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Gryniukova A, Borysko P, Myziuk I, Alieksieieva D, Hodyna D, Semenyuta I, Kovalishyn V, Metelytsia L, Rogalsky S, Tcherniuk S. Anticancer activity features of imidazole-based ionic liquids and lysosomotropic detergents: in silico and in vitro studies. Mol Divers 2024:10.1007/s11030-023-10779-4. [PMID: 38246950 DOI: 10.1007/s11030-023-10779-4] [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: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 01/23/2024]
Abstract
Long-chain imidazole-based ionic liquids (compounds 2, 4, 9) and lysosomotropic detergents (compounds 7, 3, 8) with potent anticancer activity were synthesized. Their inhibitory activities against neuroblastoma and leukaemia cell lines were predicted by the new in silico QSAR models. The cytotoxic activities of the synthesized imidazole derivatives were investigated on the SK-N-DZ (human neuroblastoma) and K-562 (human chronic myeloid leukaemia) cell lines. Compounds 2 and 7 showed the highest in vitro cytotoxic effect on both cancer cell lines. The docking procedure of compounds 2 and 7 into the NAD+ coenzyme binding site of deacetylase Sirtuin-1 (SIRT-1) showed the formation of protein-ligand complexes with calculated binding energies of - 8.0 and - 8.1 kcal/mol, respectively. The interaction of SIRT1 with compounds 2, 7 and 9 and the interaction of Bromodomain-containing protein 4 (BRD4) with compounds 7 and 9 were also demonstrated by thermal shift assay. Compounds 2, 4, 7 and 9 inhibited SIRT1 deacetylase activity in the SIRT-Glo assay. Compounds 7 and 9 showed a moderate inhibitory activity against Aurora kinase A. In addition, compounds 3, 4, 8 and 9 inhibited the Janus kinase 2 activity. The results obtained showed that long-chain imidazole derivatives exhibited cytotoxic activities on K562 leukaemia and SK-N-DZ neuroblastoma cell lines. Furthermore, these compounds inhibited a panel of molecular targets involved in leukaemia and neuroblastoma tumorigenesis. All these results suggest that both long-chain imidazole-based ionic liquids and lysosomotropic detergents may be an effective alternative for the treatment of neuroblastoma and chronic myeloid leukemia and merit further investigation.
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Affiliation(s)
- Anastasiia Gryniukova
- Department of Medical and Biological Researches, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 1 Academician Kukhar Str, Kyiv, 02094, Ukraine
- Bienta/Enamine Ltd, 78 Winston Churchill Str, Kyiv, 02094, Ukraine
| | - Petro Borysko
- Bienta/Enamine Ltd, 78 Winston Churchill Str, Kyiv, 02094, Ukraine
| | - Iryna Myziuk
- Bienta/Enamine Ltd, 78 Winston Churchill Str, Kyiv, 02094, Ukraine
| | | | - Diana Hodyna
- Department of Medical and Biological Researches, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 1 Academician Kukhar Str, Kyiv, 02094, Ukraine
| | - Ivan Semenyuta
- Department of Medical and Biological Researches, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 1 Academician Kukhar Str, Kyiv, 02094, Ukraine
| | - Vasyl Kovalishyn
- Department of Medical and Biological Researches, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 1 Academician Kukhar Str, Kyiv, 02094, Ukraine
| | - Larysa Metelytsia
- Department of Medical and Biological Researches, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 1 Academician Kukhar Str, Kyiv, 02094, Ukraine
| | - Sergiy Rogalsky
- Laboratory of Modification of Polymers, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 50 Kharkivske shose, Kyiv, 02160, Ukraine.
| | - Sergey Tcherniuk
- IdeSip, 4 Rue Pierre Fontaine, 91058, Évry-Courcouronnes, France.
- Department of Biological Sciences, Youth Academy of Sciences, 2 Nemyrovych-Danchenko Str, Kyiv, 01011, Ukraine.
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Khan S, Madhi SA, Olwagen C. Structure-based identification of novel inhibitors targeting the enoyl-ACP reductase enzyme of Acinetobacter baumannii. Sci Rep 2023; 13:21331. [PMID: 38044353 PMCID: PMC10694131 DOI: 10.1038/s41598-023-48696-z] [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: 08/15/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023] Open
Abstract
Acinetobacter baumannii is a Gram-negative multidrug-resistant bacterial pathogen primarily associated with nosocomial infections resulting in increased morbidity and mortality in adults and infants, especially in sub-Saharan Africa where the clinical burden is high. New therapeutics are needed to treat multidrug-resistant Acinetobacter baumannii infections and reduce transmission. The study used computer-integrated drug discovery approaches including pharmacophore modelling, molecular docking, and molecular dynamics simulation to screen potential inhibitors against the enoyl-acyl carrier protein reductase-FabI protein of Acinetobacter baumannii. The top three potential inhibitors: 21272541 > 89795992 > 89792657 showed favourable binding free energies including coulombic energy, van der Waals energy, and polar and non-polar energies. Furthermore, all three complexes were extremely stable and compact with reduced fluctuations during the simulations period. Inhibitor 21272541 exhibited the highest binding affinity against the Acinetobacter baumannii FabI protein. This is similar to our recent report, which also identified 21272541 as the lead inhibitor against Klebsiella pneumoniae infections. Future clinical studies evaluating drug effectiveness should prioritise inhibitor 21272541 which could be effective in treating infections caused by Gram-negative organisms.
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Affiliation(s)
- Shama Khan
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Courtney Olwagen
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
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Identification of a Family of Glycoside Derivatives Biologically Active against Acinetobacter baumannii and Other MDR Bacteria Using a QSPR Model. Pharmaceuticals (Basel) 2023. [DOI: 10.3390/ph16020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
As the rate of discovery of new antibacterial compounds for multidrug-resistant bacteria is declining, there is an urge for the search for molecules that could revert this tendency. Acinetobacter baumannii has emerged as a highly virulent Gram-negative bacterium that has acquired multiple resistance mechanisms against antibiotics and is considered of critical priority. In this work, we developed a quantitative structure-property relationship (QSPR) model with 592 compounds for the identification of structural parameters related to their property as antibacterial agents against A. baumannii. QSPR mathematical validation (R2 = 70.27, RN = −0.008, a(R2) = 0.014, and δK = 0.021) and its prediction ability (Q2LMO = 67.89, Q2EXT = 67.75, a(Q2) = −0.068, δQ = 0.0, rm2¯ = 0.229, and Δrm2 = 0.522) were obtained with different statistical parameters; additional validation was done using three sets of external molecules (R2 = 72.89, 71.64 and 71.56). We used the QSPR model to perform a virtual screening on the BIOFACQUIM natural product database. From this screening, our model showed that molecules 32 to 35 and 54 to 68, isolated from different extracts of plants of the Ipomoea sp., are potential antibacterials against A. baumannii. Furthermore, biological assays showed that molecules 56 and 60 to 64 have a wide antibacterial activity against clinically isolated strains of A. baumannii, as well as other multidrug-resistant bacteria, including Staphylococcus aureus, Escherichia coli, Klebsiella pneumonia, and Pseudomonas aeruginosa. Finally, we propose 60 as a potential lead compound due to its broad-spectrum activity and its structural simplicity. Therefore, our QSPR model can be used as a tool for the investigation and search for new antibacterial compounds against A. baumannii.
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Makarov D, Fadeeva Y, Safonova E, Shmukler L. Predictive modeling of antibacterial activity of ionic liquids by machine learning methods. Comput Biol Chem 2022; 101:107775. [DOI: 10.1016/j.compbiolchem.2022.107775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/24/2022] [Accepted: 10/03/2022] [Indexed: 11/03/2022]
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Synthesis, Characterization, Biological Evaluation, and In Silico Studies of Imidazolium-, Pyridinium-, and Ammonium-Based Ionic Liquids Containing n-Butyl Side Chains. Molecules 2022; 27:molecules27196650. [PMID: 36235187 PMCID: PMC9572234 DOI: 10.3390/molecules27196650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Ionic liquids (ILs) have emerged as active pharmaceutical ingredients because of their excellent antibacterial and biological activities. Herein, we used the green-chemistry-synthesis procedure, also known as the metathesis method, to develop three series of ionic liquids using 1-methyl-3-butyl imidazolium, butyl pyridinium, and diethyldibutylammonium as cations, and bromide (Br−), methanesulfonate (CH3SO3−), bis(trifluoromethanesulfonyl)imide (NTf2−), dichloroacetate (CHCl2CO2−), tetrafluoroborate (BF4−), and hydrogen sulfate (HSO4−) as anions. Spectroscopic methods were used to validate the structures of the lab-synthesized ILs. We performed an agar well diffusion assay by using pathogenic bacteria that cause various infections (Escherichia coli; Enterobacter aerogenes; Klebsiella pneumoniae; Proteus vulgaris; Pseudomonas aeruginosa; Streptococcus pneumoniae; Streptococcus pyogenes) to scrutinize the in vitro antibacterial activity of the ILs. It was established that the nature and unique combination of the cations and anions were responsible for the antibacterial activity of the ILs. Among the tested ionic liquids, the imidazolium cation and NTf2− and HSO4− anions exhibited the highest antibacterial activity. The antibacterial potential was further investigated by in silico studies, and it was observed that bis(trifluoromethanesulfonyl)imide (NTf2−) containing imidazolium and pyridinium ionic liquids showed the maximum inhibition against the targeted bacterial strains and could be utilized in antibiotics. These antibacterial activities float the ILs as a promising alternative to the existing antibiotics and antiseptics.
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Theoretical and Experimental Studies of Phosphonium Ionic Liquids as Potential Antibacterials of MDR Acinetobacter baumannii. Antibiotics (Basel) 2022; 11:antibiotics11040491. [PMID: 35453241 PMCID: PMC9025513 DOI: 10.3390/antibiotics11040491] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/30/2022] [Accepted: 04/02/2022] [Indexed: 11/27/2022] Open
Abstract
A previously developed model to predict antibacterial activity of ionic liquids against a resistant A. baumannii strain was used to assess activity of phosphonium ionic liquids. Their antioxidant potential was additionally evaluated with newly developed models, which were based on public data. The accuracy of the models was rigorously evaluated using cross-validation as well as test set prediction. Six alkyl triphenylphosphonium and alkyl tributylphosphonium bromides with the C8, C10, and C12 alkyl chain length were synthesized and tested in vitro. Experimental studies confirmed their activity against A. baumannii as well as showed pronounced antioxidant properties. These results suggest that phosphonium ionic liquids could be promising lead structures against A. baumannii.
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Lian X, Xia Z, Li X, Karpov P, Jin H, Tetko IV, Xia J, Wu S. Anti-MRSA drug discovery by ligand-based virtual screening and biological evaluation. Bioorg Chem 2021; 114:105042. [PMID: 34120024 DOI: 10.1016/j.bioorg.2021.105042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 10/21/2022]
Abstract
S. aureus resistant to methicillin (MRSA) is one of the most-concerned multidrug resistant bacteria, due to its role in life-threatening infections. There is an urgent need to develop new antibiotics against MRSA. In this study, we firstly compiled a data set of 2,3-diaminoquinoxalines by chemical synthesis and antibacterial screening against S. aureus, and then performed cheminformatics modeling and virtual screening. The compound with the Specs ID of AG-205/33156020 was discovered as a new antibacterial agent, and was further identified as a Gyrase B (GyrB) inhibitor. In light of the common features, we hypothesized that the 6c as the representative of 2,3-diaminoquinoxalines also inhibited GyrB and eventually proved it. Via molecular docking and molecular dynamics simulations, we identified binding modes of AG-205/33156020 and 6c to the ATPase domain of GyrB. Importantly, these GyrB inhibitors inhibited the MRSA strains and showed selectivity to HepG2 and HUVEC. Taken together, this research work provides an effective ligand-based computational workflow for scaffold hopping in anti-MRSA drug discovery, and discovers two new GyrB inhibitors that are worthy of further development.
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Affiliation(s)
- Xu Lian
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhonghua Xia
- Institute of Structural Biology, Helmholtz Zentrum München-Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Xueyao Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Pavel Karpov
- Institute of Structural Biology, Helmholtz Zentrum München-Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; BIGCHEM GmbH, Valerystr. 49, 85716 Unterschleißheim, Germany
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Igor V Tetko
- Institute of Structural Biology, Helmholtz Zentrum München-Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; BIGCHEM GmbH, Valerystr. 49, 85716 Unterschleißheim, Germany
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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