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Skariyachan S, Praveen PKU, Uttarkar A, Niranjan V. Computational design of prospective molecular targets for Burkholderia cepacia complex by molecular docking and dynamic simulation studies. Proteins 2023; 91:724-738. [PMID: 36601892 DOI: 10.1002/prot.26462] [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: 10/14/2022] [Revised: 11/27/2022] [Accepted: 01/02/2023] [Indexed: 01/06/2023]
Abstract
The study aimed to screen prospective molecular targets of BCC and potential natural lead candidates as effective binders by computational modeling, molecular docking, and dynamic (MD) simulation studies. Based on the virulent functions, tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein (mnmC) and pyrimidine/purine nucleoside phosphorylase (ppnP) were selected as the prospective molecular targets. In the absence of experimental data, the three-dimensional (3D) structures of these targets were computationally predicted. After a thorough literature survey and database search, the drug-likeness, and pharmacokinetic properties of 70 natural molecules were computationally predicted and the effectual binding of the best lead molecules against both the targets was predicted by molecular docking. The stabilities of the best-docked complexes were validated by MD simulation and the binding energy calculations were carried out by MM-GBSA approaches. The present study revealed that the hypothetical models of mnmC and ppnP showed stereochemical accuracy. The study also showed that among 70 natural compounds subjected to computational screening, Honokiol (3',5-Di(prop-2-en-1-yl) [1,1'-biphenyl]-2,4'-diol) present in Magnolia showed ideal drug-likeness, pharmacokinetic features and showed effectual binding with mnmC and ppnP (binding energies -7.3 kcal/mol and -6.6 kcal/mol, respectively). The MD simulation and GBSA calculation studies showed that the ligand-protein complexes stabilized throughout tMD simulation. The present study suggests that Honokiol can be used as a potential lead molecule against mnmC and ppnP targets of BCC and this study provides insight into further experimental validation for alternative lead development against drug resistant BCC.
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Affiliation(s)
- Sinosh Skariyachan
- Department of Microbiology, St. Pius X College Rajapuram, Kasaragod, Kerala, India
| | | | - Akshay Uttarkar
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka, India
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Ahsan U, Mushtaq F, Saleem S, Malik A, Sarfaraz H, Shahzad M, Uhlin BE, Ahmad I. Emergence of high colistin resistance in carbapenem resistant Acinetobacter baumannii in Pakistan and its potential management through immunomodulatory effect of an extract from Saussurea lappa. Front Pharmacol 2022; 13:986802. [PMID: 36188613 PMCID: PMC9523213 DOI: 10.3389/fphar.2022.986802] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/17/2022] [Indexed: 11/24/2022] Open
Abstract
Carbapenem resistant Acinetobacter baumannii has emerged as one of the most difficult to treat nosocomial bacterial infections in recent years. It was one of the major causes of secondary infections in Covid-19 patients in developing countries. The polycationic polypeptide antibiotic colistin is used as a last resort drug to treat carbapenem resistant A. baumannii infections. Therefore, resistance to colistin is considered as a serious medical threat. The purpose of this study was to assess the current status of colistin resistance in Pakistan, a country where carbapenem resistant A. bumannii infections are endemic, to understand the impact of colistin resistance on virulence in mice and to assess alternative strategies to treat such infections. Out of 150 isolates collected from five hospitals in Pakistan during 2019–20, 84% were carbapenem resistant and 7.3% were additionally resistant to colistin. There were two isolates resistant to all tested antibiotics and 83% of colistin resistant isolates were susceptible to only tetracycline family drugs doxycycline and minocycline. Doxycycline exhibited a synergetic bactericidal effect with colistin even in colistin resistant isolates. Exposure of A. baumannii 17978 to sub inhibitory concentrations of colistin identified novel point mutations associated with colistin resistance. Colistin tolerance acquired independent of mutations in lpxA, lpxB, lpxC, lpxD, and pmrAB supressed the proinflammatory immune response in epithelial cells and the virulence in a mouse infection model. Moreover, the oral administration of water extract of Saussuria lappa, although not showing antimicrobial activity against A. baumannii in vitro, lowered the number of colonizing bacteria in liver, spleen and lung of the mouse model and also lowered the levels of neutrophils and interleukin 8 in mice. Our findings suggest that the S. lappa extract exhibits an immunomodulatory effect with potential to reduce and cure systemic infections by both opaque and translucent colony variants of A. baumannii.
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Affiliation(s)
- Umaira Ahsan
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Pakistan
- Department of Microbiology, University of Health Sciences, Lahore, Pakistan
| | - Fizza Mushtaq
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Pakistan
| | - Sidrah Saleem
- Department of Microbiology, University of Health Sciences, Lahore, Pakistan
| | - Abdul Malik
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Pakistan
| | - Hira Sarfaraz
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Pakistan
| | - Muhammad Shahzad
- Department of Pharmacology, University of Health Sciences, Lahore, Pakistan
| | - Bernt Eric Uhlin
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Irfan Ahmad
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Pakistan
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- *Correspondence: Irfan Ahmad, ,
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Ramírez-Reyes T, Monribot-Villanueva JL, Jiménez-Martínez OD, Aguilar-Colorado ÁS, Bonilla-Landa I, Flores-Estévez N, Luna-Rodríguez M, Guerrero-Analco JA. Sesquiterpene Lactones and Phenols from Polyfollicles of Magnolia vovidessi and their Antimicrobial Activity. Nat Prod Commun 2018. [DOI: 10.1177/1934578x1801300502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Bioassay-guided fractionation of an active crude extract (EtOAc) of polyfollicles of Magnolia vovidessi, an endemic medicinal plant of the cloud forest of Mexico, led to the isolation and identification of shizukolidol (1), an eudesmane-type sesquiterpenoid lactone that showed antibacterial activity against the economically important phytopathogenic bacterium Chryseobacterium sp. (MIC= 400 μg/mL). In addition, 4α,8β-dihydroxy-5α(H)-eudesm-7(11)-en-8,12-olide 8 (2), rutin, scopoline and scopoletine were also isolated as were mexicanin, parthenolide, costunolide, astragalin, quercetin, hesperidin, p-coumaric acid, chlorogenic acid, vanillin, vanillic acid, 4-hydroxybenzoic acid, protocatechuic acid and shikimic acid identified by a dereplication-like procedure using LC-ESI-MS/MS. Rutin displayed mild anti-oomicite activity against phytopathogen Phytophthora cinnamomi.
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Affiliation(s)
- Thalía Ramírez-Reyes
- Laboratorio de Química de Productos Naturales, Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C.-Clúster Científico y Tecnológico BioMimic®, 91070 Xalapa, Veracruz, México
| | - Juan L. Monribot-Villanueva
- Laboratorio de Química de Productos Naturales, Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C.-Clúster Científico y Tecnológico BioMimic®, 91070 Xalapa, Veracruz, México
| | - Oscar D. Jiménez-Martínez
- Laboratorio de Química de Productos Naturales, Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C.-Clúster Científico y Tecnológico BioMimic®, 91070 Xalapa, Veracruz, México
| | - Ángel S. Aguilar-Colorado
- Laboratorio de Química de Productos Naturales, Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C.-Clúster Científico y Tecnológico BioMimic®, 91070 Xalapa, Veracruz, México
| | - Israel Bonilla-Landa
- Laboratorio de Química de Productos Naturales, Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C.-Clúster Científico y Tecnológico BioMimic®, 91070 Xalapa, Veracruz, México
| | - Norma Flores-Estévez
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa 91090, México
| | - Mauricio Luna-Rodríguez
- Laboratorio de Genética e Interacciones Planta Microorganismos, Facultad de Ciencias Agrícolas, Universidad Veracruzana, 91090, Xalapa, Veracruz, México
| | - José A. Guerrero-Analco
- Laboratorio de Química de Productos Naturales, Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C.-Clúster Científico y Tecnológico BioMimic®, 91070 Xalapa, Veracruz, México
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