1
|
Kumar N, Srivastava R, Mongre RK, Mishra CB, Kumar A, Khatoon R, Banerjee A, Ashraf-Uz-Zaman M, Singh H, Lynn AM, Lee MS, Prakash A. Identifying the Novel Inhibitors Against the Mycolic Acid Biosynthesis Pathway Target "mtFabH" of Mycobacterium tuberculosis. Front Microbiol 2022; 13:818714. [PMID: 35602011 PMCID: PMC9121832 DOI: 10.3389/fmicb.2022.818714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
Mycolic acids are the key constituents of mycobacterial cell wall, which protect the bacteria from antibiotic susceptibility, helping to subvert and escape from the host immune system. Thus, the enzymes involved in regulating and biosynthesis of mycolic acids can be explored as potential drug targets to kill Mycobacterium tuberculosis (Mtb). Herein, Kyoto Encyclopedia of Genes and Genomes is used to understand the fatty acid metabolism signaling pathway and integrative computational approach to identify the novel lead molecules against the mtFabH (β-ketoacyl-acyl carrier protein synthase III), the key regulatory enzyme of the mycolic acid pathway. The structure-based virtual screening of antimycobacterial compounds from ChEMBL library against mtFabH results in the selection of 10 lead molecules. Molecular binding and drug-likeness properties of lead molecules compared with mtFabH inhibitor suggest that only two compounds, ChEMBL414848 (C1) and ChEMBL363794 (C2), may be explored as potential lead molecules. However, the spatial stability and binding free energy estimation of thiolactomycin (TLM) and compounds C1 and C2 with mtFabH using molecular dynamics simulation, followed by molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) indicate the better activity of C2 (ΔG = -14.18 kcal/mol) as compared with TLM (ΔG = -9.21 kcal/mol) and C1 (ΔG = -13.50 kcal/mol). Thus, compound C1 may be explored as promising drug candidate for the structure-based drug designing of mtFabH inhibitors in the therapy of Mtb.
Collapse
Affiliation(s)
- Niranjan Kumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Srivastava
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Raj Kumar Mongre
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women’s University, Seoul, South Korea
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Chandra Bhushan Mishra
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States
| | - Amit Kumar
- Indian Council of Medical Research–Computational Genomics Centre, All India Institute of Medical Research, New Delhi, India
- Amity Institute of Integrative Sciences and Health, Amity University, Gurugram, India
| | - Rosy Khatoon
- Amity Institute of Biotechnology, Amity University, Gurugram, India
| | - Atanu Banerjee
- Amity Institute of Biotechnology, Amity University, Gurugram, India
| | - Md Ashraf-Uz-Zaman
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States
| | - Harpreet Singh
- Indian Council of Medical Research–Computational Genomics Centre, All India Institute of Medical Research, New Delhi, India
| | - Andrew M. Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Myeong-Sok Lee
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women’s University, Seoul, South Korea
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University, Gurugram, India
| |
Collapse
|
2
|
Troudi A, Pagès JM, Brunel JM. Chemical Highlights Supporting the Role of Lipid A in Efficient Biological Adaptation of Gram-Negative Bacteria to External Stresses. J Med Chem 2021; 64:1816-1834. [PMID: 33538159 DOI: 10.1021/acs.jmedchem.0c02185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The outer membrane (OM) of Gram-negative bacteria provides an efficient barrier against external noxious compounds such as antimicrobial agents. Associated with drug target modification, it contributes to the overall failure of chemotherapy. In the complex OM architecture, Lipid A plays an essential role by anchoring the lipopolysaccharide in the membrane and ensuring the spatial organization between lipids, proteins, and sugars. Currently, the targets of almost all antibiotics are intracellularly located and require translocation across membranes. We report herein an integrated view of Lipid A synthesis, membrane assembly, a structure comparison at the molecular structure level of numerous Gram-negative bacterial species, as well as its recent use as a target for original antibacterial molecules. This review paves the way for a new vision of a key membrane component that acts during bacterial adaptation to environmental stresses and for the development of new weapons against microbial resistance to usual antibiotics.
Collapse
Affiliation(s)
- Azza Troudi
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France.,Laboratory of Microorganisms and Active Biomolecules, Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1008, Tunisia
| | - Jean Marie Pagès
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
| | - Jean Michel Brunel
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
| |
Collapse
|
3
|
Mindrebo JT, Misson LE, Johnson C, Noel JP, Burkart MD. Activity Mapping the Acyl Carrier Protein: Elongating Ketosynthase Interaction in Fatty Acid Biosynthesis. Biochemistry 2020; 59:3626-3638. [PMID: 32857494 DOI: 10.1021/acs.biochem.0c00605] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elongating ketosynthases (KSs) catalyze carbon-carbon bond-forming reactions during the committed step for each round of chain extension in both fatty acid synthases (FASs) and polyketide synthases (PKSs). A small α-helical acyl carrier protein (ACP) shuttles fatty acyl intermediates between enzyme active sites. To accomplish this task, the ACP relies on a series of dynamic interactions with multiple partner enzymes of FAS and associated FAS-dependent pathways. Recent structures of the Escherichia coli FAS ACP, AcpP, in covalent complexes with its two cognate elongating KSs, FabF and FabB, provide high-resolution details of these interfaces, but a systematic analysis of specific interfacial interactions responsible for stabilizing these complexes has not yet been undertaken. Here, we use site-directed mutagenesis with both in vitro and in vivo activity analyses to quantitatively evaluate these contacting surfaces between AcpP and FabF. We delineate the FabF interface into three interacting regions and demonstrate the effects of point mutants, double mutants, and region deletion variants. Results from these analyses reveal a robust and modular FabF interface capable of tolerating seemingly critical interface mutations with only the deletion of an entire region significantly compromising activity. Structure and sequence analyses of FabF orthologs from related type II FAS pathways indicate significant conservation of type II FAS KS interface residues and, overall, support its delineation into interaction regions. These findings strengthen our mechanistic understanding of molecular recognition events between ACPs and FAS enzymes and provide a blueprint for engineering ACP-dependent biosynthetic pathways.
Collapse
Affiliation(s)
- Jeffrey T Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States.,Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Laetitia E Misson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Caitlin Johnson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| |
Collapse
|
4
|
Wang J, Ye X, Yang X, Cai Y, Wang S, Tang J, Sachdeva M, Qian Y, Hu W, Leeds JA, Yuan Y. Discovery of Novel Antibiotics as Covalent Inhibitors of Fatty Acid Synthesis. ACS Chem Biol 2020; 15:1826-1834. [PMID: 32568510 DOI: 10.1021/acschembio.9b00982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The steady increase in the prevalence of multidrug-resistant Staphylococcus aureus has made the search for novel antibiotics to combat this clinically important pathogen an urgent matter. In an effort to discover antibacterials with new chemical structures and mechanisms, we performed a growth inhibition screen of a synthetic library against S. aureus and discovered a promising scaffold with a 1,3,5-oxadiazin-2-one core. These compounds are potent against both methicillin-sensitive and methicillin-resistant S. aureus strains. Isolation of compound-resistant strains followed by whole genome sequencing revealed its cellular target as FabH, a key enzyme in bacterial fatty acid synthesis. Detailed mechanism of action studies suggested the compounds inhibit FabH activity by covalently modifying its active site cysteine residue with high selectivity. A crystal structure of FabH protein modified by a selected compound Oxa1 further confirmed covalency and suggested a possible mechanism for reaction. Moreover, the structural snapshot provided an explanation for compound selectivity. On the basis of the structure, we designed and synthesized Oxa1 derivatives and evaluated their antibacterial activity. The structure-activity relationship supports the hypothesis that noncovalent recognition between compounds and FabH is critical for the activity of these covalent inhibitors. We believe further optimization of the current scaffold could lead to an antibacterial with potential to treat drug-resistant bacteria in the clinic.
Collapse
Affiliation(s)
- Jia Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaoping Ye
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaohan Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Youyan Cai
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Shengjun Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jieyu Tang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Meena Sachdeva
- Novartis Institutes for Biomedical Research, Inc., Infectious Diseases Area, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Yu Qian
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wenhao Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jennifer A. Leeds
- Novartis Institutes for Biomedical Research, Inc., Infectious Diseases Area, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Yanqiu Yuan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou 510990, China
| |
Collapse
|
5
|
Navarro MOP, Simionato AS, Pérez JCB, Barazetti AR, Emiliano J, Niekawa ETG, Andreata MFDL, Modolon F, Dealis ML, Araújo EJDA, Carlos TM, Scarpelim OJ, da Silva DB, Chryssafidis AL, Bruheim P, Andrade G. Fluopsin C for Treating Multidrug-Resistant Infections: In vitro Activity Against Clinically Important Strains and in vivo Efficacy Against Carbapenemase-Producing Klebsiella pneumoniae. Front Microbiol 2019; 10:2431. [PMID: 31708901 PMCID: PMC6824035 DOI: 10.3389/fmicb.2019.02431] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 10/08/2019] [Indexed: 11/22/2022] Open
Abstract
The increasing emergence of multidrug-resistant (MDR) organisms in hospital infections is causing a global public health crisis. The development of drugs with effective antibiotic action against such agents is of the highest priority. In the present study, the action of Fluopsin C against MDR clinical isolates was evaluated under in vitro and in vivo conditions. Fluopsin C was produced in cell suspension culture of Pseudomonas aeruginosa LV strain, purified by liquid adsorption chromatography and identified by mass spectrometric analysis. Bioactivity, bacterial resistance development risk against clinically important pathogenic strains and toxicity in mammalian cell were initially determined by in vitro models. In vivo toxicity was evaluated in Tenebrio molitor larvae and mice. The therapeutic efficacy of intravenous Fluopsin C administration was evaluated in a murine model of Klebsiella pneumoniae (KPC) acute sepsis, using six different treatments. The in vitro results indicated MIC and MBC below 2 μg/mL and low bacterial resistance development frequency. Electron microscopy showed that Fluopsin C may have altered the exopolysaccharide matrix and caused disruption of the cell wall of MDR bacteria. Best therapeutic results were achieved in mice treated with a single dose of 2 mg/kg and in mice treated with two doses of 1 mg/kg, 8 h apart. Furthermore, acute and chronic histopathological studies demonstrated absent nephrotoxicity and moderate hepatotoxicity. The results demonstrated the efficacy of Fluopsin C against MDR organisms in in vitro and in vivo models, and hence it can be a novel therapeutic agent for the control of severe MDR infections.
Collapse
Affiliation(s)
| | - Ane Stefano Simionato
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | | | - André Riedi Barazetti
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | - Janaina Emiliano
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | - Erika Tyemi Goya Niekawa
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | | | - Fluvio Modolon
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | - Mickely Liuti Dealis
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | | | | | | | - Denise Brentan da Silva
- Biological and Health Sciences Centre, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Andreas Lazaros Chryssafidis
- Veterinary Toxicology Laboratory, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Galdino Andrade
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| |
Collapse
|
6
|
A Drug Repositioning Approach Reveals that Streptococcus mutans Is Susceptible to a Diverse Range of Established Antimicrobials and Nonantibiotics. Antimicrob Agents Chemother 2017; 62:AAC.01674-17. [PMID: 29061736 DOI: 10.1128/aac.01674-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/07/2017] [Indexed: 02/06/2023] Open
Abstract
Streptococcus mutans is the primary causative agent of dental caries and contributes to the multispecies biofilm known as dental plaque. An adenylate kinase-based assay was optimized for S. mutans to detect cell lysis when exposed to the Selleck library (Selleck Chemical, Houston, TX) of 853 FDA-approved drugs in, to our knowledge, the first high-throughput drug screen in S. mutans We found 126 drugs with activity against S. mutans planktonic cultures, and they were classified into six categories: antibacterials (61), antineoplastics (23), ion channel effectors (9), other antimicrobials (7), antifungals (6), and other (20). These drugs were also tested for activity against S. mutans biofilm cultures, and 24 compounds were found to inhibit biofilm formation, 6 killed preexisting biofilms, 84 exhibited biofilm inhibition and killing activity, and 12 had no activity against biofilms. The activities of 9 selected compounds that exhibited antimicrobial activity were further characterized for their activity against S. mutans planktonic and biofilm cultures. Together, our results suggest that S. mutans exhibits a susceptibility profile to a diverse array of established and novel antibacterials.
Collapse
|
7
|
Brill ZG, Condakes ML, Ting CP, Maimone TJ. Navigating the Chiral Pool in the Total Synthesis of Complex Terpene Natural Products. Chem Rev 2017; 117:11753-11795. [PMID: 28293944 PMCID: PMC5638449 DOI: 10.1021/acs.chemrev.6b00834] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The pool of abundant chiral terpene building blocks (i.e., "chiral pool terpenes") has long served as a starting point for the chemical synthesis of complex natural products, including many terpenes themselves. As inexpensive and versatile starting materials, such compounds continue to influence modern synthetic chemistry. This review highlights 21st century terpene total syntheses which themselves use small, terpene-derived materials as building blocks. An outlook to the future of research in this area is highlighted as well.
Collapse
Affiliation(s)
- Zachary G. Brill
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
| | - Matthew L. Condakes
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
| | - Chi P. Ting
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
| | - Thomas J. Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
| |
Collapse
|
8
|
Platensimycin and platencin: Inspirations for chemistry, biology, enzymology, and medicine. Biochem Pharmacol 2016; 133:139-151. [PMID: 27865713 DOI: 10.1016/j.bcp.2016.11.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/14/2016] [Indexed: 12/15/2022]
Abstract
Natural products have served as the main source of drugs and drug leads, and natural products produced by microorganisms are one of the most prevalent sources of clinical antibiotics. Their unparalleled structural and chemical diversities provide a basis to investigate fundamental biological processes while providing access to a tremendous amount of chemical space. There is a pressing need for novel antibiotics with new mode of actions to combat the growing challenge of multidrug resistant pathogens. This review begins with the pioneering discovery and biological activities of platensimycin (PTM) and platencin (PTN), two antibacterial natural products isolated from Streptomyces platensis. The elucidation of their unique biochemical mode of action, structure-activity relationships, and pharmacokinetics is presented to highlight key aspects of their biological activities. It then presents an overview of how microbial genomics has impacted the field of PTM and PTN and revealed paradigm-shifting discoveries in terpenoid biosynthesis, fatty acid metabolism, and antibiotic and antidiabetic therapies. It concludes with a discussion covering the future perspectives of PTM and PTN in regard to natural products discovery, bacterial diterpenoid biosynthesis, and the pharmaceutical promise of PTM and PTN as antibiotics and for the treatment of metabolic disorders. PTM and PTN have inspired new discoveries in chemistry, biology, enzymology, and medicine and will undoubtedly continue to do so.
Collapse
|