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Filipić B, Ušjak D, Rambaher MH, Oljacic S, Milenković MT. Evaluation of novel compounds as anti-bacterial or anti-virulence agents. Front Cell Infect Microbiol 2024; 14:1370062. [PMID: 38510964 PMCID: PMC10951914 DOI: 10.3389/fcimb.2024.1370062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
Antimicrobial resistance is a global threat, leading to an alarming increase in the prevalence of bacterial infections that can no longer be treated with available antibiotics. The World Health Organization estimates that by 2050 up to 10 million deaths per year could be associated with antimicrobial resistance, which would equal the annual number of cancer deaths worldwide. To overcome this emerging crisis, novel anti-bacterial compounds are urgently needed. There are two possible approaches in the fight against bacterial infections: a) targeting structures within bacterial cells, similar to existing antibiotics; and/or b) targeting virulence factors rather than bacterial growth. Here, for the first time, we provide a comprehensive overview of the key steps in the evaluation of potential new anti-bacterial and/or anti-virulence compounds. The methods described in this review include: a) in silico methods for the evaluation of novel compounds; b) anti-bacterial assays (MIC, MBC, Time-kill); b) anti-virulence assays (anti-biofilm, anti-quorum sensing, anti-adhesion); and c) evaluation of safety aspects (cytotoxicity assay and Ames test). Overall, we provide a detailed description of the methods that are an essential tool for chemists, computational chemists, microbiologists, and toxicologists in the evaluation of potential novel antimicrobial compounds. These methods are cost-effective and have high predictive value. They are widely used in preclinical studies to identify new molecular candidates, for further investigation in animal and human trials.
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Affiliation(s)
- Brankica Filipić
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Dušan Ušjak
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Martina Hrast Rambaher
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Slavica Oljacic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Marina T. Milenković
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
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2
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Thakur A, Sharma B, Parashar A, Sharma V, Kumar A, Mehta V. 2D-QSAR, molecular docking and MD simulation based virtual screening of the herbal molecules against Alzheimer's disorder: an approach to predict CNS activity. J Biomol Struct Dyn 2024; 42:148-162. [PMID: 36970779 DOI: 10.1080/07391102.2023.2192805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
Abstract
Acetylcholinesterase (AChE) is one of the key enzyme targets that have been used clinically for the management of Alzheimer's Disorder (AD). Numerous reports in the literature predict and demonstrate in-vitro, and in-silico anticholinergic activity of herbal molecules, however, majority of them failed to find clinical application. To address these issues, we developed a 2D-QSAR model that could efficiently predict the AChE inhibitory activity of herbal molecules along with predicting their potential to cross the blood-brain-barrier (BBB) to exert their beneficial effects during AD. Virtual screening of the herbal molecules was performed and amentoflavone, asiaticoside, astaxanthin, bahouside, biapigenin, glycyrrhizin, hyperforin, hypericin, and tocopherol were predicted as the most promising herbal molecules for inhibiting AChE. Results were validated through molecular docking, atomistic molecular dynamics simulations and Molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) studies against human AChE (PDB ID: 4EY7). To determine whether or not these molecules can cross BBB to inhibit AChE within the central nervous system (CNS) for being beneficial for the management of AD, we determined a CNS Multi-parameter Optimization (MPO) score, which was found in the range of 1 to 3.76. Overall, the best results were observed for amentoflavone and our results demonstrated a PIC50 value of 7.377 nM, molecular docking score of -11.5 kcal/mol, and CNS MPO score of 3.76. In conclusion, we successfully developed a reliable and efficient 2D-QSAR model and predicted amentoflavone to be the most promising molecule that could inhibit human AChE enzyme within the CNS and could prove beneficial for the management of AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aman Thakur
- DCO, Govt. of Rajasthan, Bharatpur, Rajasthan, India
| | - Bhanu Sharma
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India
- Biotechnology Division, CSIR-IHBT, Palampur, Himachal Pradesh, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Arun Parashar
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
| | - Vivek Sharma
- Department of Pharmacology, Govt. College of Pharmacy, Shimla, Himachal Pradesh, India
| | - Ajay Kumar
- Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra, Haryana, India
| | - Vineet Mehta
- Department of Pharmacology, Govt. College of Pharmacy, Shimla, Himachal Pradesh, India
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Ju T, Lu AL, Zhou YC, Ge M, Sun J, Han Y, Yan CG. Direct Regioselective Reductive Allylation of Imines: Application to Synthesis of Oxazines with Halogenated Reagent. Org Lett 2023. [PMID: 38032844 DOI: 10.1021/acs.orglett.3c03407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Oxazines are an important class of compounds in oxazine ligands and medical chemistry. Here, we describe a linear-selective allylation of imines with allyl electrophiles via cross-electrophile coupling reactions, followed by cyclization with halogenated reagents, providing a new strategy to afford oxazine compounds with a tetrasubstituted carbon center. Mechanistic studies indicate that α-amino carbanion, generated by successive single-electron transfer processes, is a key intermediate for nucleophile attack on π-allylpalladium in photoredox/palladium catalysis.
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Affiliation(s)
- Tao Ju
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 250002, P. R. China
| | - Ai-Ling Lu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 250002, P. R. China
| | - Yu-Chao Zhou
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 250002, P. R. China
| | - Min Ge
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 250002, P. R. China
| | - Jing Sun
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 250002, P. R. China
| | - Ying Han
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 250002, P. R. China
| | - Chao-Guo Yan
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 250002, P. R. China
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Farghaly TA, Dawood KM. Inhibitory Activities of Pyrazolo-Oxazine Heterocyclic Derivatives. Mini Rev Med Chem 2021; 22:1256-1267. [PMID: 34967287 DOI: 10.2174/1389557522666211229114446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/05/2021] [Accepted: 09/10/2021] [Indexed: 11/22/2022]
Abstract
Despite several reports and reviews addressing the biological significance of pyrazoles and oxazines, no comprehensive work on the pyrazolo oxazine fused ring system has been published so far.We report all biological evaluations on pyrazolo-oxazine derivatives in this mini-review to provide an avenue for medicinal and pharmacological researchers to conduct further in-depth exploration.
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Affiliation(s)
- Thoraya A Farghaly
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah Almukkarramah, Saudi Arabia
| | - Kamal M Dawood
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
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Deblais L, Rajashekara G. Compound Prioritization through Meta-Analysis Enhances the Discovery of Antimicrobial Hits against Bacterial Pathogens. Antibiotics (Basel) 2021; 10:antibiotics10091065. [PMID: 34572646 PMCID: PMC8471430 DOI: 10.3390/antibiotics10091065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
The development of informatic tools to improve the identification of novel antimicrobials would significantly reduce the cost and time of drug discovery. We previously screened several plant (Xanthomonas sp., Clavibacter sp., Acidovorax sp., and Erwinia sp.), animal (Avian pathogenic Escherichia coli and Mycoplasma sp.), and human (Salmonella sp. and Campylobacter sp.) pathogens against a pre-selected small molecule library (n = 4182 SM) to identify novel SM (hits) that completely inhibited the bacterial growth or attenuated at least 75% of the virulence (quorum sensing or biofilm). Our meta-analysis of the primary screens (n = 11) using the pre-selected library (approx. 10.2 ± 9.3% hit rate per screen) demonstrated that the antimicrobial activity and spectrum of activity, and type of inhibition (growth versus virulence inhibitors) correlated with several physico-chemical properties (PCP; e.g., molecular weight, molar refraction, Zagreb group indexes, Kiers shape, lipophilicity, and hydrogen bond donors and acceptors). Based on these correlations, we build an in silico model that accurately classified 80.8% of the hits (n = 1676/2073). Therefore, the pre-selected SM library of 4182 SM was narrowed down to 1676 active SM with predictable PCP. Further, 926 hits affected only one species and 1254 hits were active against specific type of pathogens; however, no correlation was detected between PCP and the type of pathogen (29%, 34%, and 46% were specific for animal, human foodborne and plant pathogens, respectively). In conclusion, our in silico model allowed rational identification of SM with potential antimicrobial activity against bacterial pathogens. Therefore, the model developed in this study may facilitate future drug discovery efforts by accelerating the identification of uncharacterized antimicrobial molecules and predict their spectrum of activity.
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Salmani MH, Garzegar S, Ehrampoush MH, Askarishahi M. Predicting anionic surfactant toxicity to Daphnia magna in aquatic environment: a green approach for evaluation of EC 50 values. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:50731-50746. [PMID: 33973114 DOI: 10.1007/s11356-021-14107-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
The median effective concentration (EC50) is the concentration of a substance expected to produce a specific effect in 50% of the populations with a certain density under defined conditions. This parameter is expressed as an acute toxicity and is obtained via chemical toxicity testing. But, the laboratory work is time-consuming, expensive, and not eco-friendly. Therefore, to predict EC50 for new anionic surfactants, a quantitative structure-activity relationship (QSAR) tool was studied for modeling the EC50 of anionic surfactants on Daphnia magna based on the molecular descriptors. The best model (R2 = 0.901 and F = 118.077, p<0.01) included 3 variables of the number of carbons, hydrogens, and the octanol-water partition coefficient logarithm. The main contribution to the toxicity was the octanol-water partition coefficient logarithm descriptor that had a negative effect on the toxicity of surfactants. The QSAR approach exhibited good results in predicting anionic surfactants EC50, which allows the building of a simple, valid, and interpretable model that can be utilized as potential tools for rapidly predicting the lnEC50 of new or untested anionic surfactants to Daphnia magna.
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Affiliation(s)
- Mohammad Hossein Salmani
- Environmental Science & Technology Research Center, Department of Environmental Health Engineering, School of Public Health, Shahid Sadoughi University of Medical Sciences, I. R, Yazd, Iran
| | - Sahar Garzegar
- Department of Environmental Health Engineering, School of Public Health, Shahid Sadoughi University of Medical Sciences, I. R, Yazd, Iran.
| | - Mohammad Hassan Ehrampoush
- Environmental Science & Technology Research Center, Department of Environmental Health Engineering, School of Public Health, Shahid Sadoughi University of Medical Sciences, I. R, Yazd, Iran
| | - Mohsen Askarishahi
- Department of Biostatistics and Epidemiology, School of Public Health, Shahid Sadoughi University of Medical Sciences, I. R, Yazd, Iran
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Zhang L, Shi M, Wang F. Practical way for the synthesis of 4H-benzo[e][1,3]oxazine by anhydride-promoted [4+2] cyclization of in situ generated o-quinone methides with amides. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Zhang J, Jin H, Wang R, Zhao L. Synthesis of 2,4‐Diaryl‐1,3‐benzoxazines via FeCl
3
‐Catalyzed Annulation of
ortho
‐Hydroxyphenyl‐Substituted
para
‐Quinone Methides with Imidates. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900842] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jing‐Ru Zhang
- School of Chemistry and Materials ScienceJiangsu Normal University Xuzhou 221116, Jiangsu People's Republic of China
| | - Hai‐Shan Jin
- School of Chemistry and Materials ScienceJiangsu Normal University Xuzhou 221116, Jiangsu People's Republic of China
| | - Ru‐Bing Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical College Beijing 100050 People's Republic of China
| | - Li‐Ming Zhao
- School of Chemistry and Materials ScienceJiangsu Normal University Xuzhou 221116, Jiangsu People's Republic of China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical College Beijing 100050 People's Republic of China
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Zamora EB, Zavala G, López A, Cevada E, Montesinos R, Vázquez F, Flores C. Quantitative Structure-Activity Relationship (QSAR) analysis of functionalized triblock copolymers with applications as dehydrating agents of crude oil. J DISPER SCI TECHNOL 2019. [DOI: 10.1080/01932691.2019.1611439] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - Gerardo Zavala
- Instituto Mexicano del Petróleo, Ciudad de México, México
| | - Alfonso López
- Instituto Mexicano del Petróleo, Ciudad de México, México
| | - Enrique Cevada
- Escuela Superior de Ingeniería Química e Industrias Extractivas, Instituto Politécnico Nacional, Ciudad de México, México
| | | | - Flavio Vázquez
- Instituto Mexicano del Petróleo, Ciudad de México, México
| | - César Flores
- Instituto Mexicano del Petróleo, Ciudad de México, México
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