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Constantinescu S, Niculescu AG, Hudiță A, Grumezescu V, Rădulescu D, Bîrcă AC, Irimiciuc SA, Gherasim O, Holban AM, Gălățeanu B, Oprea OC, Ficai A, Vasile BȘ, Grumezescu AM, Bolocan A, Rădulescu R. Silver/Graphene Oxide Nanostructured Coatings for Modulating the Microbial Susceptibility of Fixation Devices Used in Knee Surgery. Int J Mol Sci 2023; 25:246. [PMID: 38203420 PMCID: PMC10779033 DOI: 10.3390/ijms25010246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Exploring silver-based and carbon-based nanomaterials' excellent intrinsic antipathogenic effects represents an attractive alternative for fabricating anti-infective formulations. Using chemical synthesis protocols, stearate-conjugated silver (Ag@C18) nanoparticles and graphene oxide nanosheets (nGOs) were herein obtained and investigated in terms of composition and microstructure. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) characterizations revealed the formation of nanomaterials with desirable physical properties, while X-ray diffraction (XRD) analyses confirmed the high purity of synthesized nanomaterials. Further, laser-processed Ag@C18-nGO coatings were developed, optimized, and evaluated in terms of biological and microbiological outcomes. The highly biocompatible Ag@C18-nGO nanostructured coatings proved suitable candidates for the local modulation of biofilm-associated periprosthetic infections.
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Affiliation(s)
- Sorin Constantinescu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Eroii Sanitari St. 8, 050474 Bucharest, Romania; (S.C.); (D.R.); (A.B.); (R.R.)
| | - Adelina-Gabriela Niculescu
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania; (A.-G.N.); (A.M.H.)
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, Gh. Polizu St. 1-7, 060042 Bucharest, Romania; (A.C.B.); (A.F.); (B.Ș.V.)
| | - Ariana Hudiță
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania; (A.-G.N.); (A.M.H.)
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania;
| | - Valentina Grumezescu
- Lasers Department, National Institute for Lasers, Plasma and Radiation Physics, 409 Atomistilor St., 077125 Magurele, Romania; (V.G.); (S.A.I.); (O.G.)
| | - Dragoș Rădulescu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Eroii Sanitari St. 8, 050474 Bucharest, Romania; (S.C.); (D.R.); (A.B.); (R.R.)
| | - Alexandra Cătălina Bîrcă
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, Gh. Polizu St. 1-7, 060042 Bucharest, Romania; (A.C.B.); (A.F.); (B.Ș.V.)
| | - Stefan Andrei Irimiciuc
- Lasers Department, National Institute for Lasers, Plasma and Radiation Physics, 409 Atomistilor St., 077125 Magurele, Romania; (V.G.); (S.A.I.); (O.G.)
| | - Oana Gherasim
- Lasers Department, National Institute for Lasers, Plasma and Radiation Physics, 409 Atomistilor St., 077125 Magurele, Romania; (V.G.); (S.A.I.); (O.G.)
| | - Alina Maria Holban
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania; (A.-G.N.); (A.M.H.)
- Microbiology and Immunology Department, Faculty of Biology, University of Bucharest, 1-3 Portocalelor Lane, District 5, 77206 Bucharest, Romania
| | - Bianca Gălățeanu
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania;
| | - Ovidiu Cristian Oprea
- Department of Inorganic Chemistry, Physical Chemistry and Electrochemistry, University Politehnica of Bucharest, 1-7 Polizu St., 011061 Bucharest, Romania;
- Academy of Romanian Scientists, Spl. Independenței 54, 50085 Bucharest, Romania
| | - Anton Ficai
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, Gh. Polizu St. 1-7, 060042 Bucharest, Romania; (A.C.B.); (A.F.); (B.Ș.V.)
- Academy of Romanian Scientists, Spl. Independenței 54, 50085 Bucharest, Romania
| | - Bogdan Ștefan Vasile
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, Gh. Polizu St. 1-7, 060042 Bucharest, Romania; (A.C.B.); (A.F.); (B.Ș.V.)
| | - Alexandru Mihai Grumezescu
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania; (A.-G.N.); (A.M.H.)
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, Gh. Polizu St. 1-7, 060042 Bucharest, Romania; (A.C.B.); (A.F.); (B.Ș.V.)
- Academy of Romanian Scientists, Spl. Independenței 54, 50085 Bucharest, Romania
| | - Alexandra Bolocan
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Eroii Sanitari St. 8, 050474 Bucharest, Romania; (S.C.); (D.R.); (A.B.); (R.R.)
| | - Radu Rădulescu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Eroii Sanitari St. 8, 050474 Bucharest, Romania; (S.C.); (D.R.); (A.B.); (R.R.)
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Yao A, Ma Y, Sun R, Zou W, Chen X, Zhou M, Ma C, Chen T, Shaw C, Wang L. A Designed Analog of an Antimicrobial Peptide, Crabrolin, Exhibits Enhanced Anti-Proliferative and In Vivo Antimicrobial Activity. Int J Mol Sci 2023; 24:14472. [PMID: 37833918 PMCID: PMC10572522 DOI: 10.3390/ijms241914472] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/07/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Antimicrobial peptides have gradually attracted interest as promising alternatives to conventional agents to control the worldwide health threats posed by antibiotic resistance and cancer. Crabrolin is a tridecapeptide extracted from the venom of the European hornet (Vespa crabro). Its antibacterial and anticancer potentials have been underrated compared to other peptides discovered from natural resources. Herein, a series of analogs were designed based on the template sequence of crabrolin to study its structure-activity relationship and enhance the drug's potential by changing the number, type, and distribution of charged residues. The cationicity-enhanced derivatives were shown to have improved antibacterial and anticancer activities with a lower toxicity. Notably, the double-arginine-modified product, crabrolin-TR, possessed a potent capacity against Pseudomonas aeruginosa (minimum inhibitory concentration (MIC) = 4 μM), which was around thirty times stronger than the parent peptide (MIC = 128 μM). Furthermore, crabrolin-TR showed an in vivo treatment efficacy in a Klebsiella-pneumoniae-infected waxworm model and was non-toxic under its maximum MBC value (MIC = 8 μM), indicating its therapeutic potency and better selectivity. Overall, we rationally designed functional peptides by progressively increasing the number and distribution of charged residues, demonstrating new insights for developing therapeutic molecules from natural resources with enhanced properties, and proposed crabrolin-TR as an appealing antibacterial and anticancer agent candidate for development.
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Affiliation(s)
- Aifang Yao
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (Y.M.); (R.S.); (X.C.); (M.Z.); (C.M.); (T.C.); (C.S.); (L.W.)
| | - Yingxue Ma
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (Y.M.); (R.S.); (X.C.); (M.Z.); (C.M.); (T.C.); (C.S.); (L.W.)
| | - Ruize Sun
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (Y.M.); (R.S.); (X.C.); (M.Z.); (C.M.); (T.C.); (C.S.); (L.W.)
| | - Wanchen Zou
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (Y.M.); (R.S.); (X.C.); (M.Z.); (C.M.); (T.C.); (C.S.); (L.W.)
| | - Xiaoling Chen
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (Y.M.); (R.S.); (X.C.); (M.Z.); (C.M.); (T.C.); (C.S.); (L.W.)
| | - Mei Zhou
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (Y.M.); (R.S.); (X.C.); (M.Z.); (C.M.); (T.C.); (C.S.); (L.W.)
| | - Chengbang Ma
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (Y.M.); (R.S.); (X.C.); (M.Z.); (C.M.); (T.C.); (C.S.); (L.W.)
| | - Tianbao Chen
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (Y.M.); (R.S.); (X.C.); (M.Z.); (C.M.); (T.C.); (C.S.); (L.W.)
| | - Chris Shaw
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (Y.M.); (R.S.); (X.C.); (M.Z.); (C.M.); (T.C.); (C.S.); (L.W.)
| | - Lei Wang
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (Y.M.); (R.S.); (X.C.); (M.Z.); (C.M.); (T.C.); (C.S.); (L.W.)
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Abdelsalam NA, Elhadidy M, Saif NA, Elsayed SW, Mouftah SF, Sayed AA, Ziko L. Biosynthetic gene cluster signature profiles of pathogenic Gram-negative bacteria isolated from Egyptian clinical settings. Microbiol Spectr 2023; 11:e0134423. [PMID: 37707241 PMCID: PMC10580877 DOI: 10.1128/spectrum.01344-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/03/2023] [Indexed: 09/15/2023] Open
Abstract
Biosynthetic gene clusters (BGCs) are a subset of consecutive genes present within a variety of organisms to produce specialized metabolites (SMs). These SMs are becoming a cornerstone to produce multiple medications including antibacterial and anticancer agents. Natural products (NPs) also play a pivotal role in enhancing the virulence of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), which represent a global health threat. We aimed to sequence and computationally analyze the BGCs present in 66 strains pertaining to three different ESKAPE pathogenic species: 21 A. baumannii, 28 K. pneumoniae, and 17 P. aeruginosa strains recovered from clinical settings in Egypt. DNA was extracted using QIAamp DNA Mini kit and Illumina NextSeq 550 was used for whole-genome sequencing. The sequences were quality-filtered by fastp and assembled by Unicycler. BGCs were detected by antiSMASH, BAGEL, GECCO, and PRISM, and aligned using Clinker. The highest abundance of BGCs was detected in P. aeruginosa (590), then K. pneumoniae (146) and the least in A. baumannii strains (133). P. aeruginosa isolates shared mostly the non-ribosomal peptide synthase (NRPS) type, K. pneumoniae isolates shared the ribosomally synthesized and post-translationally modified peptide-like (RiPP-like) type, while A. baumannii isolates shared the siderophore type. Most of the isolates harbored non-ribosomal peptide (NRP) BGCs with few K. pneumoniae isolates encoding polyketide BGCs. Sactipeptides and bottromycin BGCs were the most frequently detected RiPP clusters. We hypothesize that each species' BGC signature confers its virulence. Future experiments will link the detected clusters with their species and determine whether the encoded SMs are produced and cause their virulence. IMPORTANCE Our study analyzes the biosynthetic gene clusters (BGCs) present in 66 assemblies from clinical ESKAPE pathogen isolates pertaining to Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa strains. We report their sequencing and assembly followed by the analysis of their BGCs using several bioinformatics tools. We then focused on the most abundant BGC type in each species and we discussed their potential roles in the virulence of each species. This study is pivotal to further build on its experimental work that deciphers the role in virulence, possible antibacterial effects, and characterization of the encoded specialized metabolites (SMs). The study highlights the importance of studying the "harmful" BGCs and understanding the pathogenicity and virulence of those species, as well as possible benefits if the SMs were used as antibacterial agents. This could be the first study of its kind from Egypt and would shed light on BGCs from ESKAPE pathogens from Egypt.
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Affiliation(s)
- Nehal Adel Abdelsalam
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mohamed Elhadidy
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Nehal A. Saif
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Salma W. Elsayed
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Shaimaa F. Mouftah
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Ahmed A. Sayed
- Genomic research program, Basic research department, Children’s Cancer Hospital Egypt, Cairo, Egypt
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Laila Ziko
- School of Life and Medical Sciences, University of Hertfordshire, Hosted by Global Academic Foundation, Cairo, Egypt
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Pompilio A, Scocchi M, Mangoni ML, Shirooie S, Serio A, Ferreira Garcia da Costa Y, Alves MS, Şeker Karatoprak G, Süntar I, Khan H, Di Bonaventura G. Bioactive compounds: a goldmine for defining new strategies against pathogenic bacterial biofilms? Crit Rev Microbiol 2023; 49:117-149. [PMID: 35313120 DOI: 10.1080/1040841x.2022.2038082] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Most human infectious diseases are caused by microorganisms growing as biofilms. These three-dimensional self-organized communities are embedded in a dense matrix allowing microorganisms to persistently inhabit abiotic and biotic surfaces due to increased resistance to both antibiotics and effectors of the immune system. Consequently, there is an urgent need for novel strategies to control biofilm-associated infections. Natural products offer a vast array of chemical structures and possess a wide variety of biological properties; therefore, they have been and continue to be exploited in the search for potential biofilm inhibitors with a specific or multi-locus mechanism of action. This review provides an updated discussion of the major bioactive compounds isolated from several natural sources - such as plants, lichens, algae, microorganisms, animals, and humans - with the potential to inhibit biofilm formation and/or to disperse established biofilms by bacterial pathogens. Despite the very large number of bioactive products, their exact mechanism of action often remains to be clarified and, in some cases, the identity of the active molecule is still unknown. This knowledge gap should be filled thus allowing development of these products not only as novel drugs to combat bacterial biofilms, but also as antibiotic adjuvants to restore the therapeutic efficacy of current antibiotics.
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Affiliation(s)
- Arianna Pompilio
- Department of Medical, Oral and Biotechnological Sciences, and Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Maria Luisa Mangoni
- Department of Biochemical Sciences, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Samira Shirooie
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Annalisa Serio
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Ygor Ferreira Garcia da Costa
- Laboratory of Cellular and Molecular Bioactivity, Pharmaceutical Research Center, Faculty of Pharmacy, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Maria Silvana Alves
- Laboratory of Cellular and Molecular Bioactivity, Pharmaceutical Research Center, Faculty of Pharmacy, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Gökçe Şeker Karatoprak
- Department of Pharmacognosy, Faculty of Pharmacy, Erciyes University, Talas, Kayseri, Turkey
| | - Ipek Süntar
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Etiler, Ankara, Turkey
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan, Pakistan
| | - Giovanni Di Bonaventura
- Department of Medical, Oral and Biotechnological Sciences, and Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
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Tiwari M, Panwar S, Tiwari V. Assessment of potassium ion channel during electric signalling in biofilm formation of Acinetobacter baumannii for finding antibiofilm molecule. Heliyon 2023; 9:e12837. [PMID: 36685419 PMCID: PMC9852675 DOI: 10.1016/j.heliyon.2023.e12837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023] Open
Abstract
Acinetobacter baumannii is an opportunistic ESKAPE pathogen which causes nosocomial infections and can produce biofilms that act as resistant determinants. The role of quorum sensing (chemical signaling) in biofilm establishment has already been studied extensively, but the existence of electrochemical signaling during biofilm formation by A. baumannii has not yet been investigated. The current study evaluated the presence of electrical signaling, types of ion channels involved, and their role in biofilm formation using spectroscopic and microbiological methods. The findings suggest that the potassium ion channel has a significant role in the electrical signaling during the biofilm formation by A. baumannii. Further, in-silico screening, molecular mechanics, and molecular dynamic simulation studies identify a potential lead, ZINC12496555(a specific inhibitor), which targets the potassium ion channel protein of A. baumannii. Mutational analysis of the interacting residues showed alterations in the unfolding rate of this protein after the selected mutation, which shows its role in the stability of this protein. It was also observed that identified lead has high antibiofilm activity, no human off-targets, and non-cytotoxicity to cell lines. Thus, identified lead against the potassium channel of A baumannii may be used as an effective therapeutic for the treatment of A. baumannii infections after further experimental validation.
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Yan X, Gu C, Yu Z, Ding L, He M, Xiao W, Zhao M, Qing Y, He L. Comprehensive analysis of transcriptome and metabolome analysis reveal new targets of Glaesserella parasuis glucose-specific enzyme IIBC (PtsG). Microb Pathog 2022; 172:105785. [PMID: 36150554 DOI: 10.1016/j.micpath.2022.105785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 10/31/2022]
Abstract
The ptsG (hpIIBCGlc) gene, belonging to the glucose-specific phosphotransferase system, encodes the bacterial glucose-specific enzyme IIBC. In this study, the effects of a deletion of the ptsG gene were investigated by metabolome and transcriptome analyses. At the transcriptional level, we identified 970 differentially expressed genes between ΔptsG and sc1401 (Padj<0.05) and 2072 co-expressed genes. Among these genes, those involved in methane metabolism, amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, pyruvate metabolism, phosphotransferase system (PTS), biotin metabolism, Two-component system and Terpenoid backbone biosynthesis showed significant changes in the ΔptsG mutant strain. Metabolome analysis revealed that a total of 310 metabolites were identified, including 20 different metabolites (p < 0.05). Among them, 15 metabolites were upregulated and 5 were downregulated in ΔptsG mutant strain. Statistical analysis revealed there were 115 individual metabolites having correlation, of which 89 were positive and 26 negative. These metabolites include amino acids, phosphates, amines, esters, nucleotides, benzoic acid and adenosine, among which amino acids and phosphate metabolites dominate. However, not all of these changes were attributable to changes in mRNA levels and must also be caused by post-transcriptional regulatory processes. The knowledge gained from this lays the foundation for further study on the role of ptsG in the pathogenic process of Glaesserella parasuis (G.parasuis).
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Affiliation(s)
- Xuefeng Yan
- School of Physical Education, Southwest Medical University, Luzhou, China
| | - Congwei Gu
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China; Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Zehui Yu
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China; Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Lingqiang Ding
- School of Life Science and Engineering, Hexi University, Zhangye, China
| | - Manli He
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China; Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Wudian Xiao
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China; Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Mingde Zhao
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China; Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China
| | - Yunfeng Qing
- Animal Disease Prevention and Control Center of Zhaohua District, Guangyuan, China
| | - Lvqin He
- Experimental Animal Center, Technology Department, Southwest Medical University, Luzhou, China; Model Animal and Human Disease Research of Luzhou Key Laboratory, Luzhou, China.
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Tiwari V. Pharmacophore screening, denovo designing, retrosynthetic analysis, and combinatorial synthesis of a novel lead VTRA1.1 against RecA protein of Acinetobacter baumannii. Chem Biol Drug Des 2022; 99:839-856. [PMID: 35278346 DOI: 10.1111/cbdd.14037] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/15/2022] [Accepted: 03/05/2022] [Indexed: 01/08/2023]
Abstract
Antibiotics and disinfectants resistance is acquired by activating RecA-mediated DNA repair, which maintains ROS-dependent DNA damage caused by the antimicrobial molecules. To increase the efficacy of different antimicrobials, an inhibitor can be developed against RecA protein. The present study aims to design a denovo inhibitor against RecA protein of Acinetobacter baumannii. Pharmacophore-based screening, molecular mechanics, molecular dynamics simulation (MDS), retrosynthetic analysis, and combinatorial synthesis were used to design lead VTRA1.1 against RecA of A. baumannii. Pharmacophore models (structure-based and ligand-based) were created, and a phase library of FDA-approved drugs was prepared. Screening of the phase library against these pharmacophore models selected thirteen lead molecules. These filtered leads were used for the denovo fragment-based design, which produced 253 combinations. These designed molecules were further analyzed for its interaction with active site of RecA that selected a hybrid VTRA1. Further, retrosynthetic analysis and combinatorial synthesis produced 1000 analogs of VTRA1 by more than 100 modifications. These analogs were used for XP docking, binding free energy calculation, and MDS analysis which finally select lead VTRA1.1 against RecA protein. Further, mutations at the interacting residues of RecA with VTRA1.1, alter the unfolding rate of RecA, which suggests the binding of VTRA1.1 to these residues may alter the stability of RecA. It is also found that VTRA1.1 had reduced interaction of RecA with LexA and ssDNA polydT, showing the lead's efficacy in controlling the SOS response. Further, it was also observed that VTRA1.1 does not contain any predicted human off-targets and no cytotoxicity to cell lines. As functional RecA is involved in antimicrobial resistance, denovo designed lead VTRA1.1 against RecA may be further developed as a significant combination for therapeutic uses against A. baumannii.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
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Inosine and D-Mannose Secreted by Drug-Resistant Klebsiella pneumoniae Affect Viability of Lung Epithelial Cells. Molecules 2022; 27:molecules27092994. [PMID: 35566345 PMCID: PMC9106066 DOI: 10.3390/molecules27092994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 11/29/2022] Open
Abstract
The antibiotic resistance rates of Klebsiella pneumoniae have been steadily increasing in recent years. Nevertheless, the metabolic features of the drug-resistant Klebsiella pneumoniae and its associated benefits for bacterial pathogenicity are far from expounded. This study aims to unravel the unique physiological and metabolic properties specific to drug-resistant K. pneumoniae. Using scanning electron microscopy (SEM), we observed a thicker extracellular mucus layer around a drug-resistant K. pneumonia strain (Kp-R) than a drug-sensitive K. pneumonia strain (Kp-S). Kp-R also produced more capsular polysaccharide (CPS) and biofilm, and appeared to have a significant competitive advantage when co-cultured with Kp-S. Moreover, Kp-R was easier to adhere to and invade A549 epithelial cells than Kp-S but caused less cell-viability damage according to cell counting kit-8 (CCK-8) tests. Immunofluorescence revealed that both Kp-R and Kp-S infection destroyed the tight junctions and F-actin of epithelial cells, while the damage caused by Kp-S was more severe than Kp-R. We detected the extracellular metabolites secreted by the two strains with UHPLC-Q-TOF MS to explore the critical secretion products. We identified 16 predominant compounds that were differentially expressed. Among them, inosine increased the viability of epithelial cells in a dose-dependent manner, and an A2AR antagonist can abolish such enhancement. D-mannose, which was secreted less in Kp-R, inhibited the viability of A549 cells in the range of low doses. These findings provide potential targets and research strategies for preventing and treating drug-resistant K. pneumoniae infections.
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Kaushik V, Tiwari M, Joshi R, Tiwari V. Therapeutic strategies against potential antibiofilm targets of multidrug-resistant Acinetobacter baumannii. J Cell Physiol 2022; 237:2045-2063. [PMID: 35083758 DOI: 10.1002/jcp.30683] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/30/2021] [Accepted: 01/07/2022] [Indexed: 12/12/2022]
Abstract
Acinetobacter baumannii is the causative agent of various hospital-acquired infections. Biofilm formation is one of the various antimicrobial resistance (AMR) strategies and is associated with high mortality and morbidity. Hence, it is essential to review the potential antibiofilm targets in A. baumannii and come up with different strategies to combat these potential targets. This review covers different pathways involved in the regulation of biofilm formation in A. baumannii like quorum sensing (QS), cyclic-di-GMP signaling, two-component system (TCS), outer-membrane protein (ompA), and biofilm-associated protein (BAP). A newly discovered mechanism of electrical signaling-mediated biofilm formation and contact-dependent biofilm modulation has also been discussed. As biofilm formation and its maintenance in A. baumannii is facilitated by these potential targets, the detailed study of these targets and pathways can bring light to different therapeutic strategies such as anti-biofilm peptides, natural and synthetic molecule inhibitors, QS molecule degrading enzymes, and other strategies. These strategies may help in suppressing the lethality of biofilm-mediated infections. Targeting essential proteins/targets which are crucial for biofilm formation and regulation may render new therapeutic strategies that can aid in combating biofilm, thus reducing the recalcitrant infections and morbidity associated with the biofilm of A. baumannii.
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Affiliation(s)
- Vaishali Kaushik
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Richa Joshi
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
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da Silva GC, de Oliveira AM, Costa WK, da Silva Filho AF, Pitta MGDR, Rêgo MJBDM, Antônia de Souza I, Paiva PMG, Napoleão TH. Antibacterial and antitumor activities of a lectin-rich preparation from Microgramma vacciniifolia rhizome. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2022; 3:100093. [PMID: 35243335 PMCID: PMC8866057 DOI: 10.1016/j.crphar.2022.100093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 02/01/2022] [Accepted: 02/13/2022] [Indexed: 01/17/2023] Open
Abstract
The rhizome of Microgramma vacciniifolia contains a lectin (carbohydrate-binding protein) called MvRL. Studies demonstrated that a MvRL-rich fraction did not show in vivo genotoxicity and acute toxicity in mice. This study aimed to evaluate the MvRL-rich fraction from M. vacciniifolia rhizome for antibacterial activity in vitro and in vivo as well as antitumor effect in vivo using the Ehrlich carcinoma model in mice. The fraction showed antibacterial activity against Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus with minimal inhibitory concentrations ranging from 31.2 to 125.0 μg/mL and minimal bactericidal concentrations from 62.5 to 200 μg/mL. The fraction was also effective in vivo against infection caused by these bacteria on Tenebrio molitor larvae considering the parameters evaluated. In regard to the antitumor activity, the treatments of Ehrlich carcinoma-bearing mice with the fraction at 100 and 200 mg/kg per os resulted in 62.58% and 75.43% of tumor inhibition, respectively. In conclusion, the MvRL-rich fraction showed in vivo antibacterial and antitumor activities and thus can be considered as an alternative of natural origin for the development of candidates for therapy. The rhizome of Microgramma vacciniifolia contains a lectin called MvRL. MvRL-rich fraction showed antibacterial activity. The fraction was also effective in vivo against bacterial infection. MvRL-rich fraction causedn 62.58–75.43% inhibition of Erlich carcinoma.
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Affiliation(s)
| | | | - Wêndeo Kennedy Costa
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Antônio Felix da Silva Filho
- Laboratório de Imunomodulação e Novas Abordagens Terapêuticas, Núcleo de Pesquisa em Inovação Terapêutica, Universidade Federal de Pernambuco, Recife, Brazil
| | - Maira Galdino da Rocha Pitta
- Laboratório de Imunomodulação e Novas Abordagens Terapêuticas, Núcleo de Pesquisa em Inovação Terapêutica, Universidade Federal de Pernambuco, Recife, Brazil
| | - Moacyr Jesus Barreto de Melo Rêgo
- Laboratório de Imunomodulação e Novas Abordagens Terapêuticas, Núcleo de Pesquisa em Inovação Terapêutica, Universidade Federal de Pernambuco, Recife, Brazil
| | - Ivone Antônia de Souza
- Departamento de Antibióticos, Centro de Ciências da Saúde, Universidade Federal de Pernambuco, Recife, Brazil
| | | | - Thiago Henrique Napoleão
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
- Corresponding author.
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Tiwari M, Joshi R, Tiwari V. Design of novel hybrid secondary metabolite targets to diguanylate cyclase of Acinetobacter baumannii. FEMS MICROBES 2021. [DOI: 10.1093/femsmc/xtab017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Biofilm formation in bacteria is a resistance determinant and is positively regulated by cyclic diguanylate signaling. This signaling is a near universal signaling, and c-di-GMP produced by diguanylate cyclase (DGC) in this signaling is involved in different bacterial behaviors. The present study aims to find a plant-based novel hybrid therapeutic agent that can target the DGC of Acinetobacter baumannii. In this study, we have tried to design a hybrid molecule from the anti-biofilm plant secondary metabolites and screened its binding with the DGC of A. baumannii. The modeled and validated DGC was used to identify the active site and docking grid. Designed hybrid compounds were analysed for their interaction with the active site residues of DGC of A. baumannii. Further, the binding free energies of the docked complexes obtained from the Generalized Born model and Solvent Accessibility (MMGBSA) were analysed. The results indicated that VR-QEg-180 has a predicted high binding affinity with enzyme DGC as compared to other hybrids, parent secondary metabolites and positive control. Molecular dynamics simulation (MDS) analysis confirmed the interaction of VR-QEg-180 with DGC of the A. baumannii. The designed lead has favorable ADMET properties, has no human off-targets and has no predicted cytotoxicity in cell lines. Therefore, the designed hybrid molecule (VR-QEg-180) targeting the DGC of A. baumannii may play a very significant role in controlling this pathogen.
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Affiliation(s)
- Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India
| | - Richa Joshi
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India
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Gherasim O, Grumezescu AM, Ficai A, Grumezescu V, Holban AM, Gălățeanu B, Hudiță A. Composite P(3HB-3HV)-CS Spheres for Enhanced Antibiotic Efficiency. Polymers (Basel) 2021; 13:989. [PMID: 33807077 PMCID: PMC8004896 DOI: 10.3390/polym13060989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 01/17/2023] Open
Abstract
Natural-derived biopolymers are suitable candidates for developing specific and selective performance-enhanced antimicrobial formulations. Composite polymeric particles based on poly(3-hydroxybutyrate-co-3-hydroxyvalerate) and chitosan, P(3HB-3HV)-CS, are herein proposed as biocompatible and biodegradable delivery systems for bioproduced antibiotics: bacitracin (Bac), neomycin (Neo) and kanamycin (Kan). The stimuli-responsive spheres proved efficient platforms for boosting the antibiotic efficiency and antibacterial susceptibility, as evidenced against Gram-positive and Gram-negative strains. Absent or reduced proinflammatory effects were evidenced on macrophages in the case of Bac-/Neo- and Kan-loaded spheres, respectively. Moreover, these systems showed superior ability to sustain and promote the proliferation of dermal fibroblasts, as well as to preserve their ultrastructure (membrane and cytoskeleton integrity) and to exhibit anti-oxidant activity. The antibiotic-loaded P(3HB-3HV)-CS spheres proved efficient alternatives for antibacterial strategies.
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Affiliation(s)
- Oana Gherasim
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, Politehnica University of Bucharest, 011061 Bucharest, Romania; (O.G.); (A.M.G.); (A.F.)
- Lasers Department, National Institute for Lasers, Plasma, and Radiation Physics, RO-77125 Magurele, Romania
| | - Alexandru Mihai Grumezescu
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, Politehnica University of Bucharest, 011061 Bucharest, Romania; (O.G.); (A.M.G.); (A.F.)
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania
| | - Anton Ficai
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, Politehnica University of Bucharest, 011061 Bucharest, Romania; (O.G.); (A.M.G.); (A.F.)
| | - Valentina Grumezescu
- Lasers Department, National Institute for Lasers, Plasma, and Radiation Physics, RO-77125 Magurele, Romania
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania
| | - Alina Maria Holban
- Microbiology & Immunology Department, Faculty of Biology, University of Bucharest, 77206 Bucharest, Romania;
| | - Bianca Gălățeanu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independentei, 050095 Bucharest, Romania; (B.G.); (A.H.)
| | - Ariana Hudiță
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independentei, 050095 Bucharest, Romania; (B.G.); (A.H.)
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Wen X, Cao J, Mi J, Huang J, Liang J, Wang Y, Ma B, Zou Y, Liao X, Liang JB, Wu Y. Metabonomics reveals an alleviation of fitness cost in resistant E. coli competing against susceptible E. coli at sub-MIC doxycycline. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124215. [PMID: 33109407 DOI: 10.1016/j.jhazmat.2020.124215] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/07/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
High concentrations of antibiotics may induce bacterial resistance mutations and further lead to fitness costs by reducing growth of resistant bacteria. However, antibiotic concentrations faced by bacteria are usually low in common environments, which leads to questions about how resistant bacteria with fitness costs regulate metabolism to coexist or compete with susceptible bacteria during sublethal challenge. Our study revealed that a low proportion (< 15%) of resistant bacteria coexisted with susceptible bacteria due to the fitness cost without doxycycline. However, the cost for the resistant strain decreased at a doxycycline concentration of 1 mg/L and even disappeared when the doxycycline concentration was 2 mg/L. Metabonomics analysis revealed that bypass carbon metabolism and biosynthesis of secondary metabolites were the primary metabolic pathways enriching various upregulated metabolites in resistant bacteria without doxycycline. Moreover, the alleviation of fitness cost for resistant bacteria competed with susceptible bacteria at 1 mg/L doxycycline was correlated with the downregulation of the biomarkers pyruvate and pilocarpine. Our study offered new insight into the metabolic mechanisms by which the fitness cost of resistant mutants was reduced at doxycycline concentrations as low as 1 mg/L and identified various potential metabolites to limit the spread of antimicrobial resistance in the environment.
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Affiliation(s)
- Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Junchao Cao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jiandui Mi
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Jielan Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jiadi Liang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Juan Boo Liang
- Laboratory of Animal Production, Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China.
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Tiwari V. Denovo designing, retro-combinatorial synthesis, and molecular dynamics analysis identify novel antiviral VTRM1.1 against RNA-dependent RNA polymerase of SARS CoV2 virus. Int J Biol Macromol 2021; 171:358-365. [PMID: 33421473 PMCID: PMC7787912 DOI: 10.1016/j.ijbiomac.2020.12.223] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 02/06/2023]
Abstract
A novel coronavirus disease (COVID-19) caused by SARS-CoV2 has now spread globally. Replication/transcription machinery of this virus consists of RNA-dependent RNA polymerase (nsp12 or RdRp) and its two cofactors nsp7 and nsp8 proteins. Hence, RdRp has emerged as a promising target to control COVID-19. In the present study, we are reporting a novel inhibitor VTRM1.1 against the RdRp protein of SARS CoV2. A series of antivirals were tested for binding to the catalytic residues of the active site of RdRp protein. In-silico screening, molecular mechanics, molecular dynamics simulation (MDS) analysis suggest ribavirin, and remdesivir have good interaction with the binding site of the RdRp protein as compared to other antiviral investigated. Hence, ribavirin and remdesivir were used for the denovo fragments based antiviral design. This design, along with docking and MDS analysis, identified a novel inhibitor VTRM1 that has better interaction with RdRp as compared to their parent molecules. Further, to produce a lead-like compound, retrosynthetic analysis, and combinatorial synthesis were performed, which produces 1000 analogs of VTRM1. These analogs were analysed by docking and MDS analysis that identified VTRM1.1 as a possible lead to inhibit RdRp protein. This lead has a good docking score, favourable binding energy and bind at catalytic residues of the active site of RdRp. The VTRM1.1 also interacts with RdRp in the presence of RNA primer and other cofactors. It was also seen that, VTRM1.1 do not have off-target in human. Therefore, the present study suggests a hybrid inhibitor VTRM1.1 for the RNA-dependent RNA polymerase of SARS CoV2 that may be useful to control infection caused by COVID-19.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India.
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Martins FG, Melo A, Sousa SF. Databases for the study of biofilms: current status and potential applications. BIOFOULING 2021; 37:96-108. [PMID: 33508968 DOI: 10.1080/08927014.2021.1876849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Biofilms play an important role in health, being associated with >80% of all microbial infections in the body and in the development of antibiotic resistance. Research in this field has continuously produced large volumes of data. Being able to handle all this information will be paramount for progress in this field. However, this places a heavy burden on the development of strategies to gather, organize and make this information available in a way that can be readily and effectively used by those requiring it. Lately, efforts towards this goal have been reported, particularly with the development of Quorumpeps, BiofOmics, BaAMPs, QSPpred, dPABBs, aBiofilm and the Biofilms Structural Database. This work reviews these databases and highlights their applicability and potential, while stressing some of the challenges for the coming years in database development and usage brought about by the use of big data and machine learning.
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Affiliation(s)
- Fábio G Martins
- UCIBIO/REQUIMTE, BioSIM - Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - André Melo
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Sérgio F Sousa
- UCIBIO/REQUIMTE, BioSIM - Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
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Recent Advances in the Pursuit of an Effective Acinetobacter baumannii Vaccine. Pathogens 2020; 9:pathogens9121066. [PMID: 33352688 PMCID: PMC7766458 DOI: 10.3390/pathogens9121066] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter baumannii has been a major cause of nosocomial infections for decades. The absence of an available vaccine coupled with emerging multidrug resistance has prevented the medical community from effectively controlling this human pathogen. Furthermore, the ongoing pandemic caused by SARS-CoV-2 has increased the risk of hospitalized patients developing ventilator-associated pneumonia caused by bacterial opportunists including A. baumannii. The shortage of antibiotics in the development pipeline prompted the World Health Organization to designate A. baumannii a top priority for the development of new medical countermeasures, such as a vaccine. There are a number of important considerations associated with the development of an A. baumannii vaccine, including strain characteristics, diverse disease manifestations, and target population. In the past decade, research efforts have revealed a number of promising new immunization strategies that could culminate in a safe and protective vaccine against A. baumannii. In this review, we highlight the recent progress in the development of A. baumannii vaccines, discuss potential challenges, and propose future directions to achieve an effective intervention against this human pathogen.
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Tiwari V. De novo design, retrosynthetic analysis and combinatorial synthesis of a hybrid antiviral (VTAR-01) to inhibit the interaction of SARS-CoV2 spike glycoprotein with human angiotensin-converting enzyme 2. Biol Open 2020; 9:bio.054056. [PMID: 32878881 PMCID: PMC7595696 DOI: 10.1242/bio.054056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin converting enzyme 2 (hACE2). Spike protein contains a receptor-binding domain (RBD) that recognizes hACE-2. In the present study, we are reporting a de novo designed novel hybrid antiviral ‘VTAR-01’ molecule that binds at the interface of RBD-hACE2 interaction. A series of antiviral molecules were tested for binding at the interface of RBD-hACE2 interaction. In silico screening, molecular mechanics and molecular dynamics simulation (MDS) analysis suggest ribavirin, ascorbate, lopinavir and hydroxychloroquine have strong interaction at the RBD-hACE2 interface. These four molecules were used for de novo fragment-based antiviral design. De novo designing, docking and MDS analysis identified a ‘VTAR’ hybrid molecule that has better interaction with this interface than all of the antivirals used to design it. We have further used retrosynthetic analysis and combinatorial synthesis to design 100 variants of VTAR molecules. Retrosynthetic analysis and combinatorial synthesis, along with docking and MDS, identified that VTAR-01 interacts with the interface of the RBD-ACE2 complex. MDS analysis confirmed its interaction with the RBD-ACE2 interface by involving Glu35 and Lys353 of ACE2, as well as Gln493 and Ser494 of RBD. Interaction of spike protein with ACE2 is essential for pathogenesis and infection of this virus; hence, this in silico designed hybrid antiviral molecule (VTAR-01) that binds at the interface of RBD-hACE2 may be further developed to control the infection of SARS-CoV2. Summary: SARS-CoV2 has caused an outbreak globally and is responsible for high mortality and morbidity. Interaction of the receptor-binding domain of spike protein of this virus with human angiotensin converting enzyme (ACE2) is vital for the infection. Hence, a de novo designed hybrid antiviral molecule (VTAR-01) targeting RBD-ACE2 interaction may play a very significant role in controlling the COVID-19 disease.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India
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Liu X, Zhang X, Zhang J, Luo Y, Xu B, Ling S, Zhang Y, Li W, Yao X. Activation of aryl hydrocarbon receptor in Langerhans cells by a microbial metabolite of tryptophan negatively regulates skin inflammation. J Dermatol Sci 2020; 100:192-200. [PMID: 33082071 DOI: 10.1016/j.jdermsci.2020.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/20/2020] [Accepted: 10/06/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Skin commensal bacteria play important roles in skin homeostasis. Langerhans cells (LCs) are epidermis-resident dendritic cells that sense environmental stimuli and are critical in the induction of immune tolerance to allergen and bacterial skin flora. However, response of LCs to the metabolites of the skin microbiota is not clear. OBJECTIVE To explore the effects of the skin microbial metabolites on LCs activation. METHODS LCs derived from CD34+ hematopoietic stem cells in the cord blood were treated with a microbial metabolite of tryptophan, indole-3-aldehyde (IAId). Activation aryl hydrocarbon receptor (AhR) signaling, production of IL-10, and expression of receptor activator of NF-κB (RANK) / receptor activator of NF-κB ligand (RANKL) in LCs or keratinocytes were analyzed using quantitative PCR, western blotting and flow cytometry. LCs maturation induced by IAId and CD4+ T cell response induced by IAId-conditioned LCs were also investigated. RESULTS IAId induced the production of indoleamine 2,3-dioxygenase (IDO) and IL-10 in LCs through the activation of AhR. IAId promoted the expression of RANK and RANKL on LCs and keratinocytes in an AhR-dependent manner respectively, which might result in activation of NF-κB signaling and production of IL-10. Moreover, a mature phenotype of LCs was induced by IAId, and IAId-activated LCs inhibited CD4+ T cell proliferation and induced IL-10 secretion. CONCLUSIONS Our study revealed a negatively regulatory function of a tryptophan metabolite on LCs through the activation of AhR, and the microbial metabolites could be utilized in future treatment for inflammatory skin diseases.
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Affiliation(s)
- Xiaochun Liu
- Department of Allergy and Rheumatology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China; Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China
| | - Xiaoning Zhang
- Department of Dermatology, The First Medical Center, Chinese PLA General Hospital, Beijing, PR China
| | - Jingxi Zhang
- Department of Allergy and Rheumatology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China; Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China
| | - Yang Luo
- Department of Allergy and Rheumatology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China; Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China
| | - Beilei Xu
- Department of Allergy and Rheumatology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China; Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China
| | - Shiqi Ling
- Department of Allergy and Rheumatology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China; Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China
| | - Yu Zhang
- Department of Allergy and Rheumatology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China; Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China
| | - Wei Li
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, PR China.
| | - Xu Yao
- Department of Allergy and Rheumatology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China; Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China.
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Novel hybrid antiviral VTRRT-13V2.1 against SARS-CoV2 main protease: retro-combinatorial synthesis and molecular dynamics analysis. Heliyon 2020; 6:e05122. [PMID: 33020742 PMCID: PMC7526676 DOI: 10.1016/j.heliyon.2020.e05122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/11/2020] [Accepted: 09/28/2020] [Indexed: 12/27/2022] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has now emerged as a global health problem and is responsible for high mortality and morbidity. The SARS-CoV-2 main protease (Mpro) emerged as a promising drug target because of its essential role in the processing of polyproteins, which is translated from viral RNA. The present study reports a designed novel hybrid antiviral molecule (VTRRT-13.V2.1) against SARS-CoV2 main protease. A series of different combinations of hybrid antiviral were generated from nonspecific antiviral molecules currently used to control COVID-19. To enhance the specificity of the designed hybrid antiviral molecule, the core pocket region of the active site of Mpro protein was targeted. In-silico screening, molecular mechanics, molecular dynamics simulation (MDS) analysis identified a hybrid VTRRT-13.V2 molecule. Retrosynthetic analysis and combinatorial synthesis generated 1000 analogs of VTRRT-13.V2 molecules. Docking, molecular mechanics, and MDS analysis selected VTRRT-13.V2.1 as a possible inhibitor for SARS-CoV2 main protease. Comparative analysis of all the results showed that VTRRT-13.V2.1 have the highest docking Glide score (-12.28 kcal/mol) and best binding energy (-52.23 kcal/mol) as compared to the other hybrid constructs such as VTRRT-13.V2 (-9.47 and -47.36 kcal/mol), VTRRT-13 (-8.9 and -47.55 kcal/mol), and current antiviral investigated. The mutational sensitivity screening showed that binding residues of Mpro are not present in mutation hotspots. It was also observed that VTRRT-13.V2.1 does not have any human off-targets. SARS-CoV2 main protease is essential for the survival of this virus; hence, a designed novel hybrid antiviral molecule (VTRRT-13.V2.1) might be useful to control the infection of COVID-19 infection.
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Tiwari M, Panwar S, Kothidar A, Tiwari V. Rational targeting of Wzb phosphatase and Wzc kinase interaction inhibits extracellular polysaccharides synthesis and biofilm formation in Acinetobacter baumannii. Carbohydr Res 2020; 492:108025. [PMID: 32402850 DOI: 10.1016/j.carres.2020.108025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/17/2020] [Accepted: 04/27/2020] [Indexed: 11/18/2022]
Abstract
Acinetobacter baumannii is an opportunistic nosocomial pathogen, and responsible for high mortality and morbidity. Biofilm formation is one of the resistance determinants, where extracellular polysaccharide (EPS) is an essential component. EPS synthesis and its export is regulated by the bacterial Wza-Wzb-Wzc system. Wzc exhibits auto-phosphorylation protein tyrosine kinase activity, while Wzb is a protein tyrosine phosphatase. Wzb mediates dephosphorylation of Wzc. Dephosphorylated Wzc is required for the export of the EPS through porin Wza-Wzc complex. It shows that the interaction of Wzb with Wzc is critical for the export of EPS. Therefore, if the Wzb-Wzc interaction is inhibited, then it might hinder the EPS transport and diminish the biofilm formation. In this study, we have modelled the Wzb, and Wzc proteins and further validated using PSVS, ProSA, RAMPAGE, and PDBsum. The modelled proteins were used for protein-protein docking. The docked protein-protein complex was minimized by Schrodinger software using OPLS_2005 force field. The binding site of the minimized Wzb-Wzc complex was identified by Sitemap. The high throughput virtual screening identified Labetalol hydrochloride and 4-{1-hydroxy-2-[(1-methyl-3-phenylpropyl) amino] propyl} phenol from FDA-approved drug library based on their interaction at the interface of Wzb-Wzc complex. The inhibitor-protein complex was further undergone molecular mechanics analysis using Generalized Born model and Solvent Accessibility (MMGBSA) to estimate the binding free energies. The lead was also used to generate the pharmacophore model and screening the molecule with antimicrobial scaffold. The identified lead was experimentally validated for its effect on EPS quantity and biofilm formation by A. baumannii. Wzb-Wzc interaction is essential for biofilm and EPS export; hence, the identified lead might be useful to regulate the biofilm formation by A. baumannii.
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Affiliation(s)
- Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Shruti Panwar
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Akansha Kothidar
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India.
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da Rosa TF, Coelho SS, Foletto VS, Bottega A, Serafin MB, Machado CDS, Franco LN, de Paula BR, Hörner R. Alternatives for the treatment of infections caused by ESKAPE pathogens. J Clin Pharm Ther 2020; 45:863-873. [PMID: 32339305 DOI: 10.1111/jcpt.13149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/11/2020] [Accepted: 04/03/2020] [Indexed: 12/21/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE The widespread use of antibiotics as therapeutic agents caused an increase of multidrug resistant bacteria (MDR) appearance. Regarding MDRs, we highlight the Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.., which are the ESKAPE group. COMMENT New treatment alternatives for infections caused by ESKAPE are under current scientific research. The main suggestions are the use of actinomycetes that produce promising substances with antibiotic activity, the synergistic effect between antimicrobials and peptides, photoinactivation, peptide rich in cationic histidine, association of new antimicrobials; besides the repositioning of drugs already approved for the treatment of other diseases. WHAT IS NEW AND CONCLUSION These selected studies showed that researchers from many countries are focused on the development of effective alternative strategies for the treatment of infections caused by these microorganisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Rosmari Hörner
- Department of Clinical and Toxicological Analysis, Federal University of Santa Maria, Santa Maria, Brazil
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Tiwari V. Post-translational modification of ESKAPE pathogens as a potential target in drug discovery. Drug Discov Today 2018; 24:814-822. [PMID: 30572117 DOI: 10.1016/j.drudis.2018.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/23/2018] [Accepted: 12/12/2018] [Indexed: 12/19/2022]
Abstract
ESKAPE pathogens are gaining clinical importance owing to their high pervasiveness and increasing resistance to various antimicrobials. These bacteria have several post-translational modifications (PTMs) that destabilize or divert host cell pathways. Prevalent PTMs of ESKAPE pathogens include addition of chemical groups (acetylation, phosphorylation, methylation and hydroxylation) or complex molecules (AMPylation, ADP-ribosylation, glycosylation and isoprenylation), covalently linked small proteins [ubiquitylation, ubiquitin-like proteins (UBL) conjugation and small ubiquitin-like modifier (SUMO)] or modification of amino acid side-chains (eliminylation and deamidation). Therefore, the understanding of different bacterial PTMs and host proteins manipulated by these PTMs provides better insight into host-pathogen interaction and will also help to develop new antibacterial agents against ESKAPE pathogens.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India.
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