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Potentiate the activity of current antibiotics by naringin dihydrochalcone targeting the AdeABC efflux pump of multidrug-resistant Acinetobacter baumannii. Int J Biol Macromol 2022; 217:592-605. [PMID: 35841965 DOI: 10.1016/j.ijbiomac.2022.07.065] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/23/2022]
Abstract
Acinetobacter baumannii is an ESKAPE pathogen responsible for severe nosocomial infections. Among all the mechanisms contributing to multidrug resistance, efflux pumps have gained significant attention due to their widespread distribution among bacterial species and broad substrate specificity. This study has investigated the diverse roles of efflux pumps present in carbapenem-resistant A. baumannii (CRAB) and screen an efflux pump inhibitor. The result showed the presence of AdeABC, AdeFGH, AdeIJK, and AbeM efflux pumps in CRAB, and experimental studies using gene mutants demonstrated the significant role of AdeABC in carbapenem resistance, biofilm formation, surface motility, pathogenesis, bacterial adherence, and invasion to the host cells. The structure-based ligand screening, molecular mechanics, molecular dynamics simulation, and experimental validation using efflux pump mutants and antibiotic accumulation assay identified naringin dihydrochalcone (NDC) as the lead against AdeB. This lead was selected as a capping agent for silver nanoparticles. The NDC-capped silver nanoparticles (NDC-AgNPs) were characterized by UV-spectroscopy, Fourier-transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), and scanning electron microscopy (SEM). The investigated molecular mechanism showed that the NDC-AgNPs possessed multiple mechanisms of action. In addition to efflux inhibitory activity, it also generates reactive oxygen and nitrogen species as well as causes change in the electrochemical gradient in CRAB. The proton gradient is important for the function of AdeABC; hence altering the electrochemical gradient also disrupts its efflux activity. Moreover, A. baumannii did not develop any resistance against NDC-AgNPs till several generations which were investigated. The NDC-AgNPs were also found to be effective against carbapenem-resistant clinical isolates of A. baumannii. Therefore, the present study provided an insight into the efflux pump mediated carbapenem resistance and possible inhibitor NDC-AgNPs to combat AdeABC efflux pump mediated resistance.
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Tiwari V. Molecular insight into the therapeutic potential of phytoconstituents targeting protein conformation and their expression. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2019; 52:225-237. [PMID: 30599902 PMCID: PMC7126799 DOI: 10.1016/j.phymed.2018.09.214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/03/2018] [Accepted: 09/25/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Native protein conformation is essential for the functional activity of the proteins and enzymes. Defects in conformation or alterations in expression of the proteins have been reported in various diseases. PURPOSE The aim of this study is to review the molecular insight into the therapeutic potential of phytoconstituents targeting protein conformations or expressions. METHODS Published literatures were searched in PubMed, Scopus, Web of Science; Article published till Dec 2017 were extracted. The literature was assessed from the Central University of Rajasthan, India. Present study evaluate article based on the role of active plant constituents on the conformation and expression of the different proteins. RESULTS Plant components play their role either at the molecular level or cellular level and exhibit antibacterial, antiviral, anti-neurodegenerative and other activities. Plant active compounds isolated from different plants may either stabilize or destabilize the conformation of proteins or alter expression level of the protein involved in these diseases, therefore, can play a significant role in preventing diseases caused by the alteration in these proteins. CONCLUSION In the present article, we have reviewed the molecular mechanism of plant active compounds, their target proteins, methods of extraction and identification, and their biological significances. Therefore, a proper understanding of the effect of these herbal molecules on the concerned proteins may help to develop new herbal-based therapeutics for various diseases.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India.
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Tiwari V, Rajeswari MR, Tiwari M. Proteomic analysis of iron-regulated membrane proteins identify FhuE receptor as a target to inhibit siderophore-mediated iron acquisition in Acinetobacter baumannii. Int J Biol Macromol 2018; 125:1156-1167. [PMID: 30579900 DOI: 10.1016/j.ijbiomac.2018.12.173] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/02/2018] [Accepted: 12/19/2018] [Indexed: 11/27/2022]
Abstract
Survival of the Acinetobacter baumannii inside host requires different micronutrients such as iron, but their bioavailability is limited because of nutritional immunity created by host. A. baumannii has to develop mechanisms to acquire nutrient iron during infection. The present study is an attempt to identify membrane proteins involved in iron sequestration mechanism of A. baumannii using two-dimensional electrophoresis and LC-MS/MS analysis. The identified iron-regulated membrane protein (IRMP) of A. baumannii was used for its interaction studies with different siderophores, and designing of the inhibitor against A. baumannii targeting this IRMP. Membrane proteomic results identified over-expression of four membrane proteins (Fhu-E receptor, ferric-acinetobactin receptor, ferrienterochelin receptor, and ferric siderophore receptor) under iron-limited condition. A. baumannii produces siderophores that have good interaction with the FhuE receptor. Result also showed that FhuE receptor has interaction with siderophores produced by other bacteria. Interaction of FhuE receptor and siderophores helps in iron sequestration and survival of Acinetobacter under nutritional immunity imposed by the host. Hence it becomes essential to find a potential inhibitor for the FhuE receptor that can inhibit the survival of A. baumannii in the host. In-silico screening, and molecular mechanics studies identified ZINC03794794 and ZINC01530652 as a likely lead to design inhibitor against the FhuE receptor of A. baumannii. The designed inhibitor is experimentally validated for its antibacterial activity on the A. baumannii. Therefore, designed inhibitor interferes with the iron acquisition mechanism of Acinetobacter hence may prove useful for preventing infection caused by A. baumannii by limiting nutrient availability.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India.
| | - Moganty R Rajeswari
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India
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Tiwari V, Meena K, Tiwari M. Differential anti-microbial secondary metabolites in different ESKAPE pathogens explain their adaptation in the hospital setup. INFECTION GENETICS AND EVOLUTION 2018; 66:57-65. [PMID: 30227225 DOI: 10.1016/j.meegid.2018.09.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/24/2018] [Accepted: 09/14/2018] [Indexed: 01/22/2023]
Abstract
Nosocomial infections are caused by ESKAPE (E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and E. cloacae) pathogens, and their co-existence is associated with their ability to survive in the hospital setup. They may produce molecules, which helps in the better survival of one ESKAPE pathogens over other. We have identified all secondary metabolite gene clusters in six ESKAPE pathogens and predicted antimicrobial and anti-biofilm properties of their product secondary metabolites. To validate our model, we have taken the secondary metabolites of ESKAPE pathogens and studied their interaction with diguanylate cyclase (involved in quorum sensing) and biofilm-associated protein (involved in biofilm formation) of Acinetobacter baumannii. Results suggest the presence of differential secondary metabolites in all ESKAPE pathogens with only three common non-antimicrobial secondary metabolites. Out of twenty-three antimicrobial secondary metabolites, TP-1161, nosiheptide and meilingmycin, showed the best antimicrobial activity and nineteen showed high anti-biofilm activity. Interaction study showed that secondary metabolites produced by other ESKAPE pathogens (non-Acinetobacter) have very good interaction with diguanylate cyclase and biofilm-associated protein of A. baumannii. This concludes that better survival of these ESKAPE pathogens in hospital setup can be correlated with differential production of antimicrobial secondary metabolites. The present study also investigates the molecular mechanism of the competition of different pathogens living in similar hospital setup (similar habitat). Therefore, the present study will initiate research that might lead to the discovery of antibiotics from one ESKAPE pathogen that controls the infection of other ESKAPE pathogens or other pathogens.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, -305817, India.
| | - Kiran Meena
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, -305817, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, -305817, India
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Biswas D, Tiwari M, Tiwari V. Comparative mechanism based study on disinfectants against multidrug-resistant Acinetobacter baumannii. J Cell Biochem 2018; 119:10314-10326. [PMID: 30145822 DOI: 10.1002/jcb.27373] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/28/2018] [Indexed: 12/19/2022]
Abstract
Acinetobacter baumannii has emerged as a hospital-acquired pathogen and has spread in the hospital settings, leading to enhanced nosocomial outbreaks associated with high death rates. Therefore, the aim of the current study is to determine the effective concentration of disinfectants like sodium hypochlorite, hydrogen peroxide, and chlorine dioxide, against multidrug-resistant (MDR) strains of A. baumannii. In this study, we have investigated the effect of disinfectants on different MDR strains i.e. RS307, RS6694, RS7434, RS10953, RS122, and sensitive strain ATCC-19606 of A. baumannii, via differential growth curves analysis, disc diffusion assay, estimation of reactive oxygen species (ROS), lipid peroxidation, and protein carbonylation. All the results collectively showed that 1% sodium hypochlorite (P value < 0.0027), 2.5% hydrogen peroxide (P value = 0.0032), and 10 mM (P value = 0.017) chlorine dioxide significantly inhibit the growth of MDR strains of A. baumannii. A significant increase in the ROS generations, altered lipid peroxidation, and a decrease in protein carbonylation was also observed after treatment with disinfectants, which confirmed its ROS-dependent damage mechanism. These disinfectants also enhance the membrane leakage of reducing sugar, protein, and DNA. The current study highlights and recommends the use of 2.5% hydrogen peroxide to control the MDR strains of A. baumannii in the hospital setup. Therefore, the present results will help in selecting concentrations of different disinfectants for regular use in hospital setups to eradicate the multidrug-resistant A. baumannii from the hospital setup.
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Affiliation(s)
- Deepika Biswas
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, India
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Targeting Outer Membrane Protein Component AdeC for the Discovery of Efflux Pump Inhibitor against AdeABC Efflux Pump of Multidrug Resistant Acinetobacter baumannii. Cell Biochem Biophys 2018; 76:391-400. [PMID: 29926429 DOI: 10.1007/s12013-018-0846-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/07/2018] [Indexed: 01/19/2023]
Abstract
The structure and functioning of multidrug efflux systems provide us with a better understanding of the transport of various antibiotics, thus giving a path for the discovery of effective compounds for combating the multidrug resistance in Acinetobacter baumannii. In the present study, a number of computational techniques have been used to search for an inhibitor for the RND efflux pump, AdeABC, of A. baumannii targeting specifically its outermost component, i.e., AdeC. We have prepared the three-dimensional structure for AdeC using MODELLER v9.16 and identified its active binding site using SiteMap. Using high-throughput virtual screening, we identified compounds from a large library of biogenic compounds on the basis of their effective interaction at the binding site of AdeC. The validation of docking step was performed by plotting ROC curve (enrichment calculations). The docked complexes were further analyzed for their binding free energies by molecular mechanics using Generalized Born model and Solvent Accessibility (MMGBSA). The molecular dynamics simulation was performed for AdeC-ZINC77257599 complex using GROMACS. The present rational drug designing, molecular mechanics and molecular dynamics data provided an inhibitor, i.e, ZINC77257599 [(3R,4Z,6E,8E)-3-hydroxy-2,2,4-trimethyl-10-oxazol-5-yl-deca-4,6,8-trienamide], for the outer membrane protein component (AdeC) of efflux pump AdeABC of A. baumannii.
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Tiwari V, Mishra N, Gadani K, Solanki PS, Shah NA, Tiwari M. Mechanism of Anti-bacterial Activity of Zinc Oxide Nanoparticle Against Carbapenem-Resistant Acinetobacter baumannii. Front Microbiol 2018; 9:1218. [PMID: 29928271 PMCID: PMC5997932 DOI: 10.3389/fmicb.2018.01218] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/18/2018] [Indexed: 11/13/2022] Open
Abstract
Acinetobacter baumannii is a multi-drug resistant opportunistic pathogen, which causes respiratory and urinary tract infections. Its prevalence increases gradually in the clinical setup. Carbapenems (beta-lactam) are most effective antibiotics till now against A. baumannii, but the development of resistance against it may lead to high mortality. Therefore, it is of utmost importance to develop an alternative drug against A. baumannii. In the present study, we have synthesized ZnO nanoparticle (ZnO-NP) and characterized by X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy and UV-Visible spectroscopy. Prepared ZnO-NPs have the size of 30 nm and have different characteristics of ZnO-NPs. Growth kinetics and disk diffusion assay showed that ZnO-NP demonstrated good antibacterial activity against carbapenem resistant A. baumannii. We have also investigated the mechanism of action of ZnO-NPs on the carbapenem resistant strain of A. baumannii. The proposed mechanism of action of ZnO involves the production of reactive oxygen species, which elevates membrane lipid peroxidation that causes membrane leakage of reducing sugars, DNA, proteins, and reduces cell viability. These results demonstrate that ZnO-NP could be developed as alternative therapeutics against A. baumannii.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Neha Mishra
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Keval Gadani
- Department of Physics, Saurashtra University, Rajkot, India
| | - P. S. Solanki
- Department of Physics, Saurashtra University, Rajkot, India
| | - N. A. Shah
- Department of Physics, Saurashtra University, Rajkot, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
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Solanki V, Tiwari M, Tiwari V. Host-bacteria interaction and adhesin study for development of therapeutics. Int J Biol Macromol 2018; 112:54-64. [PMID: 29414732 DOI: 10.1016/j.ijbiomac.2018.01.151] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/17/2018] [Accepted: 01/21/2018] [Indexed: 12/15/2022]
Abstract
Host-pathogen interaction is one of the most important areas of study to understand the adhesion of the pathogen to the host organisms. To adhere on the host cell surface, bacteria assemble the diverse adhesive structures on its surface, which play a foremost role in targeting to the host cell. We have highlighted different bacterial adhesins which are either protein mediated or glycan mediated. The present article listed examples of different bacterial adhesin proteins involved in the interactions with their host, types and subtypes of the fimbriae and non-fimbriae bacterial adhesins. Different bacterial surface adhesin subunits interact with host via different host surface biomolecules. We have also discussed the interactome of some of the pathogens with their host. Therefore, the present study will help researchers to have a detailed understanding of different interacting bacterial adhesins and henceforth, develop new therapies, adhesin specific antibodies and vaccines, which can effectively control pathogenicity of the pathogens.
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Affiliation(s)
- Vandana Solanki
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India.
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Tiwari V, Tiwari M, Biswas D. Rationale and design of an inhibitor of RecA protein as an inhibitor of Acinetobacter baumannii. J Antibiot (Tokyo) 2018; 71:522-534. [PMID: 29410519 DOI: 10.1038/s41429-018-0026-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/23/2017] [Accepted: 12/25/2017] [Indexed: 11/09/2022]
Abstract
Acinetobacter baumannii is one of the ESKAPE pathogen, which causes pneumonia, urinary tract infections, and is linked to high degree of morbidity and mortality. One-way antibiotic and disinfectant resistance is acquired by the activation of RecA-mediated DNA repair (SOS-response) that maintain ROS-dependent DNA damage caused by these anti-bacterial molecules. To increase the efficacy of different anti-microbial, there is a need to design an inhibitor against RecA of A. baumannii. We have performed homology modeling to generate the structure of RecA, followed by model refinement and validation. High-throughput virtual screening of 1,80,313 primary and secondary metabolites against RecA was performed in HTVS, SP, and XP docking modes. The selected 195 compounds were further analyzed for binding free energy by molecular mechanics approach. The selected top two molecules from molecular mechanics approach were further validated by molecular dynamics simulation (MDS). In-silico high-throughput virtual screening and MDS validation identified ZINC01530654 or (+-)-2-((4-((7-Chloro-4-quinolyl)amino)pentyl)ethylamino)ethanol sulfate (or hydroxychloroquine sulfate) as a possible lead molecule binding to RecA protein. We have experimentally determined the mechanism of ZINC01530654 to RecA protein. These findings suggest a strategy to chemically inhibit the vital process controlled by RecA that could be helpful for the development of new antibacterial agents.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India.
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Deepika Biswas
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
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Verma P, Maurya P, Tiwari M, Tiwari V. In-silico interaction studies suggest RND efflux pump mediates polymyxin resistance in Acinetobacter baumannii. J Biomol Struct Dyn 2017; 37:95-103. [DOI: 10.1080/07391102.2017.1418680] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Privita Verma
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer-305817, India
| | - Pramila Maurya
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer-305817, India
| | - Monalisa Tiwari
- 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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Tiwari V, Patel V, Tiwari M. In-silico screening and experimental validation reveal L-Adrenaline as anti-biofilm molecule against biofilm-associated protein (Bap) producing Acinetobacter baumannii. Int J Biol Macromol 2017; 107:1242-1252. [PMID: 28964839 DOI: 10.1016/j.ijbiomac.2017.09.105] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 12/15/2022]
Abstract
Acinetobacter baumannii, an ESKAPE pathogen, causes various nosocomial infections and has capacity to produce biofilm. Biofilm produced by this bacterium is highly tolerant to environmental factors and different antibiotics. Biofilm-associated protein (Bap) plays a significant role in the biofilm formation by A. baumannii and found in the extra cellular matrix of the biofilm. Therefore, it becomes essential to find a potential drug against Bap that has capacity to inhibit biofilm formation by A. baumannii. In-silico screening, molecular mechanics and molecular dynamics studies identified ZINC00039089 (L-Adrenaline) as an inhibitor for Bap of A. baumannii. Recently, it is reported that Bap can form amyloid like structure; hence we have created dimer of Bap protein. This inhibitor can bind to dimeric Bap with good affinity. It confirms that ZINC00039089 (L-Adrenaline) can bind with Bap monomer as well as oligomeric Bap, responsible for amyloid formation and biofilm formation. Hence, we have tested Adrenaline as an anti-biofilm molecule and determined its IC50 value against biofilm. The result showed Adrenaline has anti-biofilm activity with IC50 value of 75μg/ml. Therefore; our finding suggests that L-Adrenaline can be developed to inhibit biofilm formation by carbapenem resistant strain of Acinetobacter baumannii.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India.
| | - Varsha Patel
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
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Verma P, Tiwari M, Tiwari V. In silico high-throughput virtual screening and molecular dynamics simulation study to identify inhibitor for AdeABC efflux pump of Acinetobacter baumannii. J Biomol Struct Dyn 2017; 36:1182-1194. [PMID: 28393677 DOI: 10.1080/07391102.2017.1317025] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Emergence of multi-drug resistant strains of Acinetobacter baumannii has caused significant health problems and is responsible for high morbidity and mortality. Overexpression of AdeABC efflux system is one of the major mechanisms. In this study, we have focused on overcoming the drug resistance by identifying inhibitors that can effectively bind and inhibit integral membrane protein, AdeB of this efflux pump. We performed homology modeling to generate structure of AdeB using MODELLER v9.16 followed by model refinement using 3D-Refine tool and validated using PSVS, ProsaWeb, ERRAT, etc. The energy minimization of modeled protein was done using Protein preparation wizard application included in Schrodinger suite. High-throughput virtual screening of 159,868 medicinal compounds against AdeB was performed using three sequential docking modes (i.e. HTVS, SP and XP). Furthermore, absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis was done using QIKPROP. The selected 123 compounds were further analyzed for binding free energy by molecular mechanics (using prime MM-GBSA). We have also performed enrichment study (ROC curve analysis) to validate our docking results. The selected molecule and its interaction with AdeB were validated by molecular dynamics simulation (MDS) using GROMACS v5.1.4. In silico high-throughput virtual screening and MDS validation identified ZINC01155930 ((4R)-3-(cycloheptoxycarbonyl)-4-(4-etochromen-3-yl)-2-methyl-4,6,7,8-tetrahydroquinolin-5-olate) as a possible inhibitor for AdeB. Hence, it might be a suitable efflux pump inhibitor worthy of further investigation in order to be used for controlling infections caused by Acinetobacter baumannii.
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Affiliation(s)
- Privita Verma
- a Department of Biochemistry , Central University of Rajasthan , Bandarsindri, Ajmer 305817 , India
| | - Monalisa Tiwari
- a Department of Biochemistry , Central University of Rajasthan , Bandarsindri, Ajmer 305817 , India
| | - Vishvanath Tiwari
- a Department of Biochemistry , Central University of Rajasthan , Bandarsindri, Ajmer 305817 , India
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Zhang F, Xie L, Wang X, Han L, Guo X, Ni Y, Qu H, Sun J. Further Spread of bla NDM-5 in Enterobacteriaceae via IncX3 Plasmids in Shanghai, China. Front Microbiol 2016; 7:424. [PMID: 27065982 PMCID: PMC4811927 DOI: 10.3389/fmicb.2016.00424] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/16/2016] [Indexed: 01/26/2023] Open
Abstract
One hundred and two carbapenem-resistant Enterobacteriaceae (CRE) strains were isolated in a teaching hospital in Shanghai, China from 2012 to 2015. In a follow-up study, four New Delhi metallo-β-lactamase-5 (NDM-5)-producing strains were identified after screening these CRE strains, including 1 Klebsiella pneumoniae strain (RJ01), 1 Proteus mirabilis strain (RJ02), and 2 Escherichia coli strains (RJ03 and RJ04). All K. pneumoniae and E. coli isolates were resistant to carbapenems, third-generation cephalosporins, and piperacillin-tazobactam, but were susceptible to amikacin. No epidemiological links for either E. coli isolate were found by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). However, MLST revealed a novel sequence type, ST2250, of the K. pneumoniae RJ01 strain. Inc types and sizes of blaNDM-5-carrying plasmids differed among the four isolates, although in P. mirabilis RJ02 and E. coli RJ03, blaNDM-5 was carried by conjugative IncX3 plasmids of nearly the same size (∼40 kb). Investigation of the genetic background of sequences flanking the blaNDM-5 gene showed that all four isolates shared the same genetic content (IS3000-ΔISAba125-IS5-blaNDM-5-ble-trpF-dsbC-IS26-ΔumuD), which was identical to that of the pNDM_MGR194 plasmid circulating in India. This is the first identification of blaNDM-5 in P. mirabilis, which suggests its further spread to Enterobacteriaceae, and indicates that IncX3 plasmids may play an important role in potentiating the spread of blaNDM.
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Affiliation(s)
- Fangfang Zhang
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Lianyan Xie
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Xiaoli Wang
- Department of Critical Care Medicine and Respiratory Intensive Care Unit, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Lizhong Han
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Xiaokui Guo
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Yuxing Ni
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Hongping Qu
- Department of Critical Care Medicine and Respiratory Intensive Care Unit, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Jingyong Sun
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
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Tiwari M, Roy R, Tiwari V. Screening of Herbal-Based Bioactive Extract Against Carbapenem-Resistant Strain of Acinetobacter baumannii. Microb Drug Resist 2016; 22:364-71. [PMID: 26910023 DOI: 10.1089/mdr.2015.0270] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Acinetobacter baumannii is grouped in the ESKAPE pathogens by Infectious Disease Society of America, which is linked to high degree of morbidity, mortality, and increased costs. The high level of acquired and intrinsic resistance mechanisms of these bacteria makes it an urgent requirement to find a suitable alternative to carbapenem, a commonly prescribed drug for Acinetobacter infection. In this study, methanolic extracts of six medicinal plants were subjected to phytochemical screening and their antimicrobial activity was tested against two strains of A. baumannii (ATCC 19606, carbapenem-sensitive strain, and RS 307, carbapenem-resistant strain). Synergistic effect of the plant extracts and antibiotics was also tested. Bael or Aegle marmelos contains tannin, phenol, terpenoids, glycoside, alkaloids, coumarine, steroid, and quinones. Flowers of madar or Calotropis procera possess tannin, phenol, terpenoids, glycoside, quinone, anthraquinone, anthocyanin, coumarin, and steroid. An inhibitory growth curve was seen for both the bacterial strains when treated with A. marmelos, Curcuma longa, and leaves and flowers of C. procera. Antibiotics alone showed a small zone of inhibition, but when used with herbal extracts they exhibited larger zone of inhibition. Synergistic effect of A. marmelos and imipenem was the best against both the strains of A. baumannii. From this study, it can be concluded that extracts from A. marmelos and leaves and flowers of C. procera exhibited the most effective antibacterial activity. These herbal extracts may be used to screen the bioactive compound against the carbapenem-resistant strain of A. baumannii.
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Affiliation(s)
- Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan , Ajmer, India
| | - Ranita Roy
- Department of Biochemistry, Central University of Rajasthan , Ajmer, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan , Ajmer, India
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Chang Y, Luan G, Xu Y, Wang Y, Shen M, Zhang C, Zheng W, Huang J, Yang J, Jia X, Ling B. Characterization of carbapenem-resistant Acinetobacter baumannii isolates in a Chinese teaching hospital. Front Microbiol 2015; 6:910. [PMID: 26388854 PMCID: PMC4555021 DOI: 10.3389/fmicb.2015.00910] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 08/19/2015] [Indexed: 01/02/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) presents a serious therapeutic and infection control challenge. In this study, we investigated the epidemiological and molecular differences of CRAB and the threatening factors for contributing to increased CRAB infections at a hospital in western China. A total of 110 clinical isolates of A. baumannii, collected in a recent 2-year period, were tested for carbapenem antibiotic susceptibility, followed by a molecular analysis of carbapenemase genes. Genetic relatedness of the isolates was characterized by multilocus sequence typing. Sixty-seven of the 110 isolates (60.9%) were resistant to carbapenems, 80.60% (54/67) of which carried the blaOXA-23 gene. Most of these CRAB isolates (77.62%) were classified as clone complex 92 (CC92), and sequence type (ST) 92 was the most prevalent STs, followed by ST195, ST136, ST843, and ST75. One CRAB isolate of ST195 harbored plasmid pAB52 from a Chinese patient without travel history. This plasmid contains toxin–antitoxin elements related to adaptation for growth, which might have emerged as a common vehicle indirectly mediating the spread of OXA-23 in CRAB. Thus, CC92 A. baumannii carrying OXA-23 is a major drug-resistant strain spreading in China. Our findings indicate that rational application of antibiotics is indispensable for minimizing widespread of drug resistance.
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Affiliation(s)
- Yaowen Chang
- Small Molecule Drugs Sichuan Key Laboratory, Institute of Materia Medica, Chengdu Medical College Chengdu, China
| | - Guangxin Luan
- Non-coding RNA and Drug Discovery Laboratory, Chengdu Medical College Chengdu, China
| | - Ying Xu
- Clinical Laboratory, The First Affiliated Hospital, Chengdu Medical College Chengdu, China
| | - Yanhong Wang
- Non-coding RNA and Drug Discovery Laboratory, Chengdu Medical College Chengdu, China
| | - Min Shen
- Non-coding RNA and Drug Discovery Laboratory, Chengdu Medical College Chengdu, China
| | - Chi Zhang
- Small Molecule Drugs Sichuan Key Laboratory, Institute of Materia Medica, Chengdu Medical College Chengdu, China
| | - Wei Zheng
- Small Molecule Drugs Sichuan Key Laboratory, Institute of Materia Medica, Chengdu Medical College Chengdu, China
| | - Jinwei Huang
- Institute of Antibiotics, The Fifth Affiliated Hospital, Wenzhou Medical University Lishui, China
| | - Jingni Yang
- Non-coding RNA and Drug Discovery Laboratory, Chengdu Medical College Chengdu, China
| | - Xu Jia
- Non-coding RNA and Drug Discovery Laboratory, Chengdu Medical College Chengdu, China
| | - Baodong Ling
- Small Molecule Drugs Sichuan Key Laboratory, Institute of Materia Medica, Chengdu Medical College Chengdu, China
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Tiwari V, Roy R, Tiwari M. Antimicrobial active herbal compounds against Acinetobacter baumannii and other pathogens. Front Microbiol 2015; 6:618. [PMID: 26150810 PMCID: PMC4471432 DOI: 10.3389/fmicb.2015.00618] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/03/2015] [Indexed: 11/27/2022] Open
Abstract
Bacterial pathogens cause a number of lethal diseases. Opportunistic bacterial pathogens grouped into ESKAPE pathogens that are linked to the high degree of morbidity, mortality and increased costs as described by Infectious Disease Society of America. Acinetobacter baumannii is one of the ESKAPE pathogens which cause respiratory infection, pneumonia and urinary tract infections. The prevalence of this pathogen increases gradually in the clinical setup where it can grow on artificial surfaces, utilize ethanol as a carbon source and resists desiccation. Carbapenems, a β-lactam, are the most commonly prescribed drugs against A. baumannii. The high level of acquired and intrinsic carbapenem resistance mechanisms acquired by these bacteria makes their eradication difficult. The pharmaceutical industry has no solution to this problem. Hence, it is an urgent requirement to find a suitable alternative to carbapenem, a commonly prescribed drug for Acinetobacter infection. In order to do this, here we have made an effort to review the active compounds of plants that have potent antibacterial activity against many bacteria including carbapenem resistant strain of A. baumannii. We have also briefly highlighted the separation and identification methods used for these active compounds. This review will help researchers involved in the screening of herbal active compounds that might act as a replacement for carbapenem.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan Ajmer, India
| | - Ranita Roy
- Department of Biochemistry, Central University of Rajasthan Ajmer, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan Ajmer, India
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Chen Z, Li H, Feng J, Li Y, Chen X, Guo X, Chen W, Wang L, Lin L, Yang H, Yang W, Wang J, Zhou D, Liu C, Yin Z. NDM-1 encoded by a pNDM-BJ01-like plasmid p3SP-NDM in clinical Enterobacter aerogenes. Front Microbiol 2015; 6:294. [PMID: 25926823 PMCID: PMC4396501 DOI: 10.3389/fmicb.2015.00294] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/25/2015] [Indexed: 11/13/2022] Open
Abstract
A carbapenem-nonsusceptible Enterobacter aerogenes strain named 3-SP was isolated from a human case of pneumonia in a Chinese teaching hospital. NDM-1 carbapenemase is produced by a pNDM-BJ01-like conjugative plasmid designated p3SP-NDM to account for carbapenem resistance of 3-SP. p3SP-NDM was fully sequenced and compared with all publically available pNDM-BJ01-like plasmids. The genetic differences between p3SP-NDM and pNDM-BJ01 include only 18 single nucleotide polymorphisms, a 1 bp deletion and a 706 bp deletion. p3SP-NDM and pNDM-BJ01 harbor an identical Tn125 element organized as ISAba125, blaNDM−1, bleMBL, ΔtrpF, dsbC, cutA, ΔgroES, groEL, ISCR27, and ISAba125. The blaNDM−1 surrounding regions in these pNDM-BJ01-like plasmids have a conserved linear organization ISAba14-aphA6-Tn125-unknown IS, with considerable genetic differences identified within or immediately downstream of Tn125. All reported pNDM-BJ01-like plasmids are exclusively found in Acinetobacter, whereas this is the first report of identification of a pNDM-BJ01-like plasmid in Enterobacteriaceae.
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Affiliation(s)
- Zhenhong Chen
- Nanlou Respiratory Diseases Department, Chinese People's Liberation Army General Hospital Beijing, China
| | - Hongxia Li
- Nanlou Respiratory Diseases Department, Chinese People's Liberation Army General Hospital Beijing, China
| | - Jiao Feng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Yuxue Li
- The First Hospital of Shijiazhuang City Shijiazhuang, China
| | - Xin Chen
- Zhongshan School of Medicine, Sun Yat-Sen University Guangzhou, China
| | - Xuemin Guo
- Zhongshan School of Medicine, Sun Yat-Sen University Guangzhou, China
| | - Weijun Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Li Wang
- Nanlou Respiratory Diseases Department, Chinese People's Liberation Army General Hospital Beijing, China
| | - Lei Lin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Jie Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Changting Liu
- Nanlou Respiratory Diseases Department, Chinese People's Liberation Army General Hospital Beijing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
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Tiwari V, Tiwari M. Quantitative proteomics to study carbapenem resistance in Acinetobacter baumannii. Front Microbiol 2014; 5:512. [PMID: 25309531 PMCID: PMC4176082 DOI: 10.3389/fmicb.2014.00512] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/11/2014] [Indexed: 12/28/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen causing pneumonia, respiratory infections and urinary tract infections. The prevalence of this lethal pathogen increases gradually in the clinical setup where it can grow on artificial surfaces, utilize ethanol as a carbon source. Moreover it resists desiccation. Carbapenems, a β-lactam, are the most commonly prescribed drugs against A. baumannii. Resistance against carbapenem has emerged in Acinetobacter baumannii which can create significant health problems and is responsible for high morbidity and mortality. With the development of quantitative proteomics, a considerable progress has been made in the study of carbapenem resistance of Acinetobacter baumannii. Recent updates showed that quantitative proteomics has now emerged as an important tool to understand the carbapenem resistance mechanism in Acinetobacter baumannii. Present review also highlights the complementary nature of different quantitative proteomic methods used to study carbapenem resistance and suggests to combine multiple proteomic methods for understanding the response to antibiotics by Acinetobacter baumannii.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of RajasthanAjmer, India
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Phosphoproteomics as an emerging weapon to develop new antibiotics against carbapenem resistant strain of Acinetobacter baumannii. J Proteomics 2014; 112:336-8. [PMID: 25252118 DOI: 10.1016/j.jprot.2014.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 08/30/2014] [Accepted: 09/02/2014] [Indexed: 01/05/2023]
Abstract
Acinetobacter baumannii causes pneumonia, bloodstream infections, urinary tract infections, respiratory infections and meningitis. A. baumannii has developed resistance against most of the antibiotics including carbapenem. Therefore, to battle carbapenem resistance, there is a need to develop antimicrobial drugs with new modes of action. Phosphoproteomics will help identify the differentially phosphorylated protein and its crucial phosphosites which facilitate the elucidation of molecular mechanism of signaling and regulation of carbapenem resistant strain of A. baumannii as compared to carbapenem sensitive strain. This understanding might be useful for the development of new antibiotics against kinases involved in the phosphorylation of identified phosphosites in carbapenem resistant strain of A. baumannii. The proposed antibiotics selectively inhibit carbapenem resistant strain which further avoids its excessive use against carbapenem sensitive strain and thereafter reduces emergence of resistance.
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