconnected, and have activities beyond those previously reported.
Collapse
|
3
|
Santos-Júnior PFDS, Batista VDM, Nascimento IJDS, Nunes IC, Silva LR, Costa CACB, Freitas JDD, Quintans-Júnior LJ, Araújo-Júnior JXD, Freitas MEGD, Zhan P, Green KD, Garneau-Tsodikova S, Mendonça-Júnior FJB, Rodrigues-Junior VS, Silva-Júnior EFD. A consensus reverse docking approach for identification of a competitive inhibitor of acetyltransferase enhanced intracellular survival protein from Mycobacterium tuberculosis. Bioorg Med Chem 2024; 108:117774. [PMID: 38833750 DOI: 10.1016/j.bmc.2024.117774] [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: 01/24/2024] [Revised: 05/08/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024]
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), which remains a significant global health challenge. The emergence of multidrug-resistant (MDR) Mtb strains imposes the development of new therapeutic strategies. This study focuses on the identification and evaluation of potential inhibitors against Mtb H37Ra through a comprehensive screening of an in-house chemolibrary. Subsequently, a promising pyrimidine derivative (LQM495) was identified as promising and then further investigated by experimental and in silico approaches. In this context, computational techniques were used to elucidate the potential molecular target underlying the inhibitory action of LQM495. Then, a consensus reverse docking (CRD) protocol was used to investigate the interactions between this compound and several Mtb targets. Out of 98 Mtb targets investigated, the enhanced intracellular survival (Eis) protein emerged as a target for LQM495. To gain insights into the stability of the LQM495-Eis complex, molecular dynamics (MD) simulations were conducted over a 400 ns trajectory. Further insights into its binding modes within the Eis binding site were obtained through a Quantum mechanics (QM) approach, using density functional theory (DFT), with B3LYP/D3 basis set. These calculations shed light on the electronic properties and reactivity of LQM495. Subsequently, inhibition assays and kinetic studies of the Eis activity were used to investigate the activity of LQM495. Then, an IC50 value of 11.0 ± 1.4 µM was found for LQM495 upon Eis protein. Additionally, its Vmax, Km, and Ki parameters indicated that it is a competitive inhibitor. Lastly, this study presents LQM495 as a promising inhibitor of Mtb Eis protein, which could be further explored for developing novel anti-TB drugs in the future.
Collapse
Affiliation(s)
| | - Vitoria de Melo Batista
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil
| | - Igor José Dos Santos Nascimento
- Post-Graduation Program of Pharmaceutical Sciences, Pharmacy Department, State University of Paraíba, Campina Grande, Brazil
| | - Isabelle Cavalcante Nunes
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil
| | - Leandro Rocha Silva
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil
| | | | - Johnnatan Duarte de Freitas
- Department of Chemistry, Federal Institute of Alagoas, Maceió campus, Mizael Domingues Street, 57020-600 Maceió, Alagoas, Brazil
| | - Lucindo José Quintans-Júnior
- Pharmaceutical Sciences Graduate Program (PPGCS), Federal University of Sergipe, São Cristóvão, Sergipe 49100-001, Brazil
| | - João Xavier de Araújo-Júnior
- Laboratory of Medicinal Chemistry, Institute of Pharmaceutical Sciences, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil
| | | | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Keith D Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536-0596, United States
| | | | - Valnês S Rodrigues-Junior
- Department of Pharmaceutical Sciences, Federal University of Paraíba, João Pessoa, Brazil; Post-Graduation Program in Natural Products and Bioactive Synthetics, Federal University of Paraíba, João Pessoa, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil.
| |
Collapse
|
4
|
Niculescu AG, Mük GR, Avram S, Vlad IM, Limban C, Nuta D, Grumezescu AM, Chifiriuc MC. Novel strategies based on natural products and synthetic derivatives to overcome resistance in Mycobacterium tuberculosis. Eur J Med Chem 2024; 269:116268. [PMID: 38460268 DOI: 10.1016/j.ejmech.2024.116268] [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: 12/27/2023] [Revised: 02/09/2024] [Accepted: 02/18/2024] [Indexed: 03/11/2024]
Abstract
One of the biggest health challenges of today's world is the emergence of antimicrobial resistance (AMR), which renders conventional therapeutics insufficient and urgently demands the generation of novel antimicrobial strategies. Mycobacterium tuberculosis (M. tuberculosis), the pathogen causing tuberculosis (TB), is among the most successful bacteria producing drug-resistant infections. The versatility of M. tuberculosis allows it to evade traditional anti-TB agents through various acquired and intrinsic mechanisms, rendering TB among the leading causes of infectious disease-related mortality. In this context, researchers worldwide focused on establishing novel approaches to address drug resistance in M. tuberculosis, developing diverse alternative treatments with varying effectiveness and in different testing phases. Overviewing the current progress, this paper aims to briefly present the mechanisms involved in M. tuberculosis drug-resistance, further reviewing in more detail the under-development antibiotics, nanotechnological approaches, and natural therapeutic solutions that promise to overcome current treatment limitations.
Collapse
Affiliation(s)
- Adelina-Gabriela Niculescu
- Research Institute of the University of Bucharest, University of Bucharest, 90 Panduri Road, Bucharest, Romania; Department of Science and Engineering of Oxide Materials and Nanomaterials, National University of Science and Technology Politehnica Bucharest, 011061, Bucharest, Romania.
| | - Georgiana Ramona Mük
- Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, Bucharest, R-050095, Romania; St. Stephen's Pneumoftiziology Hospital, Șoseaua Ștefan cel Mare 11, Bucharest, 020122, Romania.
| | - Speranta Avram
- Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, Bucharest, R-050095, Romania.
| | - Ilinca Margareta Vlad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia, 020956, Bucharest, Romania.
| | - Carmen Limban
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia, 020956, Bucharest, Romania.
| | - Diana Nuta
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia, 020956, Bucharest, Romania.
| | - Alexandru Mihai Grumezescu
- Research Institute of the University of Bucharest, University of Bucharest, 90 Panduri Road, Bucharest, Romania; Department of Science and Engineering of Oxide Materials and Nanomaterials, National University of Science and Technology Politehnica Bucharest, 011061, Bucharest, Romania.
| | - Mariana-Carmen Chifiriuc
- Research Institute of the University of Bucharest, University of Bucharest, 90 Panduri Road, Bucharest, Romania; Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, Bucharest, R-050095, Romania.
| |
Collapse
|
5
|
Sharma D, Gautam S, Srivastava N, Khan AM, Bisht D. Comparative Proteomic Analysis of Capsule Proteins in Aminoglycoside-Resistant and Sensitive Mycobacterium tuberculosis Clinical Isolates: Unraveling Potential Drug Targets. Int J Mycobacteriol 2024; 13:197-205. [PMID: 38916392 DOI: 10.4103/ijmy.ijmy_47_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/22/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Tuberculosis (TB), a global infectious threat, has seen a concerning rise in aminoglycoside-resistant Mycobacterium tuberculosis (M.tb) strains. The potential role of capsule proteins remains largely unexplored. This layer acts as the primary barrier for tubercle bacilli, attempting to infiltrate host cells and subsequent disease development. METHODS The study aims to bridge this gap by investigating the differentially expressed capsule proteins in aminoglycoside-resistant M.tb clinical isolates compared with drug-sensitive isolates employing two-dimensional gel electrophoresis, mass spectrometry, and bioinformatic approaches. RESULTS We identified eight proteins that exhibited significant upregulation in aminoglycoside-resistant isolates. Protein Rv3029c and Rv2110c were associated with intermediary metabolism and respiration; Rv2462c with cell wall and cell processes; Rv3804c with lipid metabolism; Rv2416c and Rv2623 with virulence and detoxification/adaptation; Rv0020c with regulatory functions; and Rv0639 with information pathways. Notably, the Group-based Prediction System for Prokaryotic Ubiquitin-like Protein (GPS-PUP) algorithm identified potential pupylation sites within all proteins except Rv3804c. Interactome analysis using the STRING 12.0 database revealed potential interactive partners for these proteins, suggesting their involvement in aminoglycoside resistance. Molecular docking studies revealed suitable binding between amikacin and kanamycin drugs with Rv2462c, Rv3804c, and Rv2623 proteins. CONCLUSION As a result, our findings illustrate the multifaceted nature of aminoglycoside resistance in M.tb and the importance of understanding how capsule proteins play a role in counteracting drug efficacy. Identifying the role of these proteins in drug resistance is crucial for developing more effective treatments and diagnostics for TB.
Collapse
Affiliation(s)
- Devesh Sharma
- Department of Biochemistry, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
- School of Studies in Biochemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Sakshi Gautam
- Department of Biochemistry, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - Nalini Srivastava
- School of Studies in Biochemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Abdul Mabood Khan
- Division of Clinical Trails and Implementation Research, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - Deepa Bisht
- Department of Biochemistry, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| |
Collapse
|
6
|
Radhakrishnan L, Dani R, Navabshan I, Jamal S, Ahmed N. Targeting Aminoglycoside Acetyltransferase Activity of Mycobacterium tuberculosis (H37Rv) Derived Eis (Enhanced Intracellular Survival) Protein with Quercetin. Protein J 2024; 43:12-23. [PMID: 37932619 DOI: 10.1007/s10930-023-10165-x] [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] [Accepted: 10/10/2023] [Indexed: 11/08/2023]
Abstract
Eis (Enhanced intracellular survival) protein is an aminoglycoside acetyltransferase enzyme classified under the family - GNAT (GCN5-related family of N-acetyltransferases) secreted by Mycobacterium tuberculosis (Mtb). The enzymatic activity of Eis results in the acetylation of kanamycin, thereby impairing the drug's action. In this study, we expressed and purified recombinant Eis (rEis) to determine the enzymatic activity of Eis and its potential inhibitor. Glide-enhanced precision docking was used to perform molecular docking with chosen ligands. Quercetin was found to interact Eis with a maximum binding affinity of -8.379 kcal/mol as compared to other ligands. Quercetin shows a specific interaction between the positively charged amino acid arginine in Eis and the aromatic ring of quercetin through π-cation interaction. Further, the effect of rEis was studied on the antibiotic activity of kanamycin A in the presence and absence of quercetin. It was observed that the activity of rEis aminoglycoside acetyltransferase decreased with increasing quercetin concentration. The results from the disk diffusion assay confirmed that increasing the concentration of quercetin inhibits the rEis protein activity. In conclusion, quercetin may act as a potential Eis inhibitor.
Collapse
Affiliation(s)
- Logesh Radhakrishnan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science & Technology, Vandalur, Chennai, Tamil Nadu, 600048, India
| | - Rahul Dani
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, 600036, India
| | - Irfan Navabshan
- School of Pharmacy, BSA Crescent Institute of Science and Technology, Vandalur, Chennai, Tamil Nadu, 600048, India
| | - Shazia Jamal
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science & Technology, Vandalur, Chennai, Tamil Nadu, 600048, India
| | - Neesar Ahmed
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science & Technology, Vandalur, Chennai, Tamil Nadu, 600048, India.
| |
Collapse
|
7
|
Magaña AJ, Sklenicka J, Pinilla C, Giulianotti M, Chapagain P, Santos R, Ramirez MS, Tolmasky ME. Restoring susceptibility to aminoglycosides: identifying small molecule inhibitors of enzymatic inactivation. RSC Med Chem 2023; 14:1591-1602. [PMID: 37731693 PMCID: PMC10507813 DOI: 10.1039/d3md00226h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Growing resistance to antimicrobial medicines is a critical health problem that must be urgently addressed. Adding to the increasing number of patients that succumb to infections, there are other consequences to the rise in resistance like the compromise of several medical procedures and dental work that are heavily dependent on infection prevention. Since their introduction in the clinics, aminoglycoside antibiotics have been a critical component of the armamentarium to treat infections. Still, the increase in resistance and their side effects led to a decline in their utilization. However, numerous current factors, like the urgent need for antimicrobials and their favorable properties, led to renewed interest in these drugs. While efforts to design new classes of aminoglycosides refractory to resistance mechanisms and with fewer toxic effects are starting to yield new promising molecules, extending the useful life of those already in use is essential. For this, numerous research projects are underway to counter resistance from different angles, like inhibition of expression or activity of resistance components. This review focuses on selected examples of one aspect of this quest, the design or identification of small molecule inhibitors of resistance caused by enzymatic modification of the aminoglycoside. These compounds could be developed as aminoglycoside adjuvants to overcome resistant infections.
Collapse
Affiliation(s)
- Angel J Magaña
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Jan Sklenicka
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Clemencia Pinilla
- Center for Translational Science, Florida International University Port St. Lucie FL 34987 USA
| | - Marc Giulianotti
- Center for Translational Science, Florida International University Port St. Lucie FL 34987 USA
| | - Prem Chapagain
- Department of Physics, Florida International University Miami FL 33199 USA
- Biomolecular Sciences Institute, Florida International University Miami FL 33199 USA
| | - Radleigh Santos
- Department of Mathematics, Nova Southeastern University Fort Lauderdale FL 33314 USA
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| |
Collapse
|
8
|
Pang AH, Green KD, Tsodikov OV, Garneau-Tsodikova S. Discovery and development of inhibitors of acetyltransferase Eis to combat Mycobacterium tuberculosis. Methods Enzymol 2023; 690:369-396. [PMID: 37858535 PMCID: PMC10949404 DOI: 10.1016/bs.mie.2023.06.017] [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] [Indexed: 10/21/2023]
Abstract
Aminoglycosides are bactericidal antibiotics with a broad spectrum of activity, used to treat infections caused mostly by Gram-negative pathogens and as a second-line therapy against tuberculosis. A common resistance mechanism to aminoglycosides is bacterial aminoglycoside acetyltransferase enzymes (AACs), which render aminoglycosides inactive by acetylating their amino groups. In Mycobacterium tuberculosis, an AAC called Eis (enhanced intracellular survival) acetylates kanamycin and amikacin. When upregulated as a result of mutations, Eis causes clinically important aminoglycoside resistance; therefore, Eis inhibitors are attractive as potential aminoglycoside adjuvants for treatment of aminoglycoside-resistant tuberculosis. For over a decade, we have studied Eis and discovered several series of Eis inhibitors. Here, we provide a detailed protocol for a colorimetric assay used for high-throughput discovery of Eis inhibitors, their characterization, and testing their selectivity. We describe protocols for in vitro cell culture assays for testing aminoglycoside adjuvant properties of the inhibitors. A procedure for obtaining crystals of Eis-inhibitor complexes and determining their structures is also presented. Finally, we discuss applicability of these methods to discovery and testing of inhibitors of other AACs.
Collapse
Affiliation(s)
- Allan H Pang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, United States
| | - Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, United States
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, United States.
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, United States.
| |
Collapse
|
9
|
Singh V, Dziwornu GA, Chibale K. The implication of Mycobacterium tuberculosis-mediated metabolism of targeted xenobiotics. Nat Rev Chem 2023; 7:340-354. [PMID: 37117810 PMCID: PMC10026799 DOI: 10.1038/s41570-023-00472-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2023] [Indexed: 03/29/2023]
Abstract
Drug metabolism is generally associated with liver enzymes. However, in the case of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), Mtb-mediated drug metabolism plays a significant role in treatment outcomes. Mtb is equipped with enzymes that catalyse biotransformation reactions on xenobiotics with consequences either in its favour or as a hindrance by deactivating or activating chemical entities, respectively. Considering the range of chemical reactions involved in the biosynthetic pathways of Mtb, information related to the biotransformation of antitubercular compounds would provide opportunities for the development of new chemical tools to study successful TB infections while also highlighting potential areas for drug discovery, host-directed therapy, dose optimization and elucidation of mechanisms of action. In this Review, we discuss Mtb-mediated biotransformations and propose a holistic approach to address drug metabolism in TB drug discovery and related areas. ![]()
Mycobacterium tuberculosis-mediated metabolism of xenobiotics poses an important research question for antitubercular drug discovery. Identification of the metabolic fate of compounds can inform requisite structure–activity relationship strategies early on in a drug discovery programme towards improving the properties of the compound.
Collapse
Affiliation(s)
- Vinayak Singh
- grid.7836.a0000 0004 1937 1151Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | - Godwin Akpeko Dziwornu
- grid.7836.a0000 0004 1937 1151Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
| | - Kelly Chibale
- grid.7836.a0000 0004 1937 1151Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151Department of Chemistry, University of Cape Town, Rondebosch, South Africa
| |
Collapse
|
10
|
Pang AH, Green KD, Punetha A, Chandrika NT, Howard KC, Garneau-Tsodikova S, Tsodikov OV. Discovery and Mechanistic Analysis of Structurally Diverse Inhibitors of Acetyltransferase Eis among FDA-Approved Drugs. Biochemistry 2023; 62:710-721. [PMID: 36657084 PMCID: PMC9905294 DOI: 10.1021/acs.biochem.2c00658] [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] [Indexed: 01/21/2023]
Abstract
Over one and a half million people die of tuberculosis (TB) each year. Multidrug-resistant TB infections are especially dangerous, and new drugs are needed to combat them. The high cost and complexity of drug development make repositioning of drugs that are already in clinical use for other indications a potentially time- and money-saving avenue. In this study, we identified among existing drugs five compounds: azelastine, venlafaxine, chloroquine, mefloquine, and proguanil as inhibitors of acetyltransferase Eis from Mycobacterium tuberculosis, a causative agent of TB. Eis upregulation is a cause of clinically relevant resistance of TB to kanamycin, which is inactivated by Eis-catalyzed acetylation. Crystal structures of these drugs as well as chlorhexidine in complexes with Eis showed that these inhibitors were bound in the aminoglycoside binding cavity, consistent with their established modes of inhibition with respect to kanamycin. Among three additionally synthesized compounds, a proguanil analogue, designed based on the crystal structure of the Eis-proguanil complex, was 3-fold more potent than proguanil. The crystal structures of these compounds in complexes with Eis explained their inhibitory potencies. These initial efforts in rational drug repositioning can serve as a starting point in further development of Eis inhibitors.
Collapse
Affiliation(s)
| | | | - Ankita Punetha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Kaitlind C. Howard
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| |
Collapse
|
11
|
El-Khoury C, Mansour E, Yuliandra Y, Lai F, Hawkins BA, Du JJ, Sundberg EJ, Sluis-Cremer N, Hibbs DE, Groundwater PW. The role of adjuvants in overcoming antibacterial resistance due to enzymatic drug modification. RSC Med Chem 2022; 13:1276-1299. [PMID: 36439977 PMCID: PMC9667779 DOI: 10.1039/d2md00263a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/16/2022] [Indexed: 02/03/2023] Open
Abstract
Antibacterial resistance is a prominent issue with monotherapy often leading to treatment failure in serious infections. Many mechanisms can lead to antibacterial resistance including deactivation of antibacterial agents by bacterial enzymes. Enzymatic drug modification confers resistance to β-lactams, aminoglycosides, chloramphenicol, macrolides, isoniazid, rifamycins, fosfomycin and lincosamides. Novel enzyme inhibitor adjuvants have been developed in an attempt to overcome resistance to these agents, only a few of which have so far reached the market. This review discusses the different enzymatic processes that lead to deactivation of antibacterial agents and provides an update on the current and potential enzyme inhibitors that may restore bacterial susceptibility.
Collapse
Affiliation(s)
- Christy El-Khoury
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Elissar Mansour
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Yori Yuliandra
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Bryson A Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine Atlanta GA 30322 USA
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine Atlanta GA 30322 USA
| | - Nicolas Sluis-Cremer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine Pittsburgh PA 15213 USA
| | - David E Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Paul W Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| |
Collapse
|
12
|
Pang AH, Green KD, Chandrika NT, Garzan A, Punetha A, Holbrook SYL, Willby MJ, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Discovery of substituted benzyloxy-benzylamine inhibitors of acetyltransferase Eis and their anti-mycobacterial activity. Eur J Med Chem 2022; 242:114698. [PMID: 36037791 PMCID: PMC9481687 DOI: 10.1016/j.ejmech.2022.114698] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/30/2022]
Abstract
A clinically significant mechanism of tuberculosis resistance to the aminoglycoside kanamycin (KAN) is its acetylation catalyzed by upregulated Mycobacterium tuberculosis (Mtb) acetyltransferase Eis. In search for inhibitors of Eis, we discovered an inhibitor with a substituted benzyloxy-benzylamine scaffold. A structure-activity relationship study of 38 compounds in this structural family yielded highly potent (IC50 ∼ 1 μM) Eis inhibitors, which did not inhibit other acetyltransferases. Crystal structures of Eis in complexes with three of the inhibitors showed that the inhibitors were bound in the aminoglycoside binding site of Eis, consistent with the competitive mode of inhibition, as established by kinetics measurements. When tested in Mtb cultures, two inhibitors (47 and 55) completely abolished resistance to KAN of the highly KAN-resistant strain Mtb mc2 6230 K204, likely due to Eis inhibition as a major mechanism. Thirteen of the compounds were toxic even in the absence of KAN to Mtb and other mycobacteria, but not to non-mycobacteria or to mammalian cells. This, yet unidentified mechanism of toxicity, distinct from Eis inhibition, will merit future studies along with further development of these molecules as anti-mycobacterial agents.
Collapse
Affiliation(s)
- Allan H Pang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Atefeh Garzan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Ankita Punetha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Selina Y L Holbrook
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Melisa J Willby
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - James E Posey
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
| |
Collapse
|
13
|
M A B Alsarraf H, Lam Ung K, Johansen MD, Dimon J, Olieric V, Kremer L, Blaise M. Biochemical, structural, and functional studies reveal that MAB_4324c from Mycobacterium abscessus is an active tandem repeat N-acetyltransferase. FEBS Lett 2022; 596:1516-1532. [PMID: 35470425 DOI: 10.1002/1873-3468.14360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 11/12/2022]
Abstract
Mycobacterium abscessus is a pathogenic non-tuberculous mycobacterium that possesses an intrinsic drug-resistance profile. Several N-acetyltransferases mediate drug resistance and/or participate in M. abscessus virulence. Mining the M. abscessus genome has revealed genes encoding additional N-acetyltransferases whose functions remain uncharacterized, among them MAB_4324c. Here, we showed that the purified MAB_4324c protein is a N-acetyltransferase able to acetylate small polyamine substrates. The crystal structure of MAB_4324c was solved at high resolution in complex with its cofactor, revealing the presence of two GCN5-related N-acetyltransferase domains and a cryptic binding site for NADPH. Genetic studies demonstrate that MAB_4324c is not essential for in vitro growth of M. abscessus, however overexpression of the protein enhanced the uptake and survival of M. abscessus in THP-1 macrophages.
Collapse
Affiliation(s)
- Husam M A B Alsarraf
- IRIM, Université de Montpellier, CNRS, Montpellier, France.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kien Lam Ung
- IRIM, Université de Montpellier, CNRS, Montpellier, France.,Department of molecular biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Matt D Johansen
- IRIM, Université de Montpellier, CNRS, Montpellier, France.,Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Juliette Dimon
- IRIM, Université de Montpellier, CNRS, Montpellier, France
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen-PSI, Switzerland
| | - Laurent Kremer
- IRIM, Université de Montpellier, CNRS, Montpellier, France.,INSERM, IRIM, Montpellier, France
| | - Mickaël Blaise
- IRIM, Université de Montpellier, CNRS, Montpellier, France
| |
Collapse
|
14
|
Mujuni D, Kasemire DL, Ibanda I, Kabugo J, Nsawotebba A, Phelan JE, Majwala RK, Tugumisirize D, Nyombi A, Orena B, Turyahabwe I, Byabajungu H, Nadunga D, Musisi K, Joloba ML, Ssengooba W. Molecular characterisation of second-line drug resistance among drug resistant tuberculosis patients tested in Uganda: a two and a half-year's review. BMC Infect Dis 2022; 22:363. [PMID: 35410160 PMCID: PMC9003953 DOI: 10.1186/s12879-022-07339-w] [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] [Received: 08/11/2021] [Accepted: 04/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Second-line drug resistance (SLD) among tuberculosis (TB) patients is a serious emerging challenge towards global control of the disease. We characterized SLD-resistance conferring-mutations among TB patients with rifampicin and/or isoniazid (RIF and/or INH) drug-resistance tested at the Uganda National TB Reference Laboratory (NTRL) between June 2017 and December 2019. METHODS This was a descriptive cross-sectional secondary data analysis of 20,508 M. tuberculosis isolates of new and previously treated patients' resistant to RIF and/or INH. DNA strips with valid results to characterise the SLD resistance using the commercial Line Probe Assay Genotype MTBDRsl Version 2.0 Assay (Hain Life Science, Nehren, Germany) were reviewed. Data were analysed with STATAv15 using cross-tabulation for frequency and proportions of known resistance-conferring mutations to injectable agents (IA) and fluoroquinolones (FQ). RESULTS Among the eligible participants, 12,993/20,508 (63.4%) were male and median (IQR) age 32 (24-43). A total of 576/20,508 (2.8%) of the M. tuberculosis isolates from participants had resistance to RIF and/or INH. These included; 102/576 (17.7%) single drug-resistant and 474/576 (82.3%) multidrug-resistant (MDR) strains. Only 102 patients had test results for FQ of whom 70/102 (68.6%) and 01/102 (0.98%) had resistance-conferring mutations in the gyrA locus and gyrB locus respectively. Among patients with FQ resistance, gyrAD94G 42.6% (30.0-55.9) and gyrA A90V 41.1% (28.6-54.3) mutations were most observed. Only one mutation, E540D was detected in the gyrB locus. A total of 26 patients had resistance-conferring mutations to IA in whom, 20/26 77.0% (56.4-91.0) had A1401G mutation in the rrs gene locus. CONCLUSIONS Our study reveals a high proportion of mutations known to confer high-level fluoroquinolone drug-resistance among patients with rifampicin and/or isoniazid drug resistance. Utilizing routinely generated laboratory data from existing molecular diagnostic methods may aid real-time surveillance of emerging tuberculosis drug-resistance in resource-limited settings.
Collapse
Affiliation(s)
- Dennis Mujuni
- Makerere University, College of Health Sciences, Kampala, Uganda.,World Health Organisation Supranational Reference Laboratory, Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Dianah Linda Kasemire
- World Health Organisation Supranational Reference Laboratory, Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Ivan Ibanda
- Department of Pharmacology and Toxicology, School of Pharmacy, Kampala International University, Kampala, Uganda
| | - Joel Kabugo
- World Health Organisation Supranational Reference Laboratory, Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Andrew Nsawotebba
- World Health Organisation Supranational Reference Laboratory, Uganda National TB Reference Laboratory, Kampala, Uganda.,National Health Laboratory and Diagnostic Services, Kampala, Uganda
| | - Jody E Phelan
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Robert Kaos Majwala
- United States Agency for International Development, Defeat TB Project, Kampala, Uganda
| | - Didas Tugumisirize
- World Health Organisation Supranational Reference Laboratory, Uganda National TB Reference Laboratory, Kampala, Uganda.,National Tuberculosis and Leprosy Control Programme, Ministry of Health, Kampala, Uganda
| | - Abdunoor Nyombi
- World Health Organisation Supranational Reference Laboratory, Uganda National TB Reference Laboratory, Kampala, Uganda.,National Tuberculosis and Leprosy Control Programme, Ministry of Health, Kampala, Uganda
| | - Beatrice Orena
- World Health Organisation Supranational Reference Laboratory, Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Irene Turyahabwe
- World Health Organisation EPI Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Henry Byabajungu
- World Health Organisation Supranational Reference Laboratory, Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Diana Nadunga
- World Health Organisation Supranational Reference Laboratory, Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Kenneth Musisi
- World Health Organisation Supranational Reference Laboratory, Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Moses Lutakoome Joloba
- World Health Organisation Supranational Reference Laboratory, Uganda National TB Reference Laboratory, Kampala, Uganda.,Department of Medical Microbiology, School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Willy Ssengooba
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University, Kampala, Uganda. .,Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda.
| |
Collapse
|
15
|
Punetha A, Green KD, Garzan A, Thamban Chandrika N, Willby MJ, Pang AH, Hou C, Holbrook SYL, Krieger K, Posey JE, Parish T, Tsodikov OV, Garneau-Tsodikova S. Structure-based design of haloperidol analogues as inhibitors of acetyltransferase Eis from Mycobacterium tuberculosis to overcome kanamycin resistance. RSC Med Chem 2021; 12:1894-1909. [PMID: 34825186 DOI: 10.1039/d1md00239b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/13/2021] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a deadly bacterial disease. Drug-resistant strains of Mtb make eradication of TB a daunting task. Overexpression of the enhanced intracellular survival (Eis) protein by Mtb confers resistance to the second-line antibiotic kanamycin (KAN). Eis is an acetyltransferase that acetylates KAN, inactivating its antimicrobial function. Development of Eis inhibitors as KAN adjuvant therapeutics is an attractive path to forestall and overcome KAN resistance. We discovered that an antipsychotic drug, haloperidol (HPD, 1), was a potent Eis inhibitor with IC50 = 0.39 ± 0.08 μM. We determined the crystal structure of the Eis-haloperidol (1) complex, which guided synthesis of 34 analogues. The structure-activity relationship study showed that in addition to haloperidol (1), eight analogues, some of which were smaller than 1, potently inhibited Eis (IC50 ≤ 1 μM). Crystal structures of Eis in complexes with three potent analogues and droperidol (DPD), an antiemetic and antipsychotic, were determined. Three compounds partially restored KAN sensitivity of a KAN-resistant Mtb strain K204 overexpressing Eis. The Eis inhibitors generally did not exhibit cytotoxicity against mammalian cells. All tested compounds were modestly metabolically stable in human liver microsomes, exhibiting 30-60% metabolism over the course of the assay. While direct repurposing of haloperidol as an anti-TB agent is unlikely due to its neurotoxicity, this study reveals potential approaches to modifying this chemical scaffold to minimize toxicity and improve metabolic stability, while preserving potent Eis inhibition.
Collapse
Affiliation(s)
- Ankita Punetha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Atefeh Garzan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Melisa J Willby
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention Atlanta GA 30329 USA
| | - Allan H Pang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Caixia Hou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Selina Y L Holbrook
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Kyle Krieger
- Center for Global Infectious Disease Research, Seattle Children's Research Institute 307 Westlake Avenue N Seattle WA 98109 USA
| | - James E Posey
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention Atlanta GA 30329 USA
| | - Tanya Parish
- Center for Global Infectious Disease Research, Seattle Children's Research Institute 307 Westlake Avenue N Seattle WA 98109 USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| |
Collapse
|
16
|
Lammers M. Post-translational Lysine Ac(et)ylation in Bacteria: A Biochemical, Structural, and Synthetic Biological Perspective. Front Microbiol 2021; 12:757179. [PMID: 34721364 PMCID: PMC8556138 DOI: 10.3389/fmicb.2021.757179] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/10/2021] [Indexed: 12/21/2022] Open
Abstract
Ac(et)ylation is a post-translational modification present in all domains of life. First identified in mammals in histones to regulate RNA synthesis, today it is known that is regulates fundamental cellular processes also in bacteria: transcription, translation, metabolism, cell motility. Ac(et)ylation can occur at the ε-amino group of lysine side chains or at the α-amino group of a protein. Furthermore small molecules such as polyamines and antibiotics can be acetylated and deacetylated enzymatically at amino groups. While much research focused on N-(ε)-ac(et)ylation of lysine side chains, much less is known about the occurrence, the regulation and the physiological roles on N-(α)-ac(et)ylation of protein amino termini in bacteria. Lysine ac(et)ylation was shown to affect protein function by various mechanisms ranging from quenching of the positive charge, increasing the lysine side chains’ size affecting the protein surface complementarity, increasing the hydrophobicity and by interfering with other post-translational modifications. While N-(ε)-lysine ac(et)ylation was shown to be reversible, dynamically regulated by lysine acetyltransferases and lysine deacetylases, for N-(α)-ac(et)ylation only N-terminal acetyltransferases were identified and so far no deacetylases were discovered neither in bacteria nor in mammals. To this end, N-terminal ac(et)ylation is regarded as being irreversible. Besides enzymatic ac(et)ylation, recent data showed that ac(et)ylation of lysine side chains and of the proteins N-termini can also occur non-enzymatically by the high-energy molecules acetyl-coenzyme A and acetyl-phosphate. Acetyl-phosphate is supposed to be the key molecule that drives non-enzymatic ac(et)ylation in bacteria. Non-enzymatic ac(et)ylation can occur site-specifically with both, the protein primary sequence and the three dimensional structure affecting its efficiency. Ac(et)ylation is tightly controlled by the cellular metabolic state as acetyltransferases use ac(et)yl-CoA as donor molecule for the ac(et)ylation and sirtuin deacetylases use NAD+ as co-substrate for the deac(et)ylation. Moreover, the accumulation of ac(et)yl-CoA and acetyl-phosphate is dependent on the cellular metabolic state. This constitutes a feedback control mechanism as activities of many metabolic enzymes were shown to be regulated by lysine ac(et)ylation. Our knowledge on lysine ac(et)ylation significantly increased in the last decade predominantly due to the huge methodological advances that were made in fields such as mass-spectrometry, structural biology and synthetic biology. This also includes the identification of additional acylations occurring on lysine side chains with supposedly different regulatory potential. This review highlights recent advances in the research field. Our knowledge on enzymatic regulation of lysine ac(et)ylation will be summarized with a special focus on structural and mechanistic characterization of the enzymes, the mechanisms underlying non-enzymatic/chemical ac(et)ylation are explained, recent technological progress in the field are presented and selected examples highlighting the important physiological roles of lysine ac(et)ylation are summarized.
Collapse
Affiliation(s)
- Michael Lammers
- Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Greifswald, Germany
| |
Collapse
|
17
|
da Silva PB, Araújo VHS, Fonseca-Santos B, Solcia MC, Ribeiro CM, da Silva IC, Alves RC, Pironi AM, Silva ACL, Victorelli FD, Fernandes MA, Ferreira PS, da Silva GH, Pavan FR, Chorilli M. Highlights Regarding the Use of Metallic Nanoparticles against Pathogens Considered a Priority by the World Health Organization. Curr Med Chem 2021; 28:1906-1956. [PMID: 32400324 DOI: 10.2174/0929867327666200513080719] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/11/2020] [Accepted: 03/20/2020] [Indexed: 11/22/2022]
Abstract
The indiscriminate use of antibiotics has facilitated the growing resistance of bacteria, and this has become a serious public health problem worldwide. Several microorganisms are still resistant to multiple antibiotics and are particularly dangerous in the hospital and nursing home environment, and to patients whose care requires devices, such as ventilators and intravenous catheters. A list of twelve pathogenic genera, which especially included bacteria that were not affected by different antibiotics, was released by the World Health Organization (WHO) in 2017, and the research and development of new antibiotics against these genera has been considered a priority. The nanotechnology is a tool that offers an effective platform for altering the physicalchemical properties of different materials, thereby enabling the development of several biomedical applications. Owing to their large surface area and high reactivity, metallic particles on the nanometric scale have remarkable physical, chemical, and biological properties. Nanoparticles with sizes between 1 and 100 nm have several applications, mainly as new antimicrobial agents for the control of microorganisms. In the present review, more than 200 reports of various metallic nanoparticles, especially those containing copper, gold, platinum, silver, titanium, and zinc were analyzed with regard to their anti-bacterial activity. However, of these 200 studies, only 42 reported about trials conducted against the resistant bacteria considered a priority by the WHO. All studies are in the initial stage, and none are in the clinical phase of research.
Collapse
Affiliation(s)
- Patricia Bento da Silva
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | | | - Bruno Fonseca-Santos
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Mariana Cristina Solcia
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | | | | | - Renata Carolina Alves
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Andressa Maria Pironi
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | | | | | - Mariza Aires Fernandes
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Paula Scanavez Ferreira
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Gilmar Hanck da Silva
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Fernando Rogério Pavan
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Marlus Chorilli
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| |
Collapse
|
18
|
Structural characterization of a GNAT family acetyltransferase from Elizabethkingia anophelis bound to acetyl-CoA reveals a new dimeric interface. Sci Rep 2021; 11:1274. [PMID: 33446675 PMCID: PMC7809356 DOI: 10.1038/s41598-020-79649-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/26/2020] [Indexed: 01/13/2023] Open
Abstract
General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNATs) catalyse the acetylation of a diverse range of substrates, thereby orchestrating a variety of biological processes within prokaryotes and eukaryotes. GNAT enzymes can catalyze the transfer of an acetyl group from acetyl coenzyme A to substrates such as aminoglycoside antibiotics, amino acids, polyamines, peptides, vitamins, catecholamines, and large macromolecules including proteins. Although GNATs generally exhibit low to moderate sequence identity, they share a conserved catalytic fold and conserved structural motifs. In this current study we characterize the high-resolution X-ray crystallographic structure of a GNAT enzyme bound with acetyl-CoA from Elizabethkingia anophelis, an important multi-drug resistant bacterium. The tertiary structure is comprised of six α-helices and nine β-strands, and is similar with other GNATs. We identify a new and uncharacterized GNAT dimer interface, which is conserved in at least two other unpublished GNAT structures. This suggests that GNAT enzymes can form at least five different types of dimers, in addition to a range of other oligomers including trimer, tetramer, hexamer, and dodecamer assemblies. The high-resolution structure presented in this study is suitable for future in-silico docking and structure–activity relationship studies.
Collapse
|
19
|
Gianotti AR, Klinke S, Ermácora MR. The structure of unliganded sterol carrier protein 2 from Yarrowia lipolytica unveils a mechanism for binding site occlusion. J Struct Biol 2020; 213:107675. [PMID: 33278583 DOI: 10.1016/j.jsb.2020.107675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/21/2020] [Accepted: 11/27/2020] [Indexed: 11/19/2022]
Abstract
Isolated or as a part of multidomain proteins, Sterol Carrier Protein 2 (SCP2) exhibits high affinity and broad specificity for different lipidic and hydrophobic compounds. A wealth of structural information on SCP2 domains in all forms of life is currently available; however, many aspects of its ligand binding activity are poorly understood. ylSCP2 is a well-characterized single domain SCP2 from the yeast Yarrowia lipolytica. Herein, we report the X-ray structure of unliganded ylSCP2 refined to 2.0 Å resolution. Comparison with the previously solved liganded ylSCP2 structure unveiled a novel mechanism for binding site occlusion. The liganded ylSCP2 binding site is a large cavity with a volume of more than 800 Å3. In unliganded ylSCP2 the binding site is reduced to about 140 Å3. The obliteration is caused by a swing movement of the C-terminal α helix 5 and a subtle compaction of helices 2-4. Previous pairwise comparisons were between homologous SCP2 domains with a uncertain binding status. The reported unliganded ylSCP2 structure allows for the first time a fully controlled comparative analysis of the conformational effects of ligand occupation dispelling several doubts regarding the architecture of SCP2 binding site.
Collapse
Affiliation(s)
- Alejo R Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Argentina; Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Mario R Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Argentina; Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina.
| |
Collapse
|
20
|
Abstract
Successful treatment of tuberculosis (TB) can be hampered by Mycobacterium tuberculosis populations that are temporarily able to survive antibiotic pressure in the absence of drug resistance-conferring mutations, a phenomenon termed drug tolerance. We summarize findings on M. tuberculosis tolerance published in the past 20 years. Key M. tuberculosis responses to drug pressure are reduced growth rates, metabolic shifting, and the promotion of efflux pump activity. Metabolic shifts upon drug pressure mainly occur in M. tuberculosis's lipid metabolism and redox homeostasis, with reduced tricarboxylic acid cycle activity in favor of lipid anabolism. Increased lipid anabolism plays a role in cell wall thickening, which reduces sensitivity to most TB drugs. In addition to these general mechanisms, drug-specific mechanisms have been described. Upon isoniazid exposure, M. tuberculosis reprograms several pathways associated with mycolic acid biosynthesis. Upon rifampicin exposure, M. tuberculosis upregulates the expression of its drug target rpoB Upon bedaquiline exposure, ATP synthesis is stimulated, and the transcription factors Rv0324 and Rv0880 are activated. A better understanding of M. tuberculosis's responses to drug pressure will be important for the development of novel agents that prevent the development of drug tolerance following treatment initiation. Such agents could then contribute to novel TB treatment-shortening strategies.
Collapse
|
21
|
Asaad M, Abo-kadoum M, NZUNGIZE L, UAE M, NZAOU SA, Xie J. Methylation in Mycobacterium-host interaction and implications for novel control measures. INFECTION GENETICS AND EVOLUTION 2020; 83:104350. [DOI: 10.1016/j.meegid.2020.104350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/16/2020] [Accepted: 05/01/2020] [Indexed: 12/12/2022]
|
22
|
van Duijkeren E, Schwarz C, Bouchard D, Catry B, Pomba C, Baptiste KE, Moreno MA, Rantala M, Ružauskas M, Sanders P, Teale C, Wester AL, Ignate K, Kunsagi Z, Jukes H. The use of aminoglycosides in animals within the EU: development of resistance in animals and possible impact on human and animal health: a review. J Antimicrob Chemother 2020; 74:2480-2496. [PMID: 31002332 DOI: 10.1093/jac/dkz161] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Aminoglycosides (AGs) are important antibacterial agents for the treatment of various infections in humans and animals. Following extensive use of AGs in humans, food-producing animals and companion animals, acquired resistance among human and animal pathogens and commensal bacteria has emerged. Acquired resistance occurs through several mechanisms, but enzymatic inactivation of AGs is the most common one. Resistance genes are often located on mobile genetic elements, facilitating their spread between different bacterial species and between animals and humans. AG resistance has been found in many different bacterial species, including those with zoonotic potential such as Salmonella spp., Campylobacter spp. and livestock-associated MRSA. The highest risk is anticipated from transfer of resistant enterococci or coliforms (Escherichia coli) since infections with these pathogens in humans would potentially be treated with AGs. There is evidence that the use of AGs in human and veterinary medicine is associated with the increased prevalence of resistance. The same resistance genes have been found in isolates from humans and animals. Evaluation of risk factors indicates that the probability of transmission of AG resistance from animals to humans through transfer of zoonotic or commensal foodborne bacteria and/or their mobile genetic elements can be regarded as high, although there are no quantitative data on the actual contribution of animals to AG resistance in human pathogens. Responsible use of AGs is of great importance in order to safeguard their clinical efficacy for human and veterinary medicine.
Collapse
Affiliation(s)
| | - Christine Schwarz
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Damien Bouchard
- French Agency for Food, Environmental, and Occupational Safety, National Agency for Veterinary Medicinal Products, Fougères, France
| | - Boudewijn Catry
- Sciensano, Brussels, Belgium
- Faculty of Medicine, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Constança Pomba
- Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | | | - Miguel A Moreno
- Faculty of Veterinary Medicine, Complutense University, Madrid, Spain
| | - Merja Rantala
- Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | - Pascal Sanders
- French Agency for Food, Environmental, and Occupational Safety, Fougères Laboratory, Fougères, France
| | | | | | | | | | - Helen Jukes
- Veterinary Medicines Directorate, Addlestone, UK
| |
Collapse
|
23
|
Punetha A, Ngo HX, Holbrook SYL, Green KD, Willby MJ, Bonnett SA, Krieger K, Dennis EK, Posey JE, Parish T, Tsodikov OV, Garneau-Tsodikova S. Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis from Mycobacterium tuberculosis. ACS Chem Biol 2020; 15:1581-1594. [PMID: 32421305 DOI: 10.1021/acschembio.0c00184] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enhanced intracellular survival (Eis) protein of Mycobacterium tuberculosis (Mtb) is a versatile acetyltransferase that multiacetylates aminoglycoside antibiotics abolishing their binding to the bacterial ribosome. When overexpressed as a result of promoter mutations, Eis causes drug resistance. In an attempt to overcome the Eis-mediated kanamycin resistance of Mtb, we designed and optimized structurally unique thieno[2,3-d]pyrimidine Eis inhibitors toward effective kanamycin adjuvant combination therapy. We obtained 12 crystal structures of enzyme-inhibitor complexes, which guided our rational structure-based design of 72 thieno[2,3-d]pyrimidine analogues divided into three families. We evaluated the potency of these inhibitors in vitro as well as their ability to restore the activity of kanamycin in a resistant strain of Mtb, in which Eis was upregulated. Furthermore, we evaluated the metabolic stability of 11 compounds in vitro. This study showcases how structural information can guide Eis inhibitor design.
Collapse
Affiliation(s)
- Ankita Punetha
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Huy X. Ngo
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Selina Y. L. Holbrook
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Keith D. Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Melisa J. Willby
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Shilah A. Bonnett
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102, United States
| | - Kyle Krieger
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102, United States
- Center for Global Infectious Disease, Seattle Children’s Research Institute, Seattle Children’s Hospital, Seattle, Washington 98145, United States
| | - Emily K. Dennis
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - James E. Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102, United States
- Center for Global Infectious Disease, Seattle Children’s Research Institute, Seattle Children’s Hospital, Seattle, Washington 98145, United States
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| |
Collapse
|
24
|
Small-Molecule Acetylation by GCN5-Related N-Acetyltransferases in Bacteria. Microbiol Mol Biol Rev 2020; 84:84/2/e00090-19. [PMID: 32295819 DOI: 10.1128/mmbr.00090-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Acetylation is a conserved modification used to regulate a variety of cellular pathways, such as gene expression, protein synthesis, detoxification, and virulence. Acetyltransferase enzymes transfer an acetyl moiety, usually from acetyl coenzyme A (AcCoA), onto a target substrate, thereby modulating activity or stability. Members of the GCN5- N -acetyltransferase (GNAT) protein superfamily are found in all domains of life and are characterized by a core structural domain architecture. These enzymes can modify primary amines of small molecules or of lysyl residues of proteins. From the initial discovery of antibiotic acetylation, GNATs have been shown to modify a myriad of small-molecule substrates, including tRNAs, polyamines, cell wall components, and other toxins. This review focuses on the literature on small-molecule substrates of GNATs in bacteria, including structural examples, to understand ligand binding and catalysis. Understanding the plethora and versatility of substrates helps frame the role of acetylation within the larger context of bacterial cellular physiology.
Collapse
|
25
|
The WblC/WhiB7 Transcription Factor Controls Intrinsic Resistance to Translation-Targeting Antibiotics by Altering Ribosome Composition. mBio 2020; 11:mBio.00625-20. [PMID: 32291305 PMCID: PMC7157823 DOI: 10.1128/mbio.00625-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The emergence of antibiotic-resistant bacteria is one of the top threats in human health. Therefore, we need to understand how bacteria acquire resistance to antibiotics and continue growth even in the presence of antibiotics. Streptomyces coelicolor, an antibiotic-producing soil bacterium, intrinsically develops resistance to translation-targeting antibiotics. Intrinsic resistance is controlled by the WblC/WhiB7 transcription factor that is highly conserved within Actinobacteria, including Mycobacterium tuberculosis. Here, identification of the WblC/WhiB7 regulon revealed that WblC/WhiB7 controls ribosome maintenance genes and promotes translation in the presence of antibiotics by altering the composition of ribosome-associated proteins. Also, the WblC-mediated ribosomal alteration is indeed required for resistance to translation-targeting antibiotics. This suggests that inactivation of the WblC/WhiB7 regulon could be a potential target to treat antibiotic-resistant mycobacteria. Bacteria that encounter antibiotics can efficiently change their physiology to develop resistance. This intrinsic antibiotic resistance is mediated by multiple pathways, including a regulatory system(s) that activates specific genes. In some Streptomyces and Mycobacterium spp., the WblC/WhiB7 transcription factor is required for intrinsic resistance to translation-targeting antibiotics. Wide conservation of WblC/WhiB7 within Actinobacteria indicates a critical role of WblC/WhiB7 in developing resistance to such antibiotics. Here, we identified 312 WblC target genes in Streptomyces coelicolor, a model antibiotic-producing bacterium, using a combined analysis of RNA sequencing and chromatin immunoprecipitation sequencing. Interestingly, WblC controls many genes involved in translation, in addition to previously identified antibiotic resistance genes. Moreover, WblC promotes translation rate during antibiotic stress by altering the ribosome-associated protein composition. Our genome-wide analyses highlight a previously unappreciated antibiotic resistance mechanism that modifies ribosome composition and maintains the translation rate in the presence of sub-MIC levels of antibiotics.
Collapse
|
26
|
Green KD, Punetha A, Hou C, Garneau-Tsodikova S, Tsodikov OV. Probing the Robustness of Inhibitors of Tuberculosis Aminoglycoside Resistance Enzyme Eis by Mutagenesis. ACS Infect Dis 2019; 5:1772-1778. [PMID: 31433614 DOI: 10.1021/acsinfecdis.9b00228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Each year, millions of people worldwide contract tuberculosis (TB), the deadliest infection. The spread of infections with drug-resistant strains of Mycobacterium tuberculosis (Mtb) that are refractory to treatment poses a major global challenge. A major cause of resistance to antitubercular drugs of last resort, aminoglycosides, is overexpression of the Eis (enhanced intracellular survival) enzyme of Mtb, which inactivates aminoglycosides by acetylating them. We showed previously that this inactivation of aminoglycosides could be overcome by our recently reported Eis inhibitors that are currently in development as potential aminoglycoside adjunctive therapeutics against drug-resistant TB. To interrogate the robustness of the Eis inhibitors, we investigated the enzymatic activity of Eis and its inhibition by Eis inhibitors from three different structural families for nine single-residue mutants of Eis, including those found in the clinic. Three engineered mutations of the substrate binding site, D26A, W36A, and F84A, abolished inhibitor binding while compromising Eis enzymatic activity 2- to 3-fold. All other Eis mutants, including clinically observed ones, were potently inhibited by at least one inhibitor. This study helps position us one step ahead of Mtb resistance to Eis inhibitors as they are being developed for TB therapy.
Collapse
Affiliation(s)
- Keith D. Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Ankita Punetha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| |
Collapse
|
27
|
Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
Collapse
Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
| |
Collapse
|
28
|
Ung KL, Alsarraf HMAB, Olieric V, Kremer L, Blaise M. Crystal structure of the aminoglycosides N-acetyltransferase Eis2 from Mycobacterium abscessus. FEBS J 2019; 286:4342-4355. [PMID: 31254444 DOI: 10.1111/febs.14975] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/22/2019] [Accepted: 06/27/2019] [Indexed: 01/01/2023]
Abstract
Mycobacterium abscessus is an emerging human pathogen that is notorious for being one of the most drug-resistant species of Mycobacterium. It has developed numerous strategies to overcome the antibiotic stress response, limiting treatment options and leading to frequent therapeutic failure. The panel of aminoglycosides (AG) usually used in the treatment of M. abscessus pulmonary infections is restricted by chemical modification of the drugs by the N-acetyltransferase Eis2 protein (Mabs_Eis2). This enzyme acetylates the primary amine of AGs, preventing these antibiotics from binding ribosomal RNA and thereby impairing their activity. In this study, the high-resolution crystal structures of Mabs_Eis2 in its apo- and cofactor-bound forms were solved. The structural analysis of Mabs_Eis2, supported by the kinetic characterization of the enzyme, highlights the large substrate specificity of the enzyme. Furthermore, in silico docking and biochemical approaches attest that Mabs_Eis2 modifies clinically relevant drugs such as kanamycin and amikacin, with a better efficacy for the latter. In line with previous biochemical and in vivo studies, our work suggests that Mabs_Eis2 represents an attractive pharmacological target to be further explored. The high-resolution crystal structures presented here may pave the way to the design of Eis2-specific inhibitors with the potential to counteract the intrinsic resistance levels of M. abscessus to an important class of clinically important antibiotics. DATABASE: Structural data are available in the PDB database under the accession numbers: 6RFY, 6RFX and 6RFT.
Collapse
Affiliation(s)
- Kien Lam Ung
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, France
| | - Husam M A B Alsarraf
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, France
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, France.,INSERM, IRIM, Montpellier, France
| | - Mickaël Blaise
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, France
| |
Collapse
|
29
|
Abstract
Acetylation is a posttranslational modification conserved in all domains of life that is carried out by N-acetyltransferases. While acetylation can occur on Nα-amino groups, this review will focus on Nε-acetylation of lysyl residues and how the posttranslational modification changes the cellular physiology of bacteria. Up until the late 1990s, acetylation was studied in eukaryotes in the context of chromatin maintenance and gene expression. At present, bacterial protein acetylation plays a prominent role in central and secondary metabolism, virulence, transcription, and translation. Given the diversity of niches in the microbial world, it is not surprising that the targets of bacterial protein acetyltransferases are very diverse, making their biochemical characterization challenging. The paradigm for acetylation in bacteria involves the acetylation of acetyl-CoA synthetase, whose activity must be tightly regulated to maintain energy charge homeostasis. While this paradigm has provided much mechanistic detail for acetylation and deacetylation, in this review we discuss advances in the field that are changing our understanding of the physiological role of protein acetylation in bacteria.
Collapse
Affiliation(s)
- Chelsey M VanDrisse
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA;
| | | |
Collapse
|
30
|
Christensen DG, Baumgartner JT, Xie X, Jew KM, Basisty N, Schilling B, Kuhn ML, Wolfe AJ. Mechanisms, Detection, and Relevance of Protein Acetylation in Prokaryotes. mBio 2019; 10:e02708-18. [PMID: 30967470 PMCID: PMC6456759 DOI: 10.1128/mbio.02708-18] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Posttranslational modification of a protein, either alone or in combination with other modifications, can control properties of that protein, such as enzymatic activity, localization, stability, or interactions with other molecules. N-ε-Lysine acetylation is one such modification that has gained attention in recent years, with a prevalence and significance that rival those of phosphorylation. This review will discuss the current state of the field in bacteria and some of the work in archaea, focusing on both mechanisms of N-ε-lysine acetylation and methods to identify, quantify, and characterize specific acetyllysines. Bacterial N-ε-lysine acetylation depends on both enzymatic and nonenzymatic mechanisms of acetylation, and recent work has shed light into the regulation of both mechanisms. Technological advances in mass spectrometry have allowed researchers to gain insight with greater biological context by both (i) analyzing samples either with stable isotope labeling workflows or using label-free protocols and (ii) determining the true extent of acetylation on a protein population through stoichiometry measurements. Identification of acetylated lysines through these methods has led to studies that probe the biological significance of acetylation. General and diverse approaches used to determine the effect of acetylation on a specific lysine will be covered.
Collapse
Affiliation(s)
- D G Christensen
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
| | - J T Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - X Xie
- Buck Institute for Research on Aging, Novato, California, USA
| | - K M Jew
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - N Basisty
- Buck Institute for Research on Aging, Novato, California, USA
| | - B Schilling
- Buck Institute for Research on Aging, Novato, California, USA
| | - M L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - A J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
| |
Collapse
|
31
|
Anand S, Ganaie AA, Sharma C. Differential thermal stability, conformational stability and unfolding behavior of Eis proteins from Mycobacterium smegmatis and Mycobacterium tuberculosis. PLoS One 2019; 14:e0213933. [PMID: 30908529 PMCID: PMC6433294 DOI: 10.1371/journal.pone.0213933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/04/2019] [Indexed: 12/16/2022] Open
Abstract
Eis (Enhanced Intracellular Survival) is an important aminoglycoside N-acetyltransferase enzyme contributing to kanamycin resistance in Mtb clinical isolates. Eis proteins from M. tuberculosis (RvEis) and M. smegmatis (MsEis) have 58% identical and 69% similar amino acid sequences and acetylate aminoglycosides at multiple amines. Both the Eis proteins are hexameric and composed of two symmetric trimers. RvEis has remarkable structural stability and heat-stable aminoglycoside acetyltransferase activity. Although the structure and biochemical properties of MsEis have been studied earlier, the detailed characterization of its acetyltransferase activity and structural stability is lacking. In this study, we have performed comparative analysis of structural stability and aminoglycoside acetyltransferase activity of RvEis and MsEis proteins. Unlike RvEis, MsEis undergoes a three-state unfolding induced by heat or chemical denaturants and involves self-association of partially unfolded oligomers to form high molecular weight soluble aggregates. MsEis is highly susceptible to chemical denaturants and unfolds completely at lower concentrations of GdmCl and urea when compared to RvEis. In contrast to RvEis, the oligomeric forms of MsEis are SDS sensitive. However, SDS treatment resulted in increased helix formation in MsEis than RvEis. MsEis shows lesser thermostable activity with a decreased efficiency of kanamycin acetylation in comparison to RvEis. Furthermore, overexpression of MsEis does not provide thermal resistance to M. smegmatis unlike RvEis. Collectively, this study reveals that homologous proteins from pathogenic and nonpathogenic mycobacteria follow different modes of unfolding and demonstrate differential structural stability and activity despite highly similar sequences and oligomeric organization.
Collapse
Affiliation(s)
- Shashi Anand
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | - Charu Sharma
- CSIR-Institute of Microbial Technology, Chandigarh, India
| |
Collapse
|
32
|
Sanz-García F, Anoz-Carbonell E, Pérez-Herrán E, Martín C, Lucía A, Rodrigues L, Aínsa JA. Mycobacterial Aminoglycoside Acetyltransferases: A Little of Drug Resistance, and a Lot of Other Roles. Front Microbiol 2019; 10:46. [PMID: 30761098 PMCID: PMC6363676 DOI: 10.3389/fmicb.2019.00046] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/11/2019] [Indexed: 12/11/2022] Open
Abstract
Aminoglycoside acetyltransferases are important determinants of resistance to aminoglycoside antibiotics in most bacterial genera. In mycobacteria, however, aminoglycoside acetyltransferases contribute only partially to aminoglycoside susceptibility since they are related with low level resistance to these antibiotics (while high level aminoglycoside resistance is due to mutations in the ribosome). Instead, aminoglycoside acetyltransferases contribute to other bacterial functions, and this can explain its widespread presence along species of genus Mycobacterium. This review is focused on two mycobacterial aminoglycoside acetyltransferase enzymes. First, the aminoglycoside 2'-N-acetyltransferase [AAC(2')], which was identified as a determinant of weak aminoglycoside resistance in M. fortuitum, and later found to be widespread in most mycobacterial species; AAC(2') enzymes have been associated with resistance to cell wall degradative enzymes, and bactericidal mode of action of aminoglycosides. Second, the Eis aminoglycoside acetyltransferase, which was identified originally as a virulence determinant in M. tuberculosis (enhanced intracellular survival); Eis protein in fact controls production of pro-inflammatory cytokines and other pathways. The relation of Eis with aminoglycoside susceptibility was found after the years, and reaches clinical significance only in M. tuberculosis isolates resistant to the second-line drug kanamycin. Given the role of AAC(2') and Eis proteins in mycobacterial biology, inhibitory molecules have been identified, more abundantly in case of Eis. In conclusion, AAC(2') and Eis have evolved from a marginal role as potential drug resistance mechanisms into a promising future as drug targets.
Collapse
Affiliation(s)
- Fernando Sanz-García
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain.,Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza, Spain
| | - Esther Pérez-Herrán
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain
| | - Carlos Martín
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ainhoa Lucía
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Liliana Rodrigues
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Fundación Agencia Aragonesa para la Investigación y el Desarrollo, Zaragoza, Spain
| | - José A Aínsa
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
33
|
Shur KV, Bekker OB, Zaichikova MV, Maslov DA, Akimova NI, Zakharevich NV, Chekalina MS, Danilenko VN. Genetic Aspects of Drug Resistance and Virulence in Mycobacterium tuberculosis. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418120141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
34
|
Kashyap A, Singh PK, Silakari O. Mechanistic investigation of resistance via drug-inactivating enzymes in Mycobacterium tuberculosis. Drug Metab Rev 2018; 50:448-465. [PMID: 30343607 DOI: 10.1080/03602532.2018.1533966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Tuberculosis (TB) is a serious major health concern that has existed from millennia. According to annual WHO report 2016, it is considered as world's ninth highest killer disease by single infectious agent, ranking above HIV/AIDS. To worsen the scenario the development of multi-drug resistant tuberculosis (MDR-TB) and extremely drug-resistant tuberculosis (XDR-TB) have significantly reduced the success rate of TB treatment. Several efforts are being made to handle pharmacodynamic resistance (MDR and XDR-TB) involving designing of new inhibitors, targeting mutated target or by multi-targeting agents. However, the issue of pharmacokinetic resistance in TB is not being addressed appropriately till date. Pharmacokinetic mode of resistance involves an intrinsic mechanism of bacterial drug resistance via expression of various enzymes and efflux pumps that are responsible for the loss of activity of the therapeutic agents. Mycobacterium tuberculosis is also intrinsically resistant to various approved agents via pharmacokinetic mechanism of resistance. Several bacterial enzymes are encoded that either degrade or modifies the drugs and renders them ineffective. Targeting such inactivating bacterial enzymes provides a novel approach to make the current therapy effective and combat the problem of resistance. This review provides an insight into different bacterial enzymes which are responsible for pharmacokinetic drug resistance in TB. The structure attributes and mechanism of catalysis employed by these enzymes to inactivate drug have also been discussed which may provide basis for developing novel therapeutic agents for resistant TB.
Collapse
Affiliation(s)
- Aanchal Kashyap
- a Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala , India
| | - Pankaj Kumar Singh
- a Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala , India
| | - Om Silakari
- a Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala , India
| |
Collapse
|
35
|
Synthesis, antimicrobial activity, attenuation of aminoglycoside resistance in MRSA, and ribosomal A-site binding of pyrene-neomycin conjugates. Eur J Med Chem 2018; 163:381-393. [PMID: 30530174 DOI: 10.1016/j.ejmech.2018.11.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 01/27/2023]
Abstract
The development of new ligands that have comparable or enhanced therapeutic efficacy relative to current drugs is vital to the health of the global community in the short and long term. One strategy to accomplish this goal is to functionalize sites on current antimicrobials to enhance specificity and affinity while abating resistance mechanisms of infectious organisms. Herein, we report the synthesis of a series of pyrene-neomycin B (PYR-NEO) conjugates, their binding affinity to A-site RNA targets, resistance to aminoglycoside-modifying enzymes (AMEs), and antibacterial activity against a wide variety of bacterial strains of clinical relevance. PYR-NEO conjugation significantly alters the affinities of NEO for bacterial A-site targets. The conjugation of PYR to NEO significantly increased the resistance of NEO to AME modification. PYR-NEO conjugates exhibited broad-spectrum activity towards Gram-positive bacteria, including improved activity against NEO-resistant methicillin-resistant Staphylococcus aureus (MRSA) strains.
Collapse
|
36
|
Upadhyay S, Mittal E, Philips JA. Tuberculosis and the art of macrophage manipulation. Pathog Dis 2018; 76:4970761. [PMID: 29762680 DOI: 10.1093/femspd/fty037] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/04/2018] [Indexed: 12/24/2022] Open
Abstract
Macrophages are first-line responders against microbes. The success of Mycobacterium tuberculosis (Mtb) rests upon its ability to convert these antimicrobial cells into a permissive cellular niche. This is a remarkable accomplishment, as the antimicrobial arsenal of macrophages is extensive. Normally bacteria are delivered to an acidic, degradative lysosome through one of several trafficking pathways, including LC3-associated phagocytosis (LAP) and autophagy. Once phagocytozed, the bacilli are subjected to reactive oxygen and nitrogen species, and they induce the expression of proinflammatory cytokines, which serve to augment host responses. However, Mtb hijacks these host defense mechanisms, manipulating host cellular trafficking, innate immune responses, and cell death pathways to its benefit. The complex series of measures and countermeasures between host and pathogen ultimately determines the outcome of infection. In this review, we focus on the diverse effectors that Mtb uses in its multipronged effort to subvert the innate immune responses of macrophages. We highlight recent advances in understanding the molecular interface of the Mtb-macrophage interaction.
Collapse
Affiliation(s)
- S Upadhyay
- Division of Infectious Diseases, Department of Medicine, Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - E Mittal
- Division of Infectious Diseases, Department of Medicine, Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - J A Philips
- Division of Infectious Diseases, Department of Medicine, Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
37
|
Genetics and roadblocks of drug resistant tuberculosis. INFECTION GENETICS AND EVOLUTION 2018; 72:113-130. [PMID: 30261266 DOI: 10.1016/j.meegid.2018.09.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 11/22/2022]
Abstract
Considering the extensive evolutionary history of Mycobacterium tuberculosis, anti-Tuberculosis (TB) drug therapy exerts a recent selective pressure. However, in a microorganism devoid of horizontal gene transfer and with a strictly clonal populational structure such as M. tuberculosis the usual, but not sole, path to overcome drug susceptibility is through de novo mutations on a relatively strict set of genes. The possible allelic diversity that can be associated with drug resistance through several mechanisms such as target alteration or target overexpression, will dictate how these genes can become associated with drug resistance. The success demonstrated by this pathogenic microbe in this latter process and its ability to spread is currently one of the major obstacles to an effective TB elimination. This article reviews the action mechanism of the more important anti-TB drugs, including bedaquiline and delamanid, along with new findings on specific resistance mechanisms. With the development, validation and endorsement of new in vitro molecular tests for drug resistance, knowledge on these resistance mechanisms and microevolutionary dynamics leading to the emergence and fixation of drug resistance mutations within the host is highly important. Additionally, the fitness toll imposed by resistance development is also herein discussed together with known compensatory mechanisms. By elucidating the possible mechanisms that enable one strain to reacquire the original fitness levels, it will be theoretically possible to make more informed decisions and develop novel strategies that can force M. tuberculosis microevolutionary trajectory down through a path of decreasing fitness levels.
Collapse
|
38
|
Luthra S, Rominski A, Sander P. The Role of Antibiotic-Target-Modifying and Antibiotic-Modifying Enzymes in Mycobacterium abscessus Drug Resistance. Front Microbiol 2018; 9:2179. [PMID: 30258428 PMCID: PMC6143652 DOI: 10.3389/fmicb.2018.02179] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/24/2018] [Indexed: 11/21/2022] Open
Abstract
The incidence and prevalence of non-tuberculous mycobacterial (NTM) infections have been increasing worldwide and lately led to an emerging public health problem. Among rapidly growing NTM, Mycobacterium abscessus is the most pathogenic and drug resistant opportunistic germ, responsible for disease manifestations ranging from “curable” skin infections to only “manageable” pulmonary disease. Challenges in M. abscessus treatment stem from the bacteria’s high-level innate resistance and comprise long, costly and non-standardized administration of antimicrobial agents, poor treatment outcomes often related to adverse effects and drug toxicities, and high relapse rates. Drug resistance in M. abscessus is conferred by an assortment of mechanisms. Clinically acquired drug resistance is normally conferred by mutations in the target genes. Intrinsic resistance is attributed to low permeability of M. abscessus cell envelope as well as to (multi)drug export systems. However, expression of numerous enzymes by M. abscessus, which can modify either the drug-target or the drug itself, is the key factor for the pathogen’s phenomenal resistance to most classes of antibiotics used for treatment of other moderate to severe infectious diseases, like macrolides, aminoglycosides, rifamycins, β-lactams and tetracyclines. In 2009, when M. abscessus genome sequence became available, several research groups worldwide started studying M. abscessus antibiotic resistance mechanisms. At first, lack of tools for M. abscessus genetic manipulation severely delayed research endeavors. Nevertheless, the last 5 years, significant progress has been made towards the development of conditional expression and homologous recombination systems for M. abscessus. As a result of recent research efforts, an erythromycin ribosome methyltransferase, two aminoglycoside acetyltransferases, an aminoglycoside phosphotransferase, a rifamycin ADP-ribosyltransferase, a β-lactamase and a monooxygenase were identified to frame the complex and multifaceted intrinsic resistome of M. abscessus, which clearly contributes to complications in treatment of this highly resistant pathogen. Better knowledge of the underlying mechanisms of drug resistance in M. abscessus could improve selection of more effective chemotherapeutic regimen and promote development of novel antimicrobials which can overwhelm the existing resistance mechanisms. This article reviews the currently elucidated molecular mechanisms of antibiotic resistance in M. abscessus, with a focus on its drug-target-modifying and drug-modifying enzymes.
Collapse
Affiliation(s)
- Sakshi Luthra
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Anna Rominski
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Peter Sander
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,National Center for Mycobacteria, Zurich, Switzerland
| |
Collapse
|
39
|
Holbrook SY, Garneau-Tsodikova S. Evaluation of Aminoglycoside and Carbapenem Resistance in a Collection of Drug-Resistant Pseudomonas aeruginosa Clinical Isolates. Microb Drug Resist 2018; 24:1020-1030. [PMID: 29261405 PMCID: PMC6154764 DOI: 10.1089/mdr.2017.0101] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Pseudomonas aeruginosa, a Gram-negative bacterium, is a member of the ESKAPE pathogens and one of the leading causes of healthcare-associated infections worldwide. Aminoglycosides (AGs) are recognized for their efficacy against P. aeruginosa. The most common resistance mechanism against AGs is the acquisition of AG-modifying enzymes (AMEs) by the bacteria, including AG N-acetyltransferases (AACs), AG O-phosphotransferases (APHs), and AG O-nucleotidyltransferases (ANTs). In this study, we obtained 122 multidrug-resistant P. aeruginosa clinical isolates and evaluated the antibacterial effects of six AGs and two carbapenems alone against all clinical isolates, and in combination against eight selected strains. We further probed for four representatives of the most common AME genes [aac(6')-Ib, aac(3)-IV, ant(2")-Ia, and aph(3')-Ia] by polymerase chain reaction (PCR) and compared the AME patterns of these 122 clinical isolates to their antibiotic resistance profile. Among the diverse antibiotics resistance profile displayed by these clinical isolates, we found correlations between the resistance to various AGs as well as between the resistance to one AG and the resistance to carbapenems. PCR results revealed that the presence of aac(6')-Ib renders these isolates more resistant to a variety of antibiotics. The correlation between resistance to various AGs and carbapenems partially reflects the complex resistance strategies adapted in these pathogens and encourages the development of strategic treatment for each P. aeruginosa infection by considering the genetic information of each isolated bacteria.
Collapse
Affiliation(s)
- Selina Y.L. Holbrook
- College of Pharmacy, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky
| | - Sylvie Garneau-Tsodikova
- College of Pharmacy, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky
| |
Collapse
|
40
|
Overexpression of eis without a mutation in promoter region of amikacin- and kanamycin-resistant Mycobacterium tuberculosis clinical strain. Ann Clin Microbiol Antimicrob 2018; 17:33. [PMID: 30008266 PMCID: PMC6047124 DOI: 10.1186/s12941-018-0285-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aminoglycosides such as amikacin and kanamycin are effective injectable second-line drugs for treatment of multidrug-resistant tuberculosis. Molecular mechanisms underlying aminoglycoside resistance are not well understood. We have previously identified the amikacin- and kanamycin-resistant M. tuberculosis MT433 clinical strain, of which all known mutations related to resistance have not been found. Drug efflux pump is one of reported resistance mechanisms that might play a role in aminoglycoside resistance. METHODS The expression levels of sixteen putative efflux pump genes, including eis and one regulator gene, whiB7, of MT433 in the presence of kanamycin were determined using the reverse transcription-quantitative PCR method. The effects of upregulated genes on amikacin and kanamycin resistance were investigated by overexpression in M. tuberculosis H37Ra strain. RESULTS Upon kanamycin exposure, other than whiB7 and eis that were found extremely overexpressed, two drug efflux pump genes, namely Rv1877 and Rv2846c, showed specifically high-level of expression in M. tuberculosis MT433 strain. However, direct effect of overexpressed Rv1877 and Rv2846c on amikacin and kanamycin resistance could not be demonstrated in M. tuberculosis H37Ra overexpressed strain. CONCLUSIONS Our finding demonstrated that overexpression of eis could occur without any mutations in the promoter region and be detectable in clinical isolate. This might be a consequence of overexpressed whiB7, resulting in amikacin and kanamycin resistance in M. tuberculosis MT433 strain.
Collapse
|
41
|
Antonova AV, Gryadunov DA, Zimenkov DV. Molecular Mechanisms of Drug Tolerance in Mycobacterium tuberculosis. Mol Biol 2018. [DOI: 10.1134/s0026893318030020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
42
|
Ngo HX, Green KD, Gajadeera CS, Willby MJ, Holbrook SYL, Hou C, Garzan A, Mayhoub AS, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Potent 1,2,4-Triazino[5,6 b]indole-3-thioether Inhibitors of the Kanamycin Resistance Enzyme Eis from Mycobacterium tuberculosis. ACS Infect Dis 2018; 4:1030-1040. [PMID: 29601176 DOI: 10.1021/acsinfecdis.8b00074] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A common cause of resistance to kanamycin (KAN) in tuberculosis is overexpression of the enhanced intracellular survival (Eis) protein. Eis is an acetyltransferase that multiacetylates KAN and other aminoglycosides, rendering them unable to bind the bacterial ribosome. By high-throughput screening, a series of substituted 1,2,4-triazino[5,6 b]indole-3-thioether molecules were identified as effective Eis inhibitors. Herein, we purchased 17 and synthesized 22 new compounds, evaluated their potency, and characterized their steady-state kinetics. Four inhibitors were found not only to inhibit Eis in vitro, but also to act as adjuvants of KAN and partially restore KAN sensitivity in a Mycobacterium tuberculosis KAN-resistant strain in which Eis is upregulated. A crystal structure of Eis in complex with a potent inhibitor and CoA shows that the inhibitors bind in the aminoglycoside binding site snugly inserted into a hydrophobic cavity. These inhibitors will undergo preclinical development as novel KAN adjuvant therapies to treat KAN-resistant tuberculosis.
Collapse
Affiliation(s)
- Huy X. Ngo
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Keith D. Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Chathurada S. Gajadeera
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Melisa J. Willby
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329, United States
| | - Selina Y. L. Holbrook
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Atefeh Garzan
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Abdelrahman S. Mayhoub
- Department of Medicinal Chemistry and Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - James E. Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329, United States
| | - Oleg. V. Tsodikov
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Department of Medicinal Chemistry and Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
43
|
Chen L, Li H, Chen T, Yu L, Guo H, Chen Y, Chen M, Li Z, Wu Z, Wang X, Zhao J, Yan H, Wang X, Zhou L, Zhou J. Genome-wide DNA methylation and transcriptome changes in Mycobacterium tuberculosis with rifampicin and isoniazid resistance. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:3036-3045. [PMID: 31938429 PMCID: PMC6958063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/11/2018] [Indexed: 06/10/2023]
Abstract
We investigated the genome-wide DNA methylation and transcriptome changes in M. tuberculosis with rifampicin or isoniazid resistance. Single-molecule real-time (SMRT) sequencing and microarray technology were performed to expound DNA methylation profiles and differentially expressed genes in rifampicin or isoniazid resistant M. tuberculosis. Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis and methylated regulatory network analysis were conducted by online forecasting databases. Integrated analysis of DNA methylation and transcriptome revealed that 335 differentially methylated genes (175 hypermethylated and 160 hypomethylated) and 132 significant differentially expressed genes (68 up-regulated and 63 down-regulated) were found to be regulated by both rifampicin and isoniazid in M. tuberculosis H37Rv. Correlation analysis showed that differential methylated genes were negatively correlated with their transcriptional levels in rifampicin or isoniazid resistant strains. KEGG pathway analysis indicated that nitrogen metabolism pathway is closely related to differentially methylated genes induced by rifampicin and isoniazid. KEGG also suggested that differentially expressed genes in rifampicin or isoniazid-resistant strains may play different roles in regulating signal transduction events. Furthermore, five differentially methylated candidate genes (Rv0840c, Rv2243, Rv0644c, Rv2386c and Rv1130) in rifampicin resistant strains and three genes (Rv0405, Rv0252 and Rv0908) in isoniazid-resistant strains were verified the existence of protein-protein interaction in STRING database. Integrated DNA methylation and transcriptome analyses provide an epigenetic overview of rifampicin and isoniazid-induced antibiotic resistance in M. tuberculosis H37Rv. Several interesting genes and regulatory pathways may provide valuable resources for epigenetic studies in M. tuberculosis antibiotic resistance.
Collapse
Affiliation(s)
- Liang Chen
- Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Haicheng Li
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Tao Chen
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Li Yu
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Huixin Guo
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Yuhui Chen
- Outpatient Office, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Mu Chen
- Department of Respiration, The Sixth Affiliated Hospital of SUN YAT-SEN UniversityGuangzhou 510655, China
| | - Zhenyan Li
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Zhuhua Wu
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Xuezhi Wang
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Jiao Zhao
- Medical College of Jinan UniversityGuangzhou, China
| | - Huimin Yan
- Guangdong Medical UniversityDongguan, China
| | - Xinchun Wang
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Lin Zhou
- Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Jie Zhou
- The Forth People’s Hospital of FoshanFoshan, China
| |
Collapse
|
44
|
Demile B, Zenebu A, Shewaye H, Xia S, Guadie A. Risk factors associated with multidrug-resistant tuberculosis (MDR-TB) in a tertiary armed force referral and teaching hospital, Ethiopia. BMC Infect Dis 2018; 18:249. [PMID: 29855354 PMCID: PMC5984406 DOI: 10.1186/s12879-018-3167-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/25/2018] [Indexed: 12/12/2022] Open
Abstract
Background Ethiopia is one of the world health organization defined higher tuberculosis (TB) burden countries where the disease remains a massive public health threat. This study aimed to identify the prevalence and associated factors of multidrug-resistant tuberculosis (MDR-TB) using all armed force and civilian TB attendants in a tertiary level armed force hospital, where data for MDR-TB are previously unpublished. Methods Cross-sectional study was conducted from September 2014 to August 2015 in a tertiary level Armed Force Referral and Teaching Hospital (AFRTH), Ethiopia. Armed force members (n = 251) and civilians (n = 130) which has been undergone TB diagnosis at AFRTH were included. All the specimens collected were subjected to microscopic smear observation, culture growth and drug susceptibility testing. Data were analyzed using statistical package for social sciences following binary logistic regression and Chi-square. P-values < 0.05 were considered statistically significant. Results Among 381 TB patients, 355 (93.2%) new and 26 (6.8%) retreatment cases were identified. Culture and smear positive TB cases were identified in 297 (77.9%) and 252 (66.1%) patients, respectively. The overall prevalence of MDR-TB in AFRTH was found 1.8% (1.3% for armed force members and 0.5% for civilian patients) all of which were previously TB treated cases. The entire treatment success rates were 92.6% achieved highest in the armed force (active and pension) than the civilian patients. The failure and dead cases were also found 2.5 and 4.6%, respectively. Using bivariate analysis, category of attendants and TB contact history were strong predictors of MDR-TB in armed force and civilian patients. Moreover, human immunodeficiency virus (HIV) infection also identified a significant (OR = 14.6; 95% CI = 2.3–92.1; p = 0.004) predicting factor for MDR-TB in armed force members. However, sex, age and body mass index were not associated factor for MDR-TB. Conclusions In AFRTH, lower prevalence of MDR-TB was identified in armed force and civilian patients that were significantly associated with category of attendants, HIV infection and TB contact history. Considering armed force society as one segment of population significantly helps to plan a better MDR-TB control management, especially for countries classified as TB high burden country.
Collapse
Affiliation(s)
- Biresaw Demile
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Shanghai, China.,Department of TB/HIV, Armed Force Referral and Teaching Hospital, Addis Ababa, Ethiopia
| | - Amare Zenebu
- Department of TB/HIV, Armed Force Referral and Teaching Hospital, Addis Ababa, Ethiopia
| | - Haile Shewaye
- Department of TB/HIV, Armed Force Referral and Teaching Hospital, Addis Ababa, Ethiopia
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Awoke Guadie
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China. .,Department of Biology, College of Natural Sciences, Arba Minch University, P.O. Box 21, Arba Minch, Ethiopia.
| |
Collapse
|
45
|
Thamban Chandrika N, Garneau-Tsodikova S. Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities. Chem Soc Rev 2018; 47:1189-1249. [PMID: 29296992 PMCID: PMC5818290 DOI: 10.1039/c7cs00407a] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A systematic analysis of all synthetic and chemoenzymatic methodologies for the preparation of aminoglycosides for a variety of applications (therapeutic and agricultural) reported in the scientific literature up to 2017 is presented. This comprehensive analysis of derivatization/generation of novel aminoglycosides and their conjugates is divided based on the types of modifications used to make the new derivatives. Both the chemical strategies utilized and the biological results observed are covered. Structure-activity relationships based on different synthetic modifications along with their implications for activity and ability to avoid resistance against different microorganisms are also presented.
Collapse
Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
| | | |
Collapse
|
46
|
Eis, a novel family of arylalkylamine N-acetyltransferase (EC 2.3.1.87). Sci Rep 2018; 8:2435. [PMID: 29402941 PMCID: PMC5799202 DOI: 10.1038/s41598-018-20802-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/24/2018] [Indexed: 11/12/2022] Open
Abstract
Enhanced intracellular survival (Eis) proteins were found to enhance the intracellular survival of mycobacteria in macrophages by acetylating aminoglycoside antibiotics to confer resistance to these antibiotics and by acetylating DUSP16/MPK-7 to suppress host innate immune defenses. Eis homologs composing of two GCN5 N-acetyltransferase regions and a sterol carrier protein fold are found widely in gram-positive bacteria. In this study, we found that Eis proteins have an unprecedented ability to acetylate many arylalkylamines, are a novel type of arylalkylamine N-acetyltransferase AANAT (EC 2.3.1.87). Sequence alignment and phyletic distribution analysis confirmed Eis belongs to a new aaNAT-like cluster. Among the cluster, we studied three typical Eis proteins: Eis_Mtb from Mycobacterium tuberculosis, Eis_Msm from Mycobacterium smegmatis, and Eis_Sen from Saccharopolyspora erythraea. Eis_Mtb prefers to acetylate histamine and octopamine, while Eis_Msm uses tyramine and octopamine as substrates. Unlike them, Eis_Sen exihibits good catalytic efficiencies for most tested arylalkylamines. Considering arylalkylamines such as histamine plays a fundamental role in immune reactions, future work linking of AANAT activity of Eis proteins to their physiological function will broaden our understanding of gram-positive pathogen-host interactions. These findings shed insights into the molecular mechanism of Eis, and reveal potential clinical implications for many gram-positive pathogens.
Collapse
|
47
|
Kwon DH, Song HK. A Structural View of Xenophagy, a Battle between Host and Microbes. Mol Cells 2018; 41:27-34. [PMID: 29370690 PMCID: PMC5792709 DOI: 10.14348/molcells.2018.2274] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 02/06/2023] Open
Abstract
The cytoplasm in mammalian cells is a battlefield between the host and invading microbes. Both the living organisms have evolved unique strategies for their survival. The host utilizes a specialized autophagy system, xenophagy, for the clearance of invading pathogens, whereas bacteria secrete proteins to defend and escape from the host xenophagy. Several molecules have been identified and their structural investigation has enabled the comprehension of these mechanisms at the molecular level. In this review, we focus on one example of host autophagy and the other of bacterial defense: the autophagy receptor, NDP52, in conjunction with the sugar receptor, galectin-8, plays a critical role in targeting the autophagy machinery against Salmonella; and the cysteine protease, RavZ secreted by Legionella pneumophila cleaves the LC3-PE on the phagophore membrane. The structure-function relationships of these two examples and the directions of future research will be discussed.
Collapse
Affiliation(s)
- Do Hoon Kwon
- Department of Life Sciences, Korea University, Seoul 02841,
Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul 02841,
Korea
| |
Collapse
|
48
|
Green KD, Biswas T, Pang AH, Willby MJ, Reed MS, Stuchlik O, Pohl J, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Acetylation by Eis and Deacetylation by Rv1151c of Mycobacterium tuberculosis HupB: Biochemical and Structural Insight. Biochemistry 2018; 57:781-790. [PMID: 29345920 DOI: 10.1021/acs.biochem.7b01089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial nucleoid-associated proteins (NAPs) are critical to genome integrity and chromosome maintenance. Post-translational modifications of bacterial NAPs appear to function similarly to their better studied mammalian counterparts. The histone-like NAP HupB from Mycobacterium tuberculosis (Mtb) was previously observed to be acetylated by the acetyltransferase Eis, leading to genome reorganization. We report biochemical and structural aspects of acetylation of HupB by Eis. We also found that the SirT-family NAD+-dependent deacetylase Rv1151c from Mtb deacetylated HupB in vitro and characterized the deacetylation kinetics. We propose that activities of Eis and Rv1151c could regulate the acetylation status of HupB to remodel the mycobacterial chromosome in response to environmental changes.
Collapse
Affiliation(s)
- Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Tapan Biswas
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Allan H Pang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | | | | | | | | | | | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| |
Collapse
|
49
|
Amikacin: Uses, Resistance, and Prospects for Inhibition. Molecules 2017; 22:molecules22122267. [PMID: 29257114 PMCID: PMC5889950 DOI: 10.3390/molecules22122267] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 12/16/2022] Open
Abstract
Aminoglycosides are a group of antibiotics used since the 1940s to primarily treat a broad spectrum of bacterial infections. The primary resistance mechanism against these antibiotics is enzymatic modification by aminoglycoside-modifying enzymes that are divided into acetyl-transferases, phosphotransferases, and nucleotidyltransferases. To overcome this problem, new semisynthetic aminoglycosides were developed in the 70s. The most widely used semisynthetic aminoglycoside is amikacin, which is refractory to most aminoglycoside modifying enzymes. Amikacin was synthesized by acylation with the l-(-)-γ-amino-α-hydroxybutyryl side chain at the C-1 amino group of the deoxystreptamine moiety of kanamycin A. The main amikacin resistance mechanism found in the clinics is acetylation by the aminoglycoside 6'-N-acetyltransferase type Ib [AAC(6')-Ib], an enzyme coded for by a gene found in integrons, transposons, plasmids, and chromosomes of Gram-negative bacteria. Numerous efforts are focused on finding strategies to neutralize the action of AAC(6')-Ib and extend the useful life of amikacin. Small molecules as well as complexes ionophore-Zn+2 or Cu+2 were found to inhibit the acetylation reaction and induced phenotypic conversion to susceptibility in bacteria harboring the aac(6')-Ib gene. A new semisynthetic aminoglycoside, plazomicin, is in advance stage of development and will contribute to renewed interest in this kind of antibiotics.
Collapse
|
50
|
Anand S, Sharma C. Glycine-rich loop encompassing active site at interface of hexameric M. tuberculosis Eis protein contributes to its structural stability and activity. Int J Biol Macromol 2017; 109:124-135. [PMID: 29247728 DOI: 10.1016/j.ijbiomac.2017.12.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/23/2022]
Abstract
RvEis is a crucial thermostable hexameric aminoglycoside acetyltransferase of Mycobacterium tuberculosis, overexpression of which confers Kanamycin resistance in clinical strains. The thermostability associated with hexameric RvEis is important for the enhanced intracellular survival of mycobacteria. However, the structural determinants responsible for its thermal stability remain unexplored. In this study, we have assessed the role of glycines of conserved glycine-rich motif (G123GIYG127) present at the oligomeric interface in the hydrophobic core of RvEis in sustenance of its structural stability, oligomerization and functional activity. Substitution of glycines to alanine (G123A/G127A) result in significant decrease in melting temperature (Tm), reduction in the oligomerization with concomitant increase in the monomeric form and higher susceptibility towards the denaturants like GdmCl and urea relative to wild type. G123A/G127A mutant displayed lower catalytic efficiency (kcat/Km) and is completely inactive at 60 °C. ANS binding assay and the complete dissociation of hexameric complex into monomers at lower concentration of urea in G123A/G127A relative to wtRvEis suggests that altered hydrophobic environment could be the reason for its instability. In sum, these results demonstrate the role of G123GIYG127 motif in structural stability and activity of RvEis.
Collapse
Affiliation(s)
- Shashi Anand
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Charu Sharma
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India.
| |
Collapse
|