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Liang M, Liu X, Chen Q, Zeng B, Wang L. NMGMDA: a computational model for predicting potential microbe-drug associations based on minimize matrix nuclear norm and graph attention network. Sci Rep 2024; 14:650. [PMID: 38182635 PMCID: PMC10770326 DOI: 10.1038/s41598-023-50793-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/26/2023] [Indexed: 01/07/2024] Open
Abstract
The prediction of potential microbe-drug associations is of great value for drug research and development, especially, methods, based on deep learning, have been achieved significant improvement in bio-medicine. In this manuscript, we proposed a novel computational model named NMGMDA based on the nuclear norm minimization and graph attention network to infer latent microbe-drug associations. Firstly, we created a heterogeneous microbe-drug network in NMGMDA by fusing the drug and microbe similarities with the established drug-microbe associations. After this, by using GAT and NNM to calculate the predict scores. Lastly, we created a fivefold cross validation framework to assess the new model NMGMDA's progressiveness. According to the simulation results, NMGMDA outperforms some of the most advanced methods, with a reliable AUC of 0.9946 on both MDAD and aBioflm databases. Furthermore, case studies on Ciprofloxacin, Moxifoxacin, HIV-1 and Mycobacterium tuberculosis were carried out in order to assess the effectiveness of NMGMDA even more. The experimental results demonstrated that, following the removal of known correlations from the database, 16 and 14 medications as well as 19 and 17 microbes in the top 20 predictions were validated by pertinent literature. This demonstrates the potential of our new model, NMGMDA, to reach acceptable prediction performance.
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Affiliation(s)
- Mingmin Liang
- School of Information Engineering, Hunan Vocational College of Electronic and Technology, Changsha, 410000, China
| | - Xianzhi Liu
- School of Information Engineering, Hunan Vocational College of Electronic and Technology, Changsha, 410000, China
| | - Qijia Chen
- School of Information Engineering, Hunan Vocational College of Electronic and Technology, Changsha, 410000, China.
| | - Bin Zeng
- School of Information Engineering, Hunan Vocational College of Electronic and Technology, Changsha, 410000, China.
| | - Lei Wang
- School of Information Engineering, Hunan Vocational College of Electronic and Technology, Changsha, 410000, China.
- Big Data Innovation and Entrepreneurship Education Center of Hunan Province, Changsha University, Changsha, 410022, China.
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Paprocka R, Kołodziej P, Wiese-Szadkowska M, Helmin-Basa A, Bogucka-Kocka A. Evaluation of Anthelmintic and Anti-Inflammatory Activity of 1,2,4-Triazole Derivatives. Molecules 2022; 27:molecules27144488. [PMID: 35889357 PMCID: PMC9323247 DOI: 10.3390/molecules27144488] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 01/25/2023] Open
Abstract
Parasitic diseases, caused by intestinal helminths, remain a very serious problem in both human and veterinary medicine. While searching for new nematicides we examined a series of 1,2,4-triazole derivatives 9–22, obtained during reactions of N3-substituted amidrazones with itaconic anhydride. Two groups of compounds, 9–16 and 17–22, differed in the position of the double bond on the methacrylic acid moiety. The toxicity of derivatives 9–22 and the anti-inflammatory activity of 12 and 19–22 were studied on peripheral blood mononuclear cells (PBMC). Antiproliferative activity of compounds 12 and 19–22 was tested cytometrically in PBMC cultures stimulated by phytohemagglutinin. The influence of derivatives 12 and 19–22 on the TNF-α, IL-6, IL-10 and IFN-γ production was determined by ELISA in lipopolysaccharide-stimulated PBMC cultures. Anthelmintic activity of compounds 10–22 was studied in the Rhabditis sp. nematodes model. Most compounds (11–22) proved to be non-toxic to human PBMC. Derivatives 19–22 showed anti-inflammatory activity by inhibiting the proliferation of lymphocytes. Moreover, compounds 12 and 19–22 significantly reduced the production of TNF-α and derivatives 19–21 decreased the level of INF-γ. The strongest anti-inflammatory activity was observed for compound 21. Compounds 12 and 14 demonstrated anthelmintic activity higher than albendazole and may become promising candidates for anthelmintic drugs.
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Affiliation(s)
- Renata Paprocka
- Department of Organic Chemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza Str. 2, 85-089 Bydgoszcz, Poland
- Correspondence: (R.P.); (P.K.)
| | - Przemysław Kołodziej
- Chair and Department of Biology and Genetics, Faculty of Pharmacy, Medical University in Lublin, Chodźki Str. 4A, 20-093 Lublin, Poland;
- Correspondence: (R.P.); (P.K.)
| | - Małgorzata Wiese-Szadkowska
- Department of Immunology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, M. Curie-Sklodowska Str. 9, 85-094 Bydgoszcz, Poland; (M.W.-S.); (A.H.-B.)
| | - Anna Helmin-Basa
- Department of Immunology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, M. Curie-Sklodowska Str. 9, 85-094 Bydgoszcz, Poland; (M.W.-S.); (A.H.-B.)
| | - Anna Bogucka-Kocka
- Chair and Department of Biology and Genetics, Faculty of Pharmacy, Medical University in Lublin, Chodźki Str. 4A, 20-093 Lublin, Poland;
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Strzelecka M, Świątek P. 1,2,4-Triazoles as Important Antibacterial Agents. Pharmaceuticals (Basel) 2021; 14:ph14030224. [PMID: 33799936 PMCID: PMC7999634 DOI: 10.3390/ph14030224] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022] Open
Abstract
The global spread of drug resistance in bacteria requires new potent and safe antimicrobial agents. Compounds containing the 1,2,4-triazole ring in their structure are characterised by multidirectional biological activity. A large volume of research on triazole and their derivatives has been carried out, proving significant antibacterial activity of this heterocyclic core. This review is useful for further investigations on this scaffold to harness its optimum antibacterial potential. Moreover, rational design and development of the novel antibacterial agents incorporating 1,2,4-triazole can help in dealing with the escalating problems of microbial resistance.
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Balázs VL, Horváth B, Kerekes E, Ács K, Kocsis B, Varga A, Böszörményi A, Nagy DU, Krisch J, Széchenyi A, Horváth G. Anti- Haemophilus Activity of Selected Essential Oils Detected by TLC-Direct Bioautography and Biofilm Inhibition. Molecules 2019; 24:molecules24183301. [PMID: 31514307 PMCID: PMC6767207 DOI: 10.3390/molecules24183301] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 01/31/2023] Open
Abstract
Essential oils (EOs) are becoming increasingly popular in medical applications because of their antimicrobial effect. Direct bioautography (DB) combined with thin layer chromatography (TLC) is a screening method for the detection of antimicrobial compounds in plant extracts, for example, in EOs. Due to their lipophilic character, the common microbiological assays (etc. disk diffusion) could not provide reliable results. The aim of this study was the evaluation of antibacterial and anti-biofilm properties of the EO of cinnamon bark, clove, peppermint, thyme, and their main components against Haemophilus influenzae and H. parainfluenzae. Oil in water (O/W) type Pickering nano-emulsions stabilized with silica nanoparticles from each oil were prepared to increase their water-solubility. Samples with Tween80 surfactant and absolute ethanol were also used. Results showed that H. influenzae was more sensitive to the EOs than H. parainfluenzae (except for cinnamon bark oil). In thin layer chromatography-direct bioautography (TLC-DB) the ethanolic solutions of thyme oil presented the best activity against H. influenzae, while cinnamon oil was the most active against H. parainfluenzae. Pickering nano-emulsion of cinnamon oil inhibited the biofilm formation of H. parainfluenzae (76.35%) more efficiently than samples with Tween80 surfactant or absolute ethanol. In conclusion, Pickering nano-emulsion of EOs could inhibit the biofilm production effectively.
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Affiliation(s)
- Viktória Lilla Balázs
- Department of Pharmacognosy, Faculty of Pharmacy, University of Pécs, H-7624 Pécs, Hungary; (V.L.B.)
| | - Barbara Horváth
- Institute of Pharmaceutical Technology and Biopharmacy, Faculty of Pharmacy, University of Pécs, H-7624 Pécs, Hungary; (B.H.); (A.S.)
| | - Erika Kerekes
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary;
| | - Kamilla Ács
- Department of Pharmacognosy, Faculty of Pharmacy, University of Pécs, H-7624 Pécs, Hungary; (V.L.B.)
| | - Béla Kocsis
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, H-7624 Pécs, Hungary; (B.K.); (A.V.)
| | - Adorján Varga
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, H-7624 Pécs, Hungary; (B.K.); (A.V.)
| | - Andrea Böszörményi
- Institute of Pharmacognosy, Faculty of Pharmacy, Semmelweis University, H-1085 Budapest, Hungary;
| | - Dávid U. Nagy
- Department of Genetics and Molecular Biology, Institute of Biology, Faculty of Sciences, University of Pécs, H-7624 Pécs, Hungary;
| | - Judit Krisch
- Department of Food Engineering, Faculty of Engineering, University of Szeged, H-6724 Szeged, Hungary;
| | - Aleksandar Széchenyi
- Institute of Pharmaceutical Technology and Biopharmacy, Faculty of Pharmacy, University of Pécs, H-7624 Pécs, Hungary; (B.H.); (A.S.)
| | - Györgyi Horváth
- Department of Pharmacognosy, Faculty of Pharmacy, University of Pécs, H-7624 Pécs, Hungary; (V.L.B.)
- Correspondence: ; Tel.: +36-72-503-625 (ext. 28823)
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1,2,4-Triazole-quinoline/quinolone hybrids as potential anti-bacterial agents. Eur J Med Chem 2019; 174:1-8. [DOI: 10.1016/j.ejmech.2019.04.033] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/05/2019] [Accepted: 04/13/2019] [Indexed: 11/19/2022]
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Gao F, Wang T, Xiao J, Huang G. Antibacterial activity study of 1,2,4-triazole derivatives. Eur J Med Chem 2019; 173:274-281. [PMID: 31009913 DOI: 10.1016/j.ejmech.2019.04.043] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/14/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022]
Abstract
Antibiotics are commonly used to fight against bacterial infections, but bacteria have already been resistant to almost all antibiotics due to abuse of antibiotics. 1,2,4-Triazole derived compounds possess chemotherapeutic effects including potential antibacterial activities against drug-sensitive as well as drug-resistant pathogens. Hybridization displays a high potential to develop novel drugs with the capacity to overcome drug resistance, reduce toxicity and improve pharmacokinetic profiles. More effective antibacterial candidates might be obtained by the hybridization of 1,2,4-triazole with other antibacterial pharmacophores. This review summarizes the recent advances of 1,2,4-triazole derivatives as potential antibacterial compounds, and the structure-activity relationship is also discussed.
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Affiliation(s)
- Feng Gao
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China; Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, PR China; Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, PR China.
| | - Tengfei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
| | - Jiaqi Xiao
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China; Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, PR China.
| | - Gang Huang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, PR China.
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Influence of Thiazolidine-2,4-Dione Derivatives with Azolidine or Thiosemicarbazone Moieties on Haemophilus spp. Planktonic or Biofilm-Forming Cells. Molecules 2019; 24:molecules24061051. [PMID: 30884874 PMCID: PMC6471098 DOI: 10.3390/molecules24061051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/07/2019] [Accepted: 03/14/2019] [Indexed: 01/22/2023] Open
Abstract
Biofilm, naturally formed by microorganisms as integrated surface-bound communities, is one of the reasons for the development of antimicrobial resistance. Haemophilus spp. are common and representative opportunistic Gram-negative rods forming from the upper respiratory tract microbiota. The aim of this paper was to evaluate the influence of thiazolidine-2,4-dionebased azolidine and chlorophenylthiosemicarbazone hybrids against both planktonic and biofilm-forming Haemophilus spp. cells. The in vitro activity against planktonic and biofilm-forming cells of the tested compounds were evaluated by using the broth microdilution method. These activities were detected against reference and clinical strains of Haemophilus spp. on the basis of MICs (minimal inhibitory concentrations) and MBICs (minimal biofilm inhibitory concentrations). In addition, anti-adhesive properties of these compounds were examined. The target compounds showed potential activity against planktonic cells with MIC = 62.5–500 mg/L and biofilm-forming cells with MBIC = 62.5–1000 mg/L. The observed anti-adhesive properties of the tested compounds were reversible during long-term incubation in a lower concentration of compounds.
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