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Rizo J, Encarnación-Guevara S. Bacterial protein acetylation: mechanisms, functions, and methods for study. Front Cell Infect Microbiol 2024; 14:1408947. [PMID: 39027134 PMCID: PMC11254643 DOI: 10.3389/fcimb.2024.1408947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Lysine acetylation is an evolutionarily conserved protein modification that changes protein functions and plays an essential role in many cellular processes, such as central metabolism, transcriptional regulation, chemotaxis, and pathogen virulence. It can alter DNA binding, enzymatic activity, protein-protein interactions, protein stability, or protein localization. In prokaryotes, lysine acetylation occurs non-enzymatically and by the action of lysine acetyltransferases (KAT). In enzymatic acetylation, KAT transfers the acetyl group from acetyl-CoA (AcCoA) to the lysine side chain. In contrast, acetyl phosphate (AcP) is the acetyl donor of chemical acetylation. Regardless of the acetylation type, the removal of acetyl groups from acetyl lysines occurs only enzymatically by lysine deacetylases (KDAC). KATs are grouped into three main superfamilies based on their catalytic domain sequences and biochemical characteristics of catalysis. Specifically, members of the GNAT are found in eukaryotes and prokaryotes and have a core structural domain architecture. These enzymes can acetylate small molecules, metabolites, peptides, and proteins. This review presents current knowledge of acetylation mechanisms and functional implications in bacterial metabolism, pathogenicity, stress response, translation, and the emerging topic of protein acetylation in the gut microbiome. Additionally, the methods used to elucidate the biological significance of acetylation in bacteria, such as relative quantification and stoichiometry quantification, and the genetic code expansion tool (CGE), are reviewed.
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Affiliation(s)
| | - Sergio Encarnación-Guevara
- Laboratorio de Proteómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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2
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Rahman MM, Islam MR, Talukder MEK, Atif MF, Alam R, Uddin AFMS, Anis-Ul-Haque KM, Islam MS, Uddn MJ, Akhter S. Unveiling therapeutic efficacy of extract and multi-targeting phytocompounds from Christella dentata (Forssk.) Brownsey & Jermy against multidrug-resistant Pseudomonas aeruginosa. RSC Adv 2024; 14:6096-6111. [PMID: 38370460 PMCID: PMC10871032 DOI: 10.1039/d3ra08367e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/09/2024] [Indexed: 02/20/2024] Open
Abstract
Christella dentata (Forssk.) Brownsey & Jermy has been commonly used in traditional medicinal practices but its effects on multi-drug-resistant (MDR) bacteria have remained unexplored. We aimed to assess the in vitro antibacterial potential of the ethanol extract of Christella dentata (EECD) against MDR Pseudomonas aeruginosa and to identify potential multi-targeting antibacterial phytocompounds through computer-aided drug design focusing on the LasR and LpxC proteins. PPS, FT-IR and GC-MS were used for profiling of the phytocompounds in EECD. The antimicrobial activity of EECD was assessed using in vitro agar well diffusion, disc diffusion, MIC and MBC. Computer-aided drug design was used to identify multi-targeting leads from GC-MS-annotated phytocompounds. EECD exhibited dose-dependent antibacterial activity and revealed the presence of 51 phytocompounds in GC-MS analysis. Among these, three phytocompounds; (2E,4E)-N-isobutylhexadeca-2,4-dienamide (CID 6442402), bicyclo[4.3.0]nonane, 2,2,6,7-tetramethyl-7-hydroxy- (CID 536446) and 1,4-diethylbenzene (CID 7734) were identified as promising antibacterial phytocompounds as they strongly bonded with LasR and LpxC. Of them, CID 536446 and CID 7734 exhibited multiple targeting abilities with LasR and LpxC. On further screening, both CID 536446 and CID 7734 exhibited favorable drug-able, pharmacokinetics and toxicity properties. Finally, molecular dynamics (MD) simulation proved the binding stability of bicyclo[4.3.0]nonane, 2,2,6,7-tetramethyl-7-hydroxy- and 1,4-diethylbenzene to active pockets of LasR and LpxC. The results of this study offer scientific validation for the traditional use of Christella dentata in bacterial infection-related diseases. It also suggests that bicyclo[4.3.0]nonane, 2,2,6,7-tetramethyl-7-hydroxy- and 1,4-diethylbenzene from Christella dentata might be responsible for the antibacterial activity and could act as phytopharmacological leads for the development of LasR and LpxC inhibitors against MDR P. aeruginosa.
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Affiliation(s)
- Md Mashiar Rahman
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Md Rakibul Islam
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Md Enamul Kabir Talukder
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Md Farhan Atif
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Rahat Alam
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - A F M Shahab Uddin
- Department of Computer Science and Engineering, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - K M Anis-Ul-Haque
- Department of Chemistry, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Md Saidul Islam
- Korea Institute of Radiological & Medical Sciences 75, Nowon-ro, Nowon-gu Seoul South Korea
| | - Mohammad Jashim Uddn
- Department of Pharmacy, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Shahina Akhter
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC) Foy's Lake Chittagong 4202 Bangladesh
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3
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Ostroumova OS, Efimova SS. Lipid-Centric Approaches in Combating Infectious Diseases: Antibacterials, Antifungals and Antivirals with Lipid-Associated Mechanisms of Action. Antibiotics (Basel) 2023; 12:1716. [PMID: 38136750 PMCID: PMC10741038 DOI: 10.3390/antibiotics12121716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
One of the global challenges of the 21st century is the increase in mortality from infectious diseases against the backdrop of the spread of antibiotic-resistant pathogenic microorganisms. In this regard, it is worth targeting antibacterials towards the membranes of pathogens that are quite conservative and not amenable to elimination. This review is an attempt to critically analyze the possibilities of targeting antimicrobial agents towards enzymes involved in pathogen lipid biosynthesis or towards bacterial, fungal, and viral lipid membranes, to increase the permeability via pore formation and to modulate the membranes' properties in a manner that makes them incompatible with the pathogen's life cycle. This review discusses the advantages and disadvantages of each approach in the search for highly effective but nontoxic antimicrobial agents. Examples of compounds with a proven molecular mechanism of action are presented, and the types of the most promising pharmacophores for further research and the improvement of the characteristics of antibiotics are discussed. The strategies that pathogens use for survival in terms of modulating the lipid composition and physical properties of the membrane, achieving a balance between resistance to antibiotics and the ability to facilitate all necessary transport and signaling processes, are also considered.
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Affiliation(s)
- Olga S. Ostroumova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia;
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Imon RR, Kabir Talukder ME, Akhter S, Islam MS, Ahammad F, Anis-Ul-Haque KM, Moniruzzaman M, Afroze M, Khan M, Hena Mostofa Jamal MA, Wani TA, Uddin MJ, Rahman MM. Natural defense against multi-drug resistant Pseudomonas aeruginosa: Cassia occidentalis L. in vitro and in silico antibacterial activity. RSC Adv 2023; 13:28773-28784. [PMID: 37790109 PMCID: PMC10543200 DOI: 10.1039/d3ra03923d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023] Open
Abstract
Cassia occidentalis L. is widely used in indigenous and traditional medicine, but its impact on multi-drug resistant (MDR) bacterial infections mostly remains unknown. Therefore, this study aimed to evaluate the in vitro antibacterial efficiency of methanol and ethyl acetate extracts of C. occidentalis L. leaves (MECOL and EAECOL) against multi-drug resistant Pseudomonas aeruginosa and to identify potential antibacterial agents through computational studies targeting the LasR protein. Initially, 82 compounds were identified using GC-MS analysis, and the functional groups were determined through FT-IR analysis. Both extracts of the plant exhibited dose-dependent antibacterial activity, with MICs of 104.16 ± 36.08 μg mL-1 for MECOL and 83.33 ± 36.08 μg mL-1 for EAECOL, and an MBC of 125 μg mL-1. Among the 82 compounds, 12 potential compounds were identified based on binding scores using molecular docking with the LasR protein and MM-GBSA analysis. Furthermore, screening for ADME properties, including physicochemical features, water solubility, lipophilicity, RO5 compliance, and toxicity, identified the top three compounds: methyl dihydrojasmonate, methyl benzoate, and 4a-methyl-4,4a,5,6,7,8-hexahydro-2(3H)-naphthalenone, which also demonstrated binding affinity with the active site residues of the LpxC protein of the bacteria. Additionally, molecular dynamics (MD) simulations confirmed the binding reliability of these three phytochemicals to LasR's active pocket, comparable to the protein native inhibitory ligands (C12-HSL). The study offers scientific support for the traditional use of C. occidentalis in treating bacterial infections, highlighting the potential of the three compounds as leads for developing LasR inhibitors to combat multi-drug resistant P. aeruginosa.
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Affiliation(s)
- Raihan Rahman Imon
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Md Enamul Kabir Talukder
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Shahina Akhter
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong Foy's Lake Chittagong 4202 Bangladesh
| | - Md Saidul Islam
- Korea Institute of Radiological & Medical Sciences 75, Nowon-ro, Nowon-gu Seoul South Korea
| | - Foysal Ahammad
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre) Jashore 7408 Bangladesh
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU) Doha Qatar
| | - K M Anis-Ul-Haque
- Department of Chemistry, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Md Moniruzzaman
- Bangladesh Reference Institute for Chemical Measurements (BRICM), Bangladesh Council of Scientific and Industrial Research Dr Qudrat-i-Khuda Road, Dhanmondi Dhaka 1205 Bangladesh
| | - Mirola Afroze
- Bangladesh Reference Institute for Chemical Measurements (BRICM), Bangladesh Council of Scientific and Industrial Research Dr Qudrat-i-Khuda Road, Dhanmondi Dhaka 1205 Bangladesh
| | - Mala Khan
- Bangladesh Reference Institute for Chemical Measurements (BRICM), Bangladesh Council of Scientific and Industrial Research Dr Qudrat-i-Khuda Road, Dhanmondi Dhaka 1205 Bangladesh
| | | | - Tanveer A Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University PO Box 2457 Riyadh 11451 Saudi Arabia
| | - Mohammad Jashim Uddin
- Department of Pharmacy, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Md Mashiar Rahman
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
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5
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Kumar Pal S, Kumar S. Indole-based LpxC (UDP-3-O-(R-3-hydroxyacyl)-N-acetylglucosaminedeacetylase) inhibitors for Salmonella typhi: rational drug discovery through in silico screening. 3 Biotech 2023; 13:281. [PMID: 37496977 PMCID: PMC10366066 DOI: 10.1007/s13205-023-03699-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023] Open
Abstract
Salmonella typhi is an infectious bacteria that causes typhoid fever and poses a significant risk to human health. The emergence of antibiotic resistance has become a growing concern in the management of this disease. In this work, a structure-based drug design approach was used to identify inhibitors for zinc-dependent metalloamidase LpxC, the enzyme responsible for the biosynthesis of lipid A. Using an in silico approach (virtual screening, docking, and molecular dynamics (MD) simulations), from a library of 59,000 indole derivatives, we were able to identify promising lead molecules with high binding affinity to the LpxC. Of these, five molecules (compound 435 (CID: 12253558), compound 436 (CID: 122514279), compound 1812 (CID: 90797680), compound 2584 (CID: 57056726), and compound 2545 (CID: 59897361)) have passed all the filtering criteria. This finding was verified by molecular dynamics (MD) simulation as well as post-dynamics free energy calculations. The five compounds that have been identified have shown the most promise compared to other compounds that are already recognized. To further validate the positive outcome of this study, experimental validation and optimization are necessary. These lead compounds may help to develop new antibiotics for antibiotic-resistant Salmonella typhi and improve typhoid fever treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03699-5.
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Affiliation(s)
- Sudhir Kumar Pal
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, 632014 Tamil Nadu India
| | - Sanjit Kumar
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, 632014 Tamil Nadu India
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Kumar Pal S, Kumar S. LpxC (UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase) inhibitors: A long path explored for potent drug design. Int J Biol Macromol 2023; 234:122960. [PMID: 36565833 DOI: 10.1016/j.ijbiomac.2022.12.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Microbial infections are becoming resistant to traditional antibiotics. As novel resistance mechanisms are developed and disseminated across the world, our ability to treat the most common infectious diseases is becoming increasingly compromised. As existing antibiotics are losing their effectiveness, especially treatment of bacterial infections, is difficult. In order to combat this issue, it is of utmost importance to identify novel pharmacological targets or antibiotics. LpxC, a zinc-dependent metalloamidase that catalyzes the committed step in the biosynthesis of lipid A (endotoxin) in bacteria, is a prime candidate for drug/therapeutic target. So far, the rate-limiting metallo-amidase LpxC has been the most-targeted macromolecule in the Raetz pathway. This is because it is important for the growth of these bacterial infections. This review showcases on the research done to develop efficient drugs in this area before and after the 2015.
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Affiliation(s)
- Sudhir Kumar Pal
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India.
| | - Sanjit Kumar
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India.
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7
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Niu Z, Lei P, Wang Y, Wang J, Yang J, Zhang J. Small molecule LpxC inhibitors against gram-negative bacteria: Advances and future perspectives. Eur J Med Chem 2023; 253:115326. [PMID: 37023679 DOI: 10.1016/j.ejmech.2023.115326] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/18/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Uridine diphosphate-3-O-(hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a metalloenzyme with zinc ions as cofactors and is a key enzyme in the essential structural outer membrane lipid A synthesis commitment step of gram-negative bacteria. As LpxC is extremely homologous among different Gram-negative bacteria, it is conserved in almost all gram-negative bacteria, which makes LpxC a promising target. LpxC inhibitors have been reported extensively in recent years, such as PF-5081090 and CHIR-090 were found to have broad-spectrum antibiotic activity against P. aeruginosa and E. coli. They are mainly classified into hydroxamate inhibitors and non-hydroxamate inhibitors based on their structure, but no LpxC inhibitors have been marketed due to safety and activity issues. This review, therefore, focuses on small molecule inhibitors of LpxC against gram-negative pathogenic bacteria and covers recent advances in LpxC inhibitors, focusing on their structural optimization process, structure-activity relationships, and future directions, with the aim of providing ideas for the development of LpxC inhibitors and clinical research.
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Basak S, Li Y, Tao S, Daryaee F, Merino J, Gu C, Delker SL, Phan JN, Edwards TE, Walker SG, Tonge PJ. Structure-Kinetic Relationship Studies for the Development of Long Residence Time LpxC Inhibitors. J Med Chem 2022; 65:11854-11875. [PMID: 36037447 PMCID: PMC10182817 DOI: 10.1021/acs.jmedchem.2c00974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a promising drug target in Gram-negative bacteria. Previously, we described a correlation between the residence time of inhibitors on Pseudomonas aeruginosa LpxC (paLpxC) and the post-antibiotic effect (PAE) caused by the inhibitors on the growth of P. aeruginosa. Given that drugs with prolonged activity following compound removal may have advantages in dosing regimens, we have explored the structure-kinetic relationship for paLpxC inhibition by analogues of the pyridone methylsulfone PF5081090 (1) originally developed by Pfizer. Several analogues have longer residence times on paLpxC than 1 (41 min) including PT913, which has a residence time of 124 min. PT913 also has a PAE of 4 h, extending the original correlation observed between residence time and PAE. Collectively, the studies provide a platform for the rational modulation of paLpxC inhibitor residence time and the potential development of antibacterial agents that cause prolonged suppression of bacterial growth.
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Affiliation(s)
- Sneha Basak
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Yong Li
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Suyuan Tao
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Fereidoon Daryaee
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Jonathan Merino
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Chendi Gu
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | | | - Jenny N. Phan
- McGill University Montreal, Quebec H3A 0G4, Canada Canada
| | | | - Stephen G. Walker
- Department of Oral Biology and Pathology, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Peter J. Tonge
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Radiology, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
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Branch AH, Stoudenmire JL, Seib KL, Cornelissen CN. Acclimation to Nutritional Immunity and Metal Intoxication Requires Zinc, Manganese, and Copper Homeostasis in the Pathogenic Neisseriae. Front Cell Infect Microbiol 2022; 12:909888. [PMID: 35846739 PMCID: PMC9280163 DOI: 10.3389/fcimb.2022.909888] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/18/2022] [Indexed: 12/15/2022] Open
Abstract
Neisseria gonorrhoeae and Neisseria meningitidis are human-specific pathogens in the Neisseriaceae family that can cause devastating diseases. Although both species inhabit mucosal surfaces, they cause dramatically different diseases. Despite this, they have evolved similar mechanisms to survive and thrive in a metal-restricted host. The human host restricts, or overloads, the bacterial metal nutrient supply within host cell niches to limit pathogenesis and disease progression. Thus, the pathogenic Neisseria require appropriate metal homeostasis mechanisms to acclimate to such a hostile and ever-changing host environment. This review discusses the mechanisms by which the host allocates and alters zinc, manganese, and copper levels and the ability of the pathogenic Neisseria to sense and respond to such alterations. This review will also discuss integrated metal homeostasis in N. gonorrhoeae and the significance of investigating metal interplay.
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Affiliation(s)
- Alexis Hope Branch
- Center for Translational Immunology, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, United States
| | - Julie L. Stoudenmire
- Center for Translational Immunology, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, United States
| | - Kate L. Seib
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Cynthia Nau Cornelissen
- Center for Translational Immunology, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, United States
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Garcia-Vello P, Di Lorenzo F, Zucchetta D, Zamyatina A, De Castro C, Molinaro A. Lipopolysaccharide lipid A: A promising molecule for new immunity-based therapies and antibiotics. Pharmacol Ther 2022; 230:107970. [PMID: 34454000 DOI: 10.1016/j.pharmthera.2021.107970] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022]
Abstract
Lipopolysaccharides (LPS) are the main components of the external leaflet of the Gram-negative outer membrane and consist of three different moieties: lipid A, core oligosaccharide, and O-polysaccharide. The lipid A is a glucosamine disaccharide with different levels of acylation and phosphorylation, beside carrying, in certain cases, additional substituents on the sugar backbone. It is also the main immunostimulatory part of the LPS, as its recognition by the host immune system represents a fundamental event for detection of perilous microorganisms. Moreover, an uncontrolled immune response caused by a large amount of circulating LPS can lead to dramatic outcomes for human health, such as septic shock. The immunostimulant properties of an LPS incredibly vary depending on lipid A chemical structure, and for this reason, natural and synthetic variants of the lipid A are under study to develop new drugs that mimic or antagonise its natural effects. Here, we review past and recent findings on the lipid A as an antibiotic target and immune-therapeutic molecule, with a special attention on the crucial role of the chemical structure and its exploitation for conceiving novel strategies for treatment of several immune-related pathologies.
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Affiliation(s)
- Pilar Garcia-Vello
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy.
| | - Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - Daniele Zucchetta
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Alla Zamyatina
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy.
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11
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Fan S, Li D, Yan M, Feng X, Lv G, Wu G, Jin Y, Wang Y, Yang Z. The Complex Structure of Protein AaLpxC from Aquifex aeolicus with ACHN-975 Molecule Suggests an Inhibitory Mechanism at Atomic-Level against Gram-Negative Bacteria. Molecules 2021; 26:molecules26051451. [PMID: 33800069 PMCID: PMC7962117 DOI: 10.3390/molecules26051451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 11/16/2022] Open
Abstract
New drugs with novel antibacterial targets for Gram-negative bacterial pathogens are desperately needed. The protein LpxC is a vital enzyme for the biosynthesis of lipid A, an outer membrane component of Gram-negative bacterial pathogens. The ACHN-975 molecule has high enzymatic inhibitory capacity against the infectious diseases, which are caused by multidrug-resistant bacteria, but clinical research was halted because of its inflammatory response in previous studies. In this work, the structure of the recombinant UDP-3-O-(R-3-hydroxymyristol)-N-acetylglucosamine deacetylase from Aquifex aeolicus in complex with ACHN-975 was determined to a resolution at 1.21 Å. According to the solved complex structure, ACHN-975 was docked into the AaLpxC’s active site, which occupied the site of AaLpxC substrate. Hydroxamate group of ACHN-975 forms five-valenced coordination with resides His74, His226, Asp230, and the long chain part of ACHN-975 containing the rigid alkynyl groups docked in further to interact with the hydrophobic area of AaLpxC. We employed isothermal titration calorimetry for the measurement of affinity between AaLpxC mutants and ACHN-975, and the results manifest the key residues (His74, Thr179, Tyr212, His226, Asp230 and His253) for interaction. The determined AaLpxC crystal structure in complex with ACHN-975 is expected to serve as a guidance and basis for the design and optimization of molecular structures of ACHN-975 analogues to develop novel drug candidates against Gram-negative bacteria.
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Affiliation(s)
- Shuai Fan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Danyang Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Maocai Yan
- School of Pharmacy, Jining Medical University, Rizhao, Shandong 276800, China;
| | - Xiao Feng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Guangxin Lv
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Guangteng Wu
- ArNuXon Pharm-Sci Co., Ltd., Beijing 100085, China;
| | - Yuanyuan Jin
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
- Correspondence: (Y.W.); (Z.Y.)
| | - Zhaoyong Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
- Correspondence: (Y.W.); (Z.Y.)
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12
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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.
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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
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13
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Damale MG, Pathan SK, Patil RB, Sangshetti JN. Pharmacoinformatics approaches to identify potential hits against tetraacyldisaccharide 4'-kinase (LpxK) of Pseudomonas aeruginosa. RSC Adv 2020; 10:32856-32874. [PMID: 35516480 PMCID: PMC9056689 DOI: 10.1039/d0ra06675c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 08/24/2020] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas aeruginosa infection can cause pneumonia and urinary tract infection and the management of Pseudomonas aeruginosa infection is critical in multidrug resistance, hospital-acquired bacteremia and ventilator-associated pneumonia. The key enzymes of lipid A biosynthesis in Pseudomonas aeruginosa are promising drug targets. However, the enzyme tetraacyldisaccharide 4'-kinase (LpxK) has not been explored as a drug target so far. Several pharmacoinformatics tools such as comparative metabolic pathway analysis (Metacyc), data mining from a database of essential genes (DEG), homology modeling, molecular docking, pharmacophore based virtual screening, ADMET prediction and molecular dynamics simulation were used in identifying novel lead compounds against this target. The top virtual hits STOCK6S-33288, 43621, 39892, 37164 and 35740 may serve as the templates for the design and synthesis of potent LpxK inhibitors in the management of serious Pseudomonas aeruginosa infection.
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Affiliation(s)
- Manoj G Damale
- Y.B. Chavan College of Pharmacy Dr. Rafiq Zakaria Campus, Rauza Baugh Aurangabad MS 431001 India
- Srinath College of Pharmacy Aurangabad MS India
| | - Shahebaaz K Pathan
- Y.B. Chavan College of Pharmacy Dr. Rafiq Zakaria Campus, Rauza Baugh Aurangabad MS 431001 India
| | - Rajesh B Patil
- Sinhgad Technical Education Society's, Smt. Kashibai Navale College of Pharmacy Pune-Saswad Road, Kondhwa (Bk) Pune 411048 India
| | - Jaiprakash N Sangshetti
- Y.B. Chavan College of Pharmacy Dr. Rafiq Zakaria Campus, Rauza Baugh Aurangabad MS 431001 India
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14
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Pasala C, Katari SK, Nalamolu RM, Bitla AR, Amineni U. Hierarchical-Clustering, Scaffold-Mining Exercises and Dynamics Simulations for Effectual Inhibitors Against Lipid-A Biosynthesis of Helicobacter pylori. Cell Mol Bioeng 2019; 12:255-274. [PMID: 31719913 DOI: 10.1007/s12195-019-00572-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 04/23/2019] [Indexed: 12/19/2022] Open
Abstract
Introduction Treatment failures of standard regimens and new strains egression are due to the augmented drug resistance conundrum. These confounding factors now became the drug designers spotlight to implement therapeutics against Helicobacter pylori strains and to safeguard infected victims with devoid of adverse drug reactions. Thereby, to navigate the chemical space for medicine, paramount vital drug target opting considerations should be imperative. The study is therefore aimed to develop potent therapeutic variants against an insightful extrapolative, common target LpxC as a follow-up to previous studies. Methods We explored the relationships between existing inhibitors and novel leads at the scaffold level in an appropriate conformational plasticity for lead-optimization campaign. Hierarchical-clustering and shape-based screening against an in-house library of > 21 million compounds resulted in panel of 11,000 compounds. Rigid-receptor docking through virtual screening cascade, quantum-polarized-ligand, induced-fit dockings, post-docking processes and system stability assessments were performed. Results After docking experiments, an enrichment performance unveiled seven ranked actives better binding efficiencies with Zinc-binding potency than substrate and in-actives (decoy-set) with ROC (1.0) and area under accumulation curve (0.90) metrics. Physics-based membrane permeability accompanied ADME/T predictions and long-range dynamic simulations of 250 ns chemical time have depicted good passive diffusion with no toxicity of leads and sustained consistency of lead1-LpxC in the physiological milieu respectively. Conclusions In the study, as these static outcomes obtained from this approach competed with the substrate and existing ligands in binding affinity estimations as well as positively correlated from different aspects of predictions, which could facilitate promiscuous new chemical entities against H. pylori.
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Affiliation(s)
- Chiranjeevi Pasala
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, 517507 AP India
| | - Sudheer Kumar Katari
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, 517507 AP India
| | | | - Aparna R Bitla
- Department of Biochemistry, SVIMS University, Tirupati, 517507 AP India
| | - Umamaheswari Amineni
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, 517507 AP India
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15
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González-Bello C. The Inhibition of Lipid A Biosynthesis-The Antidote Against Superbugs? ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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16
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Rubab M, Chellia R, Saravanakumar K, Mandava S, Khan I, Tango CN, Hussain MS, Daliri EBM, Kim SH, Ramakrishnan SR, Wang MH, Lee J, Kwon JH, Chandrashekar S, Oh DH. Preservative effect of Chinese cabbage (Brassica rapa subsp. pekinensis) extract on their molecular docking, antioxidant and antimicrobial properties. PLoS One 2018; 13:e0203306. [PMID: 30281596 PMCID: PMC6169867 DOI: 10.1371/journal.pone.0203306] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/17/2018] [Indexed: 12/25/2022] Open
Abstract
This study aimed at investigating the antimicrobial activity of different solvent extracts of Chinese cabbage Brassica rapa subsp. pekinensis (BRARP) and their antioxidant and cytotoxicity properties. Of the different solvents extracts, the chloroform extracts (CE) were significantly inhibited the bacterial pathogens at minimum inhibitory concentration (MIC) of 16.5 mg.mL-1. Biochemical analysis revealed that total phenol (62.6 ± 0.05 mg GAE.g-1) and flavonoids (27.6 ± 0.04 mg QE.g-1) were higher in the extracts of BRARP, which resulted in enhanced antioxidant activity in CE. A total of eight dominant compounds were detected in the potent antimicrobial extract from BRARP based on GC-MS analysis. The molecular interactions study revealed that, among the screened compounds the 1,2-benzenedicarboxylic acid and 2,3-dicyanopropionamide interacted with the active site of pathogenicity and survival related protein with lipopolysaccharide (LpxC) with higer binding energy. This work concluded that the 1, 2-Benzenedicarboxylic acid and 2, 3-Dicyanopropionamide from BRARP was reported to be good non-cytotoxic and antioxidant antimicrobials against bacterial pathogens.
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Affiliation(s)
- Momna Rubab
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
| | - Ramachandran Chellia
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
| | - Kandasamy Saravanakumar
- Department of Medical Biotechnology, College of Biomedical Sciences, Kangwon National University, Chuncheon, South Korea
| | - Suresh Mandava
- College of Pharmacy, Kangwon National University, Chuncheon, South Korea
| | - Imran Khan
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
| | - Charles Nkufi Tango
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
| | - Mohammad Shakhawat Hussain
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
| | - Eric Banan-Mwine Daliri
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
| | - Se-Hun Kim
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
| | | | - Myeong-Hyeon Wang
- Department of Medical Biotechnology, College of Biomedical Sciences, Kangwon National University, Chuncheon, South Korea
| | - Jongkook Lee
- College of Pharmacy, Kangwon National University, Chuncheon, South Korea
| | - Joong-Ho Kwon
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, South Korea
| | | | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
- * E-mail:
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17
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Sharma A, Kumar V, Pratap S, Kumar P. The inhibitory and binding studies of methyl-sulfone hydroxamate based inhibitors against LpxC from drug resistant Moraxella catarrhalis using biophysical, biochemical and in silico approaches. Int J Biol Macromol 2018; 118:1747-1762. [DOI: 10.1016/j.ijbiomac.2018.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 01/17/2023]
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18
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Ahmad S, Navid A, Akhtar AS, Azam SS, Wadood A, Pérez-Sánchez H. Subtractive Genomics, Molecular Docking and Molecular Dynamics Simulation Revealed LpxC as a Potential Drug Target Against Multi-Drug Resistant Klebsiella pneumoniae. Interdiscip Sci 2018; 11:508-526. [PMID: 29721784 DOI: 10.1007/s12539-018-0299-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/11/2018] [Accepted: 04/24/2018] [Indexed: 12/17/2022]
Abstract
The emergence and dissemination of pan drug resistant clones of Klebsiella pneumoniae are great threat to public health. In this regard new therapeutic targets must be highlighted to pave the path for novel drug discovery and development. Subtractive proteomic pipeline brought forth UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC), a Zn+2 dependent cytoplasmic metalloprotein and catalyze the rate limiting deacetylation step of lipid A biosynthesis pathway. Primary sequence analysis followed by 3-dimensional (3-D) structure elucidation of the protein led to the detection of K. pneumoniae LpxC (KpLpxC) topology distinct from its orthologous counterparts in other bacterial species. Molecular docking study of the protein recognized receptor antagonist compound 106, a uridine-based LpxC inhibitory compound, as a ligand best able to fit the binding pocket with a Gold Score of 67.53. Molecular dynamics simulation of docked KpLpxC revealed an alternate binding pattern of ligand in the active site. The ligand tail exhibited preferred binding to the domain I residues as opposed to the substrate binding hydrophobic channel of subdomain II, usually targeted by inhibitory compounds. Comparison with the undocked KpLpxC system demonstrated ligand induced high conformational changes in the hydrophobic channel of subdomain II in KpLpxC. Hence, ligand exerted its inhibitory potential by rendering the channel unstable for substrate binding.
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Affiliation(s)
- Sajjad Ahmad
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Afifa Navid
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Amina Saleem Akhtar
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University-Mardan, Shankar Campus, Mardan, Khyber Pukhtoonkhwa, Pakistan
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
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19
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Bendaif H, Melhaoui A, Ramdani M, Elmsellem H, Douez C, El Ouadi Y. Antibacterial activity and virtual screening by molecular docking of lycorine from Pancratium foetidum Pom (Moroccan endemic Amaryllidaceae). Microb Pathog 2017; 115:138-145. [PMID: 29253598 DOI: 10.1016/j.micpath.2017.12.037] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 11/18/2022]
Abstract
Lycorine is an alkaloid isolated from bulbs of Pancratium foetidum Pom Amaryllidaceae of the genus Lycoris. It has very strong pharmacodynamics properties and biological effects, among others, antimalarial, antiviral, antitumor, and anti-inflammatory. Lycorine has been identified and characterized by thin layer chromatography, IR and NMR (1H and 13C NMR, COZY, HMBC, HSQC and NOESY). The antibacterial activity of lycorine has been evaluated. Lycorine has a moderate antibacterial activity on the majority of strains studied, nevertheless it is more effective than Streptomycin and Ampicillin against bacteria: P. aeruginosa, En. cloacae. To confirm these results, it is necessary to use qualitative techniques and methods, etc… We performed a virtual docking ligand-lycorine protein screening study to predict and characterize their mode of interaction with the LpxC receptor. Docking results have shown that lycorine can interact with target amino residues studied by hydrogen and metal-ion bonds. In addition, the ADME-Tox profile study has shown that lycorine is all in agreement, either with Lipinski's critics or with the toxicity standards.
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Affiliation(s)
- H Bendaif
- Laboratory of Macromolecular Organic Chemistry and Natural Products (URAC25), Faculty of Science, 60000 Oujda, Morocco.
| | - A Melhaoui
- Laboratory of Macromolecular Organic Chemistry and Natural Products (URAC25), Faculty of Science, 60000 Oujda, Morocco
| | - M Ramdani
- Laboratory of Applied Analytical Chemistry Materials and Environment (LA2CME-URAC18), Faculty of Science, B.P. 717, 60000 Oujda, Morocco
| | - H Elmsellem
- Laboratory of Applied Analytical Chemistry Materials and Environment (LA2CME-URAC18), Faculty of Science, B.P. 717, 60000 Oujda, Morocco
| | - C Douez
- Université d'Artois, 62000, Arras, France
| | - Y El Ouadi
- Laboratory of Applied Analytical Chemistry Materials and Environment (LA2CME-URAC18), Faculty of Science, B.P. 717, 60000 Oujda, Morocco.
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20
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Moreira LM, Soares MR, Facincani AP, Ferreira CB, Ferreira RM, Ferro MIT, Gozzo FC, Felestrino ÉB, Assis RAB, Garcia CCM, Setubal JC, Ferro JA, de Oliveira JCF. Proteomics-based identification of differentially abundant proteins reveals adaptation mechanisms of Xanthomonas citri subsp. citri during Citrus sinensis infection. BMC Microbiol 2017; 17:155. [PMID: 28693412 PMCID: PMC5504864 DOI: 10.1186/s12866-017-1063-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 07/01/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Xanthomonas citri subsp. citri (Xac) is the causal agent of citrus canker. A proteomic analysis under in planta infectious and non-infectious conditions was conducted in order to increase our knowledge about the adaptive process of Xac during infection. RESULTS For that, a 2D-based proteomic analysis of Xac at 1, 3 and 5 days after inoculation, in comparison to Xac growth in NB media was carried out and followed by MALDI-TOF-TOF identification of 124 unique differentially abundant proteins. Among them, 79 correspond to up-regulated proteins in at least one of the three stages of infection. Our results indicate an important role of proteins related to biofilm synthesis, lipopolysaccharides biosynthesis, and iron uptake and metabolism as possible modulators of plant innate immunity, and revealed an intricate network of proteins involved in reactive oxygen species adaptation during Plants` Oxidative Burst response. We also identified proteins previously unknown to be involved in Xac-Citrus interaction, including the hypothetical protein XAC3981. A mutant strain for this gene has proved to be non-pathogenic in respect to classical symptoms of citrus canker induced in compatible plants. CONCLUSIONS This is the first time that a protein repertoire is shown to be active and working in an integrated manner during the infection process in a compatible host, pointing to an elaborate mechanism for adaptation of Xac once inside the plant.
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Affiliation(s)
- Leandro M Moreira
- Departamento de Ciências Biológicas (DECBI), Instituto de Ciências Exatas e Biológicas (ICEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil. .,Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.
| | - Márcia R Soares
- Departamento de Bioquímica (DBq), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Agda P Facincani
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, Jaboticabal, SP, Brazil.
| | - Cristiano B Ferreira
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Rafael M Ferreira
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Maria I T Ferro
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Fábio C Gozzo
- Instituto de Química, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Érica B Felestrino
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Renata A B Assis
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Camila Carrião M Garcia
- Departamento de Ciências Biológicas (DECBI), Instituto de Ciências Exatas e Biológicas (ICEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil.,Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - João C Setubal
- Departamento de Bioquímica (DB), Instituto de Química (IQ), Universidade de São Paulo (USP), São Paulo, SP, Brazil.,Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA
| | - Jesus A Ferro
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Julio C F de Oliveira
- Departamento de Ciências Biológicas (DCB), Universidade Federal de São Paulo (UNIFESP), Diadema, SP, Brazil
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21
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Zhang J, Chan A, Lippa B, Cross JB, Liu C, Yin N, Romero JAC, Lawrence J, Heney R, Herradura P, Goss J, Clark C, Abel C, Zhang Y, Poutsiaka KM, Epie F, Conrad M, Mahamoon A, Nguyen K, Chavan A, Clark E, Li TC, Cheng RK, Wood M, Andersen OA, Brooks M, Kwong J, Barker J, Parr IB, Gu Y, Ryan MD, Coleman S, Metcalf CA. Structure-based discovery of LpxC inhibitors. Bioorg Med Chem Lett 2017; 27:1670-1680. [DOI: 10.1016/j.bmcl.2017.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 10/20/2022]
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23
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Erwin AL. Antibacterial Drug Discovery Targeting the Lipopolysaccharide Biosynthetic Enzyme LpxC. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a025304. [PMID: 27235477 DOI: 10.1101/cshperspect.a025304] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The enzyme LpxC (UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase) is broadly conserved across Gram-negative bacteria and is essential for synthesis of lipid A, the membrane anchor of the lipopolysaccharides (LPSs), which are a major component of the outer membrane in nearly all Gram-negative bacteria. LpxC has been the focus of target-directed antibiotic discovery projects in numerous pharmaceutical and academic groups for more than 20 years. Despite intense effort, no LpxC inhibitor has been approved for therapeutic use, and only one has yet reached human studies. This article will summarize the history of LpxC as a drug target and the parallel history of research on LpxC biology. Both academic and industrial researchers have used LpxC inhibitors as tool compounds, leading to increased understanding of the differing mechanisms for regulation of LPS synthesis in Escherichia coli and Pseudomonas aeruginosa.
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24
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Miller MD, Gao N, Ross PL, Olivier NB. Crystal structure of A. aeolicus LpxC with bound product suggests alternate deacetylation mechanism. Proteins 2015; 83:1706-19. [PMID: 26177919 DOI: 10.1002/prot.24856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/08/2015] [Accepted: 07/01/2015] [Indexed: 11/07/2022]
Abstract
UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) is the first committed step to form lipid A, an essential component of the outer membrane of Gram-negative bacteria. As it is essential for the survival of many pathogens, LpxC is an attractive target for antibacterial therapeutics. Herein, we report the product-bound co-crystal structure of LpxC from the acheal Aquifex aeolicus solved to 1.6 Å resolution. We identified interactions by hydroxyl and hydroxymethyl substituents of the product glucosamine ring that may enable new insights to exploit waters in the active site for structure-based design of LpxC inhibitors with novel scaffolds. By using this product structure, we have performed quantum mechanical modeling on the substrate in the active site. Based on our results and published experimental data, we propose a new mechanism that may lead to a better understanding of LpxC catalysis and inhibition.
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Affiliation(s)
- Matthew D Miller
- AstraZeneca R&D Boston, Infection Innovative Medicines Unit, Waltham, Massachusetts, 02451
| | - Ning Gao
- AstraZeneca R&D Boston, Discovery Sciences, Waltham, Massachusetts, 02451
| | - Philip L Ross
- AstraZeneca R&D Boston, Discovery Sciences, Waltham, Massachusetts, 02451
| | - Nelson B Olivier
- AstraZeneca R&D Cambridge-UK, Discovery Sciences, Cambridge, CB4 0FZ, United Kingdom
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Gao N, McLeod SM, Hajec L, Olivier NB, Lahiri SD, Bryan Prince D, Thresher J, Ross PL, Whiteaker JD, Doig P, Li AH, Hill PJ, Cornebise M, Reck F, Hale MR. Overexpression of Pseudomonas aeruginosa LpxC with its inhibitors in an acrB-deficient Escherichia coli strain. Protein Expr Purif 2014; 104:57-64. [DOI: 10.1016/j.pep.2014.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/27/2014] [Accepted: 09/09/2014] [Indexed: 10/24/2022]
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26
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Szermerski M, Melesina J, Wichapong K, Löppenberg M, Jose J, Sippl W, Holl R. Synthesis, biological evaluation and molecular docking studies of benzyloxyacetohydroxamic acids as LpxC inhibitors. Bioorg Med Chem 2014; 22:1016-28. [DOI: 10.1016/j.bmc.2013.12.057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/21/2013] [Accepted: 12/18/2013] [Indexed: 11/28/2022]
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27
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Lee CJ, Liang X, Gopalaswamy R, Najeeb J, Ark ED, Toone EJ, Zhou P. Structural basis of the promiscuous inhibitor susceptibility of Escherichia coli LpxC. ACS Chem Biol 2014; 9:237-46. [PMID: 24117400 DOI: 10.1021/cb400067g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The LpxC enzyme in the lipid A biosynthetic pathway is one of the most promising and clinically unexploited antibiotic targets for treatment of multidrug-resistant Gram-negative infections. Progress in medicinal chemistry has led to the discovery of potent LpxC inhibitors with a variety of chemical scaffolds and distinct antibiotic profiles. The vast majority of these compounds, including the nanomolar inhibitors L-161,240 and BB-78485, are highly effective in suppressing the activity of Escherichia coli LpxC (EcLpxC) but not divergent orthologs such as Pseudomonas aeruginosa LpxC (PaLpxC) in vitro. The molecular basis for such promiscuous inhibition of EcLpxC has remained poorly understood. Here, we report the crystal structure of EcLpxC bound to L-161,240, providing the first molecular insight into L-161,240 inhibition. Additionally, structural analysis of the EcLpxC/L-161,240 complex together with the EcLpxC/BB-78485 complex reveals an unexpected backbone flipping of the Insert I βa-βb loop in EcLpxC in comparison with previously reported crystal structures of EcLpxC complexes with l-threonyl-hydroxamate-based broad-spectrum inhibitors. Such a conformational switch, which has only been observed in EcLpxC but not in divergent orthologs such as PaLpxC, results in expansion of the active site of EcLpxC, enabling it to accommodate LpxC inhibitors with a variety of head groups, including compounds containing single (R- or S-enantiomers) or double substitutions at the neighboring Cα atom of the hydroxamate warhead group. These results highlight the importance of understanding inherent conformational plasticity of target proteins in lead optimization.
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Affiliation(s)
- Chul-Jin Lee
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Structural Biology & Biophysics Program, Duke University, Durham, North Carolina 27710, United States
| | - Xiaofei Liang
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Ramesh Gopalaswamy
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Javaria Najeeb
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Structural Biology & Biophysics Program, Duke University, Durham, North Carolina 27710, United States
| | - Eugene D. Ark
- Trinity College of Arts & Sciences, Duke University, Durham, North Carolina 27708, United States
| | - Eric J. Toone
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Structural Biology & Biophysics Program, Duke University, Durham, North Carolina 27710, United States
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Pei Zhou
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Structural Biology & Biophysics Program, Duke University, Durham, North Carolina 27710, United States
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
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28
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Clayton GM, Klein DJ, Rickert KW, Patel SB, Kornienko M, Zugay-Murphy J, Reid JC, Tummala S, Sharma S, Singh SB, Miesel L, Lumb KJ, Soisson SM. Structure of the bacterial deacetylase LpxC bound to the nucleotide reaction product reveals mechanisms of oxyanion stabilization and proton transfer. J Biol Chem 2013; 288:34073-34080. [PMID: 24108127 DOI: 10.1074/jbc.m113.513028] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The emergence of antibiotic-resistant strains of pathogenic bacteria is an increasing threat to global health that underscores an urgent need for an expanded antibacterial armamentarium. Gram-negative bacteria, such as Escherichia coli, have become increasingly important clinical pathogens with limited treatment options. This is due in part to their lipopolysaccharide (LPS) outer membrane components, which dually serve as endotoxins while also protecting Gram-negative bacteria from antibiotic entry. The LpxC enzyme catalyzes the committed step of LPS biosynthesis, making LpxC a promising target for new antibacterials. Here, we present the first structure of an LpxC enzyme in complex with the deacetylation reaction product, UDP-(3-O-(R-3-hydroxymyristoyl))-glucosamine. These studies provide valuable insight into recognition of substrates and products by LpxC and a platform for structure-guided drug discovery of broad spectrum Gram-negative antibiotics.
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Affiliation(s)
- Gina M Clayton
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Daniel J Klein
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Keith W Rickert
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Sangita B Patel
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Maria Kornienko
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Joan Zugay-Murphy
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - John C Reid
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Srivanya Tummala
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Sujata Sharma
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Sheo B Singh
- Discovery Chemistry, Merck Research Laboratories, Kenilworth, New Jersey 07033
| | - Lynn Miesel
- Infectious Diseases, Merck Research Laboratories, Kenilworth, New Jersey 07033
| | - Kevin J Lumb
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Stephen M Soisson
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486.
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29
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Schitter G, Wrodnigg TM. Update on carbohydrate-containing antibacterial agents. Expert Opin Drug Discov 2013; 4:315-56. [PMID: 23489128 DOI: 10.1517/17460440902778725] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Since the first known use of antibiotics > 2,500 years ago, a research field with immense importance for the welfare of mankind has been developed. After a decrease in interest in this topic by the end of the 20th century the occurrence of (poly-)resistant strains of bacteria induced a revival of antibiotics research. Health systems have been seeking viable and reliable solutions to this dangerous and expansive threat. OBJECTIVE This review will focus on carbohydrate-containing antibiotics and will give an outline of recently published novel isolated, semisynthetic as well as synthetic structures, their mechanism of action, if known, and the strategies for the design of compounds with potential by improved antibacterial properties. METHODS The literature between 2000 and 2008 was screened with main focus on recent examples of novel structures and strategies for the lead finding of exclusively antibacterial agents. RESULTS/CONCLUSION With the explanation of the role of the carbohydrate moieties in the respective antibacterial agents together with better synthetic strategies in carbohydrate chemistry as well as improvements in assay development for high throughput screening methods, carbohydrate-containing antibiotics can be used for the finding of potential drug leads that contribute to the fight against infections and diseases caused by (resistant) bacterial pathogens.
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Affiliation(s)
- Georg Schitter
- Technical University Graz, Institute of Organic Chemistry, Univ.-Doz. TMW, Dip.-Ing. GS, Glycogroup, A-8010 Graz, Austria +43 316 873 8744 ; +43 316 873 8740 ;
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30
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Hale MR, Hill P, Lahiri S, Miller MD, Ross P, Alm R, Gao N, Kutschke A, Johnstone M, Prince B, Thresher J, Yang W. Exploring the UDP pocket of LpxC through amino acid analogs. Bioorg Med Chem Lett 2013; 23:2362-7. [PMID: 23499237 DOI: 10.1016/j.bmcl.2013.02.055] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 02/06/2013] [Accepted: 02/12/2013] [Indexed: 11/19/2022]
Abstract
Lipopolysaccharide (LPS) biosynthesis is an attractive antibacterial target as it is both conserved and essential for the survival of key pathogenic bacteria. Lipid A is the hydrophobic anchor for LPS and a key structural component of the outer membrane of Gram-negative bacteria. Lipid A biosynthesis is performed in part by a unique zinc dependent metalloamidase, LpxC (UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase), which catalyzes the first non-reversible step in lipid A biosynthesis. The UDP portion of the LpxC substrate-binding pocket has been relatively unexplored. We have designed and evaluated a series of hydroxamate based inhibitors which explore the SAR of substitutions directed into the UDP pocket with a range of substituted α-amino acid based linkers. We also provide the first wild type structure of Pseudomonas aeruginosa LpxC which was utilized in the design of many of these analogs.
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Affiliation(s)
- Michael R Hale
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.
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31
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Pradhan D, Priyadarshini V, Munikumar M, Swargam S, Umamaheswari A, Bitla A. Para-(benzoyl)-phenylalanine as a potential inhibitor against LpxC of Leptospira spp.: homology modeling, docking, and molecular dynamics study. J Biomol Struct Dyn 2013; 32:171-85. [PMID: 23383626 DOI: 10.1080/07391102.2012.758056] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Leptospira interrogans, a Gram-negative bacterial pathogen is the main cause of human leptospirosis. Lipid A is a highly immunoreactive endotoxic center of lipopolysaccharide (LPS) that anchors LPS into the outer membrane of Leptospira. Discovery of compounds inhibiting lipid-A biosynthetic pathway would be promising for dissolving the structural integrity of membrane leading to cell lysis and death of Leptospira. LpxC, a unique enzyme of lipid-A biosynthetic pathway was identified as common drug target of Leptospira. Herein, homology modeling, docking, and molecular dynamics (MD) simulations were employed to discover potential inhibitors of LpxC. A reliable tertiary structure of LpxC in complex with inhibitor BB-78485 was constructed in Modeller 9v8. A data-set of BB-78485 structural analogs were docked with LpxC in Maestro v9.2 virtual screening workflow, which implements three stage Glide docking protocol. Twelve lead molecules with better XP Gscore compared to BB-78485 were proposed as potential inhibitors of LpxC. Para-(benzoyl)-phenylalanine - that showed lowest XP Gscore (-10.35 kcal/mol) - was predicted to have best binding affinity towards LpxC. MD simulations were performed for LpxC and para-(benzoyl)-phenylalanine docking complex in Desmond v3.0. Trajectory analysis showed the docking complex and inter-molecular interactions was stable throughout the entire production part of MD simulations. The results indicate para-(benzoyl)-phenylalanine as a potent drug molecule against leptospirosis. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:10.
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Affiliation(s)
- Dibyabhaba Pradhan
- a Department of Bioinformatics , SVIMS Bioinformatics Centre, SVIMS University , Tirupati , 517507 , AP , India
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32
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Warmus JS, Quinn CL, Taylor C, Murphy ST, Johnson TA, Limberakis C, Ortwine D, Bronstein J, Pagano P, Knafels JD, Lightle S, Mochalkin I, Brideau R, Podoll T. Structure based design of an in vivo active hydroxamic acid inhibitor of P. aeruginosa LpxC. Bioorg Med Chem Lett 2012; 22:2536-43. [PMID: 22401863 DOI: 10.1016/j.bmcl.2012.01.140] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 01/30/2012] [Accepted: 01/31/2012] [Indexed: 11/28/2022]
Abstract
Lipid A is an essential component of the Gram negative outer membrane, which protects the bacterium from attack of many antibiotics. The Lipid A biosynthesis pathway is essential for Gram negative bacterial growth and is unique to these bacteria. The first committed step in Lipid A biosynthesis is catalysis by LpxC, a zinc dependent deacetylase. We show the design of an LpxC inhibitor utilizing a robust model which directed efficient design of picomolar inhibitors. Analysis of physiochemical properties drove design to focus on an optimal lipophilicity profile. Further structure based design took advantage of a conserved water network over the active site, and with the optimal lipophilicity profile, led to an improved LpxC inhibitor with in vivo activity against wild type Pseudomonas aeruginosa.
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Affiliation(s)
- Joseph S Warmus
- Department of Chemistry, Pfizer Global Research and Development, Ann Arbor, MI 48105, USA.
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33
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Montgomery JI, Brown MF, Reilly U, Price LM, Abramite JA, Arcari J, Barham R, Che Y, Chen JM, Chung SW, Collantes EM, Desbonnet C, Doroski M, Doty J, Engtrakul JJ, Harris TM, Huband M, Knafels JD, Leach KL, Liu S, Marfat A, McAllister L, McElroy E, Menard CA, Mitton-Fry M, Mullins L, Noe MC, O'Donnell J, Oliver R, Penzien J, Plummer M, Shanmugasundaram V, Thoma C, Tomaras AP, Uccello DP, Vaz A, Wishka DG. Pyridone methylsulfone hydroxamate LpxC inhibitors for the treatment of serious gram-negative infections. J Med Chem 2012; 55:1662-70. [PMID: 22257165 DOI: 10.1021/jm2014875] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The synthesis and biological activity of a new series of LpxC inhibitors represented by pyridone methylsulfone hydroxamate 2a is presented. Members of this series have improved solubility and free fraction when compared to compounds in the previously described biphenyl methylsulfone hydroxamate series, and they maintain superior Gram-negative antibacterial activity to comparator agents.
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Affiliation(s)
- Justin I Montgomery
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States.
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34
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Brown MF, Reilly U, Abramite JA, Arcari JT, Oliver R, Barham RA, Che Y, Chen JM, Collantes EM, Chung SW, Desbonnet C, Doty J, Doroski M, Engtrakul JJ, Harris TM, Huband M, Knafels JD, Leach KL, Liu S, Marfat A, Marra A, McElroy E, Melnick M, Menard CA, Montgomery JI, Mullins L, Noe MC, O'Donnell J, Penzien J, Plummer MS, Price LM, Shanmugasundaram V, Thoma C, Uccello DP, Warmus JS, Wishka DG. Potent inhibitors of LpxC for the treatment of Gram-negative infections. J Med Chem 2012; 55:914-23. [PMID: 22175825 DOI: 10.1021/jm2014748] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this paper, we present the synthesis and SAR as well as selectivity, pharmacokinetic, and infection model data for representative analogues of a novel series of potent antibacterial LpxC inhibitors represented by hydroxamic acid.
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Affiliation(s)
- Matthew F Brown
- Worldwide Medicinal Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States.
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35
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Page MGP. The role of the outer membrane of Gram-negative bacteria in antibiotic resistance: Ajax' shield or Achilles' heel? Handb Exp Pharmacol 2012:67-86. [PMID: 23090596 DOI: 10.1007/978-3-642-28951-4_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There has been an enormous increase in our knowledge of the fundamental steps in the biosynthesis and assembly of the outer membrane of Gram-negative bacteria. Lipopolysaccharide is a major component of the outer membrane of Gram-negative bacteria as is peptidoglycan. Porins, efflux pumps and other transport proteins of the outer membrane are also present. It is clear that there are numerous essential proteins that have the potential to be targets for novel antimicrobial agents. Progress, however, has been slow. Much of the emphasis has been on cytoplasmic processes that were better understood earlier on, but have the drawback that two penetration barriers, with different permeability properties, have to be crossed. With the increased understanding of the late-stage events occurring in the periplasm, it may be possible to shift focus to these more accessible targets. Nevertheless, getting drugs across the outer membrane will remain a challenge to the ingenuity of the medicinal chemist.
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36
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Liang X, Lee CJ, Chen X, Chung HS, Zeng D, Raetz CRH, Li Y, Zhou P, Toone EJ. Syntheses, structures and antibiotic activities of LpxC inhibitors based on the diacetylene scaffold. Bioorg Med Chem 2011; 19:852-60. [PMID: 21194954 PMCID: PMC3035996 DOI: 10.1016/j.bmc.2010.12.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/01/2010] [Accepted: 12/02/2010] [Indexed: 11/27/2022]
Abstract
Compounds inhibiting LpxC in the lipid A biosynthetic pathway are promising leads for novel antibiotics against multidrug-resistant Gram-negative pathogens. We report the syntheses and structural and biochemical characterizations of LpxC inhibitors based on a diphenyl-diacetylene (1,4-diphenyl-1,3-butadiyne) threonyl-hydroxamate scaffold. These studies provide a molecular interpretation for the differential antibiotic activities of compounds with a substituted distal phenyl ring as well as the absolute stereochemical requirement at the C2, but not C3, position of the threonyl group.
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Affiliation(s)
- Xiaofei Liang
- Department of Chemistry, Jilin University, Changchun, Jilin 130021, P.R. China
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Chul-Jin Lee
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Structural Biology & Biophysics Program, Duke University, Durham, NC 27710, USA
| | - Xin Chen
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Hak Suk Chung
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Daina Zeng
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Yaoxian Li
- Department of Chemistry, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Pei Zhou
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Structural Biology & Biophysics Program, Duke University, Durham, NC 27710, USA
| | - Eric J. Toone
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Structural Biology & Biophysics Program, Duke University, Durham, NC 27710, USA
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37
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Cole KE, Gattis SG, Angell HD, Fierke CA, Christianson DW. Structure of the metal-dependent deacetylase LpxC from Yersinia enterocolitica complexed with the potent inhibitor CHIR-090 . Biochemistry 2010; 50:258-65. [PMID: 21171638 DOI: 10.1021/bi101622a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first committed step of lipid A biosynthesis is catalyzed by UDP-(3-O-((R)-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase, a metal-dependent deacetylase also known as LpxC. Because lipid A is essential for bacterial viability, the inhibition of LpxC is an appealing therapeutic strategy for the treatment of Gram-negative bacterial infections. Here we report the 1.79 Å resolution X-ray crystal structure of LpxC from Yersinia enterocolitica (YeLpxC) complexed with the potent hydroxamate inhibitor CHIR-090. This enzyme is a nearly identical orthologue of LpxC from Yersinia pestis (99.7% sequence identity), the pathogen that causes bubonic plague. Similar to the inhibition of LpxC from Escherichia coli, CHIR-090 inhibits YeLpxC via a two-step slow, tight-binding mechanism with an apparent K(i) of 0.54 ± 0.14 nM followed by conversion of the E·I to E·I* species with a rate constant of 0.11 ± 0.01 min(-1). The structure of the LpxC complex with CHIR-090 shows that the inhibitor hydroxamate group chelates the active site zinc ion, and the "tail" of the inhibitor binds in the hydrophobic tunnel in the active site. This hydrophobic tunnel is framed by a βαβ subdomain that exhibits significant conformational flexibility as it accommodates inhibitor binding. CHIR-090 displays a 27 mm zone of inhibition against Y. enterocolitica in a Kirby-Bauer antibiotic assay, which is comparable to its reported activity against other Gram-negative species including E. coli and Pseudomonas aeruginosa. This study demonstrates that the inhibition of LpxC should be explored as a potential therapeutic and/or prophylatic response to infection by weaponized Yersinia species.
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Affiliation(s)
- Kathryn E Cole
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, 19104-6323, United States
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38
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Lee CJ, Liang X, Chen X, Zeng D, Joo SH, Chung HS, Barb AW, Swanson SM, Nicholas RA, Li Y, Toone EJ, Raetz CRH, Zhou P. Species-specific and inhibitor-dependent conformations of LpxC: implications for antibiotic design. ACTA ACUST UNITED AC 2010; 18:38-47. [PMID: 21167751 DOI: 10.1016/j.chembiol.2010.11.011] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 11/15/2010] [Accepted: 11/16/2010] [Indexed: 10/18/2022]
Abstract
LpxC is an essential enzyme in the lipid A biosynthetic pathway in gram-negative bacteria. Several promising antimicrobial lead compounds targeting LpxC have been reported, though they typically display a large variation in potency against different gram-negative pathogens. We report that inhibitors with a diacetylene scaffold effectively overcome the resistance caused by sequence variation in the LpxC substrate-binding passage. Compound binding is captured in complex with representative LpxC orthologs, and structural analysis reveals large conformational differences that mostly reflect inherent molecular features of distinct LpxC orthologs, whereas ligand-induced structural adaptations occur at a smaller scale. These observations highlight the need for a molecular understanding of inherent structural features and conformational plasticity of LpxC enzymes for optimizing LpxC inhibitors as broad-spectrum antibiotics against gram-negative infections.
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Affiliation(s)
- Chul-Jin Lee
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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39
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Dowling DP, Gattis SG, Fierke CA, Christianson DW. Structures of metal-substituted human histone deacetylase 8 provide mechanistic inferences on biological function . Biochemistry 2010; 49:5048-56. [PMID: 20545365 DOI: 10.1021/bi1005046] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The metal-dependent histone deacetylases (HDACs) adopt an alpha/beta protein fold first identified in rat liver arginase. Despite insignificant overall amino acid sequence identity, these enzymes share a strictly conserved metal binding site with divergent metal specificity and stoichiometry. HDAC8, originally thought to be a Zn(2+)-metallohydrolase, exhibits increased activity with Co(2+) and Fe(2+) cofactors based on k(cat)/K(M) (Gantt, S. L., Gattis, S. G., and Fierke, C. A. (2006) Biochemistry 45, 6170-6178). Here, we report the first X-ray crystal structures of metallo-substituted HDAC8, Co(2+)-HDAC8, D101L Co(2+)-HDAC8, D101L Mn(2+)-HDAC8, and D101L Fe(2+)-HDAC8, each complexed with the inhibitor M344. Metal content of protein samples in solution is confirmed by inductively coupled plasma mass spectrometry. For the crystalline enzymes, peaks in Bijvoet difference Fourier maps calculated from X-ray diffraction data collected near the respective elemental absorption edges confirm metal substitution. Additional solution studies confirm incorporation of Cu(2+); Fe(3+) and Ni(2+) do not bind under conditions tested. The metal dependence of the substrate K(M) values and the K(i) values of hydroxamate inhibitors that chelate the active site metal are consistent with substrate-metal coordination in the precatalytic Michaelis complex that enhances catalysis. Additionally, although HDAC8 binds Zn(2+) nearly 10(6)-fold more tightly than Fe(2+), the affinities for both metal ions are comparable to the readily exchangeable metal concentrations estimated in living cells, suggesting that HDAC8 could bind either or both Fe(2+) or Zn(2+) in vivo.
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Affiliation(s)
- Daniel P Dowling
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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40
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Barb AW, Jiang L, Raetz CRH, Zhou P. Assignment of 1H, 13C and 15N backbone resonances of Escherichia coli LpxC bound to L-161,240. BIOMOLECULAR NMR ASSIGNMENTS 2010; 4:37-40. [PMID: 19941092 PMCID: PMC3631426 DOI: 10.1007/s12104-009-9201-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 11/05/2009] [Indexed: 05/28/2023]
Abstract
The UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase LpxC catalyzes the committed reaction of lipid A biosynthesis, an essential pathway in Gram-negative bacteria. We report the backbone resonance assignments of the 34 kDa LpxC from Escherichia coli in complex with the antibiotic L-161,240 using multidimensional, multinuclear NMR experiments. The (1)H chemical shifts of complexed L-161,240 are also determined.
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Affiliation(s)
- Adam W Barb
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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41
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Hernick M, Gattis SG, Penner-Hahn JE, Fierke CA. Activation of Escherichia coli UDP-3-O-[(R)-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase by Fe2+ yields a more efficient enzyme with altered ligand affinity. Biochemistry 2010; 49:2246-55. [PMID: 20136146 DOI: 10.1021/bi902066t] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The metal-dependent deacetylase UDP-3-O-[(R)-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase (LpxC) catalyzes the first committed step in lipid A biosynthesis, the hydrolysis of UDP-3-O-myristoyl-N-acetylglucosamine to form UDP-3-O-myristoylglucosamine and acetate. Consequently, LpxC is a target for the development of antibiotics, nearly all of which coordinate the active site metal ion. Here we examine the ability of Fe(2+) to serve as a cofactor for wild-type Escherichia coli LpxC and a mutant enzyme (EcC63A), in which one of the ligands for the inhibitory metal binding site has been removed. LpxC exhibits higher activity (6-8-fold) with a single bound Fe(2+) as the cofactor compared to Zn(2+)-LpxC; both metalloenzymes have a bell-shaped dependence on pH with similar pK(a) values, indicating that at least two ionizations are important for maximal activity. X-ray absorption spectroscopy experiments suggest that the catalytic metal ion bound to Fe(2+)-EcLpxC is five-coordinate, suggesting that catalytic activity may correlate with coordination number. Furthermore, the ligand affinity of Fe(2+)-LpxC compared to the Zn(2+) enzyme is altered by up to 6-fold. In contrast to Zn(2+)-LpxC, the activity of Fe(2+)-LpxC is redox-sensitive, and a time-dependent decrease in activity is observed under aerobic conditions. The LpxC activity of crude E. coli cell lysates is also aerobically sensitive, consistent with the presence of Fe(2+)-LpxC. These data indicate that EcLpxC can use either Fe(2+) or Zn(2+) to activate catalysis in vitro and possibly in vivo, which may allow LpxC to function in E. coli grown under different environmental conditions.
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Affiliation(s)
- Marcy Hernick
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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Narberhaus F, Obrist M, Führer F, Langklotz S. Degradation of cytoplasmic substrates by FtsH, a membrane-anchored protease with many talents. Res Microbiol 2009; 160:652-9. [DOI: 10.1016/j.resmic.2009.08.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 08/17/2009] [Accepted: 08/17/2009] [Indexed: 12/01/2022]
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Bartling CM, Raetz CRH. Crystal structure and acyl chain selectivity of Escherichia coli LpxD, the N-acyltransferase of lipid A biosynthesis. Biochemistry 2009; 48:8672-83. [PMID: 19655786 PMCID: PMC2748855 DOI: 10.1021/bi901025v] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
LpxD catalyzes the third step of lipid A biosynthesis, the R-3-hydroxyacyl-ACP-dependent N-acylation of UDP-3-O-(acyl)-alpha-D-glucosamine, and is a target for new antibiotic development. Here we report the 2.6 A crystal structure of the Escherichia coli LpxD homotrimer (EcLpxD). As is the case in Chlamydia trachomatis LpxD (CtLxpD), each EcLpxD chain consists of an N-terminal uridine-binding region, a left-handed parallel beta-helix (LbetaH), and a C-terminal alpha-helical domain. The backbones of the LbetaH domains of the two enzymes are similar, as are the positions of key active site residues. The N-terminal nucleotide binding domains are oriented differently relative to the LbetaH regions, but are similar when overlaid on each other. The orientation of the EcLpxD tripeptide (residues 303-305), connecting the distal end of the LbetaH and the proximal end of the C-terminal helical domains, differs from its counterpart in CtLpxD (residues 311-312); this results in a 120 degrees rotation of the C-terminal domain relative to the LbetaH region in EcLpxD versus CtLpxD. M290 of EcLpxD appears to cap the distal end of a hydrophobic cleft that binds the acyl chain of the R-3-hydroxyacyl-ACP donor substrate. Under standard assay conditions, wild-type EcLpxD prefers R,S-3-hydroxymyristoyl-ACP over R,S-3-hydroxypalmitoyl-ACP by a factor of 3, whereas the M290A mutant has the opposite selectivity. Both wild-type and M290A EcLpxD rescue the conditional lethality of E. coli RL25, a temperature-sensitive strain harboring point mutations in lpxD. Complementation with wild-type EcLpxD restores normal lipid A containing only N-linked hydroxymyristate to RL25 at 42 degrees C, as judged by mass spectrometry, whereas the M290A mutant generates multiple lipid A species containing one or two longer hydroxy fatty acids in place of the usual R-3-hydroxymyristate at positions 2 and 2'.
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Affiliation(s)
- Craig M. Bartling
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
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Cuny GD. A new class of UDP-3-O-(R-3-hydroxymyristol)-N-acetylglucosamine deacetylase (LpxC) inhibitors for the treatment of Gram-negative infections: PCT application WO 2008027466. Expert Opin Ther Pat 2009; 19:893-9. [PMID: 19473108 DOI: 10.1517/13543770902766829] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Human infections due to Gram-negative bacteria cause significant morbidity and mortality. Identification of new strategies, molecular targets, and agents for the treatment of Gram-negative bacterial infections are needed urgently. Lipid A is a necessary component of the lipopolysaccharide-containing outer membrane of Gram-negative bacteria. The zinc-dependent hydrolase UDP-3-O-(R-3-hydroxymyristol)-N-acetylglucosamine deacetylase (LpxC) involved in the first committed step in the biosynthetic pathway of lipid A has no sequence homology to any known mammalian enzymes and has emerged as an attractive Gram-negative antibacterial molecular target. Most previously described LpxC inhibitors contain a hydroxamic acid, which can lead to low specificity vs. other metal-dependent enzymes and can consequently result in unwanted side effects. OBJECTIVE This review examines a new reported class of nonhydroxamic LpxC inhibitors for the treatment of Gram-negative infections. METHODS The new class of inhibitor is compared with several previously reported LpxC inhibitors. CONCLUSION The LpxC inhibitors disclosed in PCT application WO 2008027466 contain hydantoins in place of the hydroxamic acids commonly found in most previously described inhibitors. These molecules could represent a means of treating Gram-negative infections via a more selective inhibition of LpxC.
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Affiliation(s)
- Gregory D Cuny
- Brigham & Women's Hospital, Harvard Medical School, Partners Center for Drug Discovery, Laboratory for Drug Discovery in Neurodegeneration, 65 Landsdowne Street, Cambridge, MA 02139, USA.
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Barb AW, Leavy TM, Robins LI, Guan Z, Six DA, Zhou P, Hangauer MJ, Bertozzi CR, Raetz CRH. Uridine-based inhibitors as new leads for antibiotics targeting Escherichia coli LpxC. Biochemistry 2009; 48:3068-77. [PMID: 19256534 DOI: 10.1021/bi900167q] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The UDP-3-O-(R-3-hydroxyacyl)-N-acetylglucosamine deacetylase LpxC catalyzes the committed reaction of lipid A (endotoxin) biosynthesis in Gram-negative bacteria and is a validated antibiotic target. Although several previously described compounds bind to the unique acyl chain binding passage of LpxC with high affinity, strategies to target the enzyme's UDP-binding site have not been reported. Here the identification of a series of uridine-based LpxC inhibitors is presented. The most potent examined, 1-68A, is a pH-dependent, two-step, covalent inhibitor of Escherichia coli LpxC that competes with UDP to bind the enzyme in the first step of inhibition. Compound 1-68A exhibits a K(I) of 54 muM and a maximal rate of inactivation (k(inact)) of 1.7 min(-1) at pH 7.4. Dithiothreitol, glutathione and the C207A mutant of E. coli LpxC prevent the formation of a covalent complex by 1-68A, suggesting a role for Cys-207 in inhibition. The inhibitory activity of 1-68A and a panel of synthetic analogues identified moieties necessary for inhibition. 1-68A and a 2-dehydroxy analogue, 1-68Aa, inhibit several purified LpxC orthologues. These compounds may provide new scaffolds for extension of existing LpxC-inhibiting antibiotics to target the UDP binding pocket.
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Affiliation(s)
- Adam W Barb
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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