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Karabacak Atay Ç, Dilek Ö, Tilki T, Dede B. A novel imidazole-based azo molecule: synthesis, characterization, quantum chemical calculations, molecular docking, molecular dynamics simulations and ADMET properties. J Mol Model 2023; 29:226. [PMID: 37405575 DOI: 10.1007/s00894-023-05625-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
CONTEXT Today, the treatment or prevention of cancer, which is one of the most important causes of death, has a very important place. On the other hand, the discovery of new antimicrobial agents is also important because of antibiotic resistance that can occur in humans. For these reasons, in this study, the synthesis, quantum chemical calculations, and in silico studies of a novel azo molecule with high bioactive potential were carried out. In the first step of the synthesis part, (3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)aniline compound, which is the raw material of the drug used in cancer treatments, was synthesized. In the second step, a novel product 2-hydroxy-5-((3-(4-methyl-1H-imidazol-1-yl)-5-trifluoromethyl)phenyl)diazenyl)benzaldehyde (HTB) was obtained as a result of the reaction of salicylaldehyde coupling to this compound. Then, as it was being spectroscopically described, its geometry was optimized. In order to perform quantum chemical calculations, the molecular structure, vibrational spectroscopic data, electronic transition absorption wavelengths, HOMO and LUMO analyses, molecular electrostatic potential (MEP) and potential energy surface (PES) of the molecule were all taken into consideration. Using molecular docking simulations, in silico interactions of the HTB molecule with some anticancer and antibacterial-related proteins were studied. In addition, the ADMET parameters of the HTB were also predicted. METHODS The structure of the synthesized compound was elucidated using 1H-NMR, 13C-NMR (APT), 19F-NMR, FT-IR and UV-vis spectroscopic methods. The optimized geometry, molecular electrostatic potential diagram and vibrational frequencies of the HTB molecule were calculated at the DFT/B3LYP/6-311G(d,p) level. The TD-DFT method was used to calculate HOMOs-LUMOs and electronic transitions, and the GIAO method was used to calculate chemical shift values. It was observed that the experimental spectral data were in good agreement with the theoretical ones. Molecular docking simulations of the HTB molecule using 4 different proteins were investigated. Two of these proteins were involved in simulating anticancer activity and the other two in simulating antibacterial activity. According to molecular docking studies, the binding energies of the complexes formed by the HTB compound with the 4 selected proteins were between -9.6 and -8.7 kcal/mol. HTB showed the best affinity with VEGFR2 protein (PDB ID: 2XIR) and the binding energy of this interaction was found to be -9.6 kcal/mol. The HTB-2XIR interaction was examined with molecular dynamics simulation for 25 ns and it was determined that this complex was stable during this time. In addition, the ADMET parameters of the HTB were also calculated, and from these values, it was determined that the compound has very low toxicity and high oral bioavailability.
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Affiliation(s)
- Çiğdem Karabacak Atay
- Department of Basic Education, Faculty of Education, Burdur Mehmet Akif Ersoy University, 15030, Burdur, Turkey.
| | - Ömer Dilek
- Central Research Laboratory Application and Research Center, Isparta University of Applied Sciences, 32200, Isparta, Turkey
| | - Tahir Tilki
- Department of Chemistry, Faculty of Science & Art, Süleyman Demirel University, 32260, Isparta, Turkey
| | - Bülent Dede
- Department of Chemistry, Faculty of Science & Art, Süleyman Demirel University, 32260, Isparta, Turkey
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Verma V, Singh A, Tyagi P, Kumar V, Prasad AK. Synthesis of 1,2,3‐Triazole‐Linked Hexopyranosylpyrimidine Nucleosides and Their Application as Hepatitis B Viral DNA, HBsAg and HBeAg Suppressants. ChemistrySelect 2023. [DOI: 10.1002/slct.202204982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Gökalp M, Tilki T, Karabacak Atay Ç. Newly Synthesized Aminothiazole Based Disazo Dyes and Their Theoretical Calculations. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2181828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Merve Gökalp
- Department of Chemistry, Süleyman Demirel University, Isparta, Turkey
| | - Tahir Tilki
- Department of Chemistry, Süleyman Demirel University, Isparta, Turkey
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Insight into potent TLR2 inhibitors for the treatment of disease caused by Mycoplasma pneumoniae based on machine learning approaches. Mol Divers 2023; 27:371-387. [PMID: 35488091 DOI: 10.1007/s11030-022-10433-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/01/2022] [Indexed: 02/08/2023]
Abstract
Mycoplasma pneumoniae (MP) is one of the most common pathogens that causes acute respiratory tract infections. Children experiencing MP infection often suffer severe complications, lung injury, and even death. Previous studies have demonstrated that Toll-like receptor 2 (TLR2) is a potential therapeutic target for treating the MP-induced inflammatory response. However, the screening of natural compounds has received more attention for the treatment of bacterial infections to reduce the likelihood of bacterial resistance. Herein, we screened compounds by combining molecular docking and machine learning approaches to find potential lead compounds for treating MP infection. First, all compounds were docked with the TLR2 receptor protein to screen for potential candidates. To predict drug bioactivity, a machine learning model (random forest) was trained for TLR2 inhibitors to obtain the predictive model. The model achieved significant squared correlation coefficient (R2) values for the training set (0.85) and validation set (0.84) of compounds. The developed machine learning model was then used to predict the pIC50 values of the top 50 candidates from the Traditional Chinese compounds and Discovery Diversity sets of compounds. As a result, these compounds are capable of inhibiting the inflammatory response induced by MP. However, prior to bringing these compounds to market, it is necessary to verify these results with additional biological testing, including preclinical and clinical studies. Moreover, the present study provides a theoretical basis for the use of natural compounds as potential candidates to treat pneumonia caused by MP.
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Yi SZ, Li BN, Fu PY, Pan M, Su CY. Interplay of Dual-Proton Transfer Relay to Achieve Full-Color Panel Luminescence in Excited-State Intramolecular Proton Transfer (ESIPT) Fluorophores. ACS APPLIED MATERIALS & INTERFACES 2023; 15:3172-3181. [PMID: 36621007 DOI: 10.1021/acsami.2c20129] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
A new design was applied for the facile synthesis of pure organic photoluminescent molecules with dual excited-state intramolecular proton transfer (ESIPT) sites. In this novel class of emitters, full-color panel emission from blue, green, and yellow to red, including white light, can be achieved in different solvents as modulated by the enol-keto(1st)-keto(2nd) tautomer emissions. A comprehensive transient photophysical study verifies that keto(1st) and keto(2nd) have a precursor (<0.8 ps)-successor (∼20 ps)-relayed absorbance relationship, and then a fast equilibrium between the two is established, resulting in dual emissions in the nanosecond scale (∼1900 ps). Through the research on copper ions' selective PL response, the dual-ESIPT mechanism was further verified; in addition, the study of solid-state PL changes upon the stimulus of organic vapor manifests the potential application sensitivity of the molecules as dual-ESIPT sensors. Theoretical results including reaction potential energy surface analyses manifest the fact that dual-proton transfer goes along a sequential route with a smaller energy barrier, firmly supporting the experimental results. An intrinsic system that undergoes intramolecular double proton relayed transfer is thus established for the achievement of much broadened optical responses and full-color display, providing reference for the design and application of advanced dual-ESIPT optical materials.
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Affiliation(s)
- Shao-Zhe Yi
- Lehn Institute of Functional Materials, MOE Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, 132 East Waihuan Road, Panyu District, Guangzhou 510006, P. R. China
| | - Bao-Ning Li
- School of Chemistry and Chemical Engineering, Yulin University, Yulin 719000, P. R. China
| | - Peng-Yan Fu
- Lehn Institute of Functional Materials, MOE Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, 132 East Waihuan Road, Panyu District, Guangzhou 510006, P. R. China
| | - Mei Pan
- Lehn Institute of Functional Materials, MOE Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, 132 East Waihuan Road, Panyu District, Guangzhou 510006, P. R. China
| | - Cheng-Yong Su
- Lehn Institute of Functional Materials, MOE Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, 132 East Waihuan Road, Panyu District, Guangzhou 510006, P. R. China
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Zhu Z, Rahman Z, Aamir M, Shah SZA, Hamid S, Bilawal A, Li S, Ishfaq M. Insight into TLR4 receptor inhibitory activity via QSAR for the treatment of Mycoplasma pneumonia disease. RSC Adv 2023; 13:2057-2069. [PMID: 36712602 PMCID: PMC9833105 DOI: 10.1039/d2ra06178c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/14/2022] [Indexed: 01/13/2023] Open
Abstract
Mycoplasma pneumoniae (MP) is one of the most common pathogenic organisms causing upper and lower respiratory tract infections, lung injury, and even death in young children. Toll-like receptors (TLRs) play an important role in innate immunity by allowing the host to recognize pathogens invading the body. Previous studies demonstrated that TLR4 is a potential therapeutic target for the treatment of MP pneumonia. Therefore, the present study aimed to screen biologically active ingredients that target the TLR4 receptor pathway. We first used molecular docking to screen out the active compounds inhibiting the TLR4 pathway, and then used regression and classification machine learning algorithms to establish a quantitative structure-activity relationship (QSAR) model to predict the biological activity of the screened compounds. A total of 78 molecules were used in QSAR modelling, which were retrieved from the ChEMBL database. The QSAR models had acceptable correlation coefficients of R 2 on the training and testing dataset in the range of 0.96 to 0.91 and 0.93 to 0.76, respectively. The multiclass classification models showed accuracy on training and testing data within ranges of 1.0 to 0.70, 0.96 to 0.63, and log loss ranges from 0.27 to 8.63, respectively. In addition, molecular descriptors and fingerprints have been studied as structural elements involved in increased and decreased inhibitory activities. These results provide a quantitative analysis of QSAR and classification models applicable for high-throughput screening, as well as insights into the mechanisms of inhibition of TLR4 antagonists.
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Affiliation(s)
- Zemin Zhu
- College of Computer Science, Huanggang Normal UniversityHuanggang 438000China+86 15972855212
| | - Ziaur Rahman
- College of Computer Science, Huanggang Normal UniversityHuanggang 438000China+86 15972855212
| | - Muhammad Aamir
- College of Computer Science, Huanggang Normal UniversityHuanggang 438000China+86 15972855212
| | - Syed Zahid Ali Shah
- Department of Pathology, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur-PakistanPakistan
| | - Sattar Hamid
- The University of Agriculture PeshawarKhyber Pakhtunkhwa25130Pakistan
| | - Akhunzada Bilawal
- College of Food Science, Northeast Agricultural UniversityHarbinChina
| | - Sihong Li
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F UniversityHangzhou 311300China
| | - Muhammad Ishfaq
- College of Computer Science, Huanggang Normal UniversityHuanggang 438000China+86 15972855212
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Sezgin B, Tilki T, Karabacak Atay Ç, Dede B. Comparative in vitro and DFT antioxidant studies of phenolic group substituted pyridine-based azo derivatives. J Biomol Struct Dyn 2022; 40:4921-4932. [DOI: 10.1080/07391102.2020.1863264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Barış Sezgin
- Faculty of Science & Art, Department of Chemistry, Süleyman Demirel University, Isparta, Turkey
| | - Tahir Tilki
- Faculty of Science & Art, Department of Chemistry, Süleyman Demirel University, Isparta, Turkey
| | - Çiğdem Karabacak Atay
- Faculty of Education, Department of Basic Education, Burdur Mehmet Akif Ersoy University, Burdur, Turkey
| | - Bülent Dede
- Faculty of Science & Art, Department of Chemistry, Süleyman Demirel University, Isparta, Turkey
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Theoretical Investigation on the ESIPT Process and Detection Mechanism for Dual-Proton Type Fluorescent Probe. Int J Mol Sci 2022; 23:ijms23042132. [PMID: 35216247 PMCID: PMC8876953 DOI: 10.3390/ijms23042132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 02/06/2023] Open
Abstract
Recently, a new fluorescent probe AE-Phoswas reported to detect the activity of alkaline phosphatases (ALP) in different living cell lines. Here, we present an in-depth computational analysis of the mechanism and source of the fluorescence of the AE-Phos probe. There is an intermediate product (AE-OH-Phos) in the experiment as well as a different configuration of products that may emit fluorescence. It is essential to investigate the origin of fluorescence and the detection mechanism of the probe, which could help us eliminate the interference of other substances (including an intermediate product and possible isomers) on fluorescence during the experiment. According to the change of geometric parameters and Infrared spectra, we deduce that the dual intramolecular hydrogen bonds of salicylaldehyde azine (SA) were enhanced at the excited state, while AE-OH-Phos was attenuated. Considering the complex ESIPT behavior of the dual proton-type probe, the potential energy surfaces were further discussed. It can be concluded that the single proton transfer structure of SA (SA-SPT) is the most stable form. Both the concerted double proton transfer process and stepwise single proton transfer process of SA were forbidden. The fluorescence for SA was 438 nm, while that of SA-SPT was 521 nm, which agrees with the experimentally measured fluorescence wavelength (536 nm). The conclusion that single proton transfer occurs in SA is once again verified. In addition, the distribution of electron-hole and relative index was analyzed to investigate the intrinsic mechanism for the fluorescence quenching of the probe and the intermediate product. The identification of the origin of fluorescence sheds light on the design and use of dual-proton type fluorescent probes in the future.
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Sun H, Deng L, Hu W, Liao T, Liao W, Chai H, Zhao C. Synthesis, crystal structure, vibrational properties and DFT studies of 4-(furan-2-ylmethyl)-1-(thiomorpholinomethyl)-[1,2,4]triazolo[4,3-a]quinazon-5(4H)-one. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Wu Q, Zheng Z, Ye W, Guo Q, Liao T, Yang D, Zhao C, Liao W, Chai H, Zhou Z. Synthesis, crystal and molecular structure, vibrational spectroscopic, DFT and molecular docking of 4-(2-chlorobenzyl)-1-(4‑hydroxy-3- ((4-hydroxypiperidin-1-yl) methyl-5-methoxyphenyl)-[1,2,4] triazolo [4,3-a] quinazolin-5(4H)-one. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Sezgin B, Dede B, Tilki T. Structural, theoretical and enzyme-like activities of novel Cu(II) and Mn(II) complexes with coumarin based bidentate ligand. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Synthesis, crystal structure, DFT, molecular docking and antitumor activity of 4-(2-chlorobenzyl)-1-(5-fluoro-2-hydroxy-3-((4-methylpiperidin-1-yl)methyl)phenyl)-[1,2,4]triazolo[4,3-a]quinazolin-5(4H)-one. RESEARCH ON CHEMICAL INTERMEDIATES 2021. [DOI: 10.1007/s11164-021-04491-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Raajaraman BR, Sheela NR, Muthu S. Quantum Chemical, Vibrational Spectroscopic and Molecular Docking Studies of 1-(Diphenylmethyl)Piperazine. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1852273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- B R. Raajaraman
- Department of Physics, Sri Venkateswara College of Engineering, Sriperumbudur, Tamilnadu, India
| | - N. R. Sheela
- Department of Physics, Sri Venkateswara College of Engineering, Sriperumbudur, Tamilnadu, India
| | - S. Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, Tamilnadu, India
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Kaur H, Singh J, Narasimhan B. Indole hybridized diazenyl derivatives: synthesis, antimicrobial activity, cytotoxicity evaluation and docking studies. BMC Chem 2019; 13:65. [PMID: 31384812 PMCID: PMC6661771 DOI: 10.1186/s13065-019-0580-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/02/2019] [Indexed: 02/07/2023] Open
Abstract
Background In search of effective antimicrobial and cytotoxic agents, a series of indole hybridized diazenyl derivatives (DS-1 to DS-21) was efficiently prepared by condensation of diazotized p-aminoacetophenone with indole or nitroindole followed by reaction with different aromatic/heteroaromatic amines of biological significance. The synthesized derivatives were characterized by various spectroscopic techniques. Methodology The antimicrobial evaluation of DS-1 to DS-23 was done by tube dilution method against various pathogenic bacterial and fungal strains. The active antimicrobial derivatives were further evaluated for cytotoxicity against human lung carcinoma cell line (HCT-116), breast cancer cell line (MDAMB231), leukemic cancer cell line (K562), and normal cell line (HEK293) by MTT assay using doxorubicin as the standard drug. The test derivatives were additionally docked for the B-subunit of enzyme DNA gyrase from E. coli at the ATPase binding site to study the molecular interactions using Schrodinger maestro v11.5 software. Results and discussion Most of the synthesized derivatives have shown high activity against Gram-negative bacteria particularly E. coli and K. pneumonia with MIC ranging from 1.95 to 7.81 μg/ml. The derivatives have demonstrated very less activity against tested Gram positive bacterial and fungal strains. The derivatives DS-14 and DS-20 have been found to active against breast cancer cell line and human colon carcinoma cell line having IC50 in the range of 19–65 µg/ml. All the derivatives were found to less potent against leukemic cancer cell line. The synthesized derivatives have revealed their safety by exhibiting very less cytotoxicity against the normal cell line (HEK-293) with IC50 > 100 µg/ml. Most of the active derivatives have shown good docking scores in comparison to the standard drugs against DNA gyrase from E. coli. Further ADME predictions by Qikprop module of the Schrodinger confirmed these molecules have drug like properties. Conclusion The derivatives DS-14 and DS-20 have shown potential against Gram-negative bacteria and breast cancer cell line and can be used as a lead for rational drug designing of the antimicrobial and cytotoxic agents. .
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Affiliation(s)
- Harmeet Kaur
- 1Faculty of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, 124001 India
| | - Jasbir Singh
- 2College of Pharmacy, Postgraduate Institute of Medical Sciences, Rohtak, 124001 India
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