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Altamimi M, Syed SA, Tuzun B, Alhazani MR, Alnemer O, Bari A. Synthesis biological evaluation and molecular docking of isatin hybrids as anti-cancer and anti-microbial agents. J Enzyme Inhib Med Chem 2024; 39:2288548. [PMID: 38073431 DOI: 10.1080/14756366.2023.2288548] [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: 09/28/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Isatin, known as 1H-indole-2,3-dione, was originally recognised as a synthetic molecule until its discovery in the fruits of the cannonball tree, Couroupita guianensis. It is naturally occurring in plants of the genus Isatis and serves as a metabolic derivative of adrenaline in humans. Isatin possesses significant pharmacological importance, and its synthetic versatility has prompted extensive interest in its derivative compounds due to their diverse biological and pharmacological properties. These derivatives represent a valuable class of heterocyclic compounds with potential applications as precursors for synthesizing numerous valuable drugs. In the pursuit of advancing our research on isatin hybrids, we investigate the utilisation of readily available hydrazonoindolin-2-one and isatin as starting materials for the synthesis of a wide range of analogues. Characterisation of the synthesized compounds was carried out through various analytical techniques. Furthermore, the obtained compounds were subjected to extensive testing to evaluate their anticancer and antimicrobial activities. Specifically, their efficacy against key proteins, namely Staphylococcus aureus protein (PDB ID: 1JIJ), Escherichia coli protein (PDB ID: 1T9U), Pseudomonas aeruginosa protein (PDB ID: 2UV0), and Acinetobacter baumannii protein (PDB ID: 4HKG), was examined through molecular docking calculations. Several molecules, such as 3, 4, 6, 16, and 19, displayed remarkable activity against the renal cancer cell line UO-31. Additionally, the results of antimicrobial activity testing revealed that compound 16 exhibited significant cytotoxicity against Candida albicans and Cryptococcus neoformans. Subsequently, ADME/T calculations were performed to gain insights into the potential effects and reactions of these molecules within human metabolism. This comprehensive study provides valuable insights into the potential pharmacological applications of isatin derivatives and underscores their significance in drug development.
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Affiliation(s)
- Mohammad Altamimi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Saeed Ali Syed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Burak Tuzun
- Plant and Animal Production Department, Technical Sciences Vocational School of Sivas, Sivas Cumhuriyet University, Sivas, Turkey
| | | | - Osamah Alnemer
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Seyfi S, Salarinejad S, Moghimi S, Toolabi M, Sadeghian N, Tüzün B, Firoozpour L, Ketabforoosh SHME, Taslimi P, Foroumadi A. Synthesis, biological activities, and molecular docking studies of triazolo[4,3-b]triazine derivatives as a novel class of α-glucosidase and α-amylase inhibitors. Arch Pharm (Weinheim) 2024; 357:e2300628. [PMID: 38501879 DOI: 10.1002/ardp.202300628] [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: 10/29/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/20/2024]
Abstract
In diabetes mellitus, amylase and glucosidase enzymes are the primary triggers. The main function of these enzymes is to break macromolecules into simple sugar units, which directly affect blood sugar levels by increasing blood permeability. To overcome this metabolic effect, there is a need for a potent and effective inhibitor capable of suppressing the enzymatic conversion of sugar macromolecules into their smaller units. Herein, we reported the discovery of a series of substituted triazolo[4,3-b][1,2,4]triazine derivatives as α-glucosidase and α-amylase inhibitors. All target compounds demonstrated significant inhibitory activities against α-glucosidase and α-amylase enzymes compared with acarbose as the positive control. The most potent compound 10k, 2-[(6-phenyl-[1,2,4]triazolo[4,3-b][1,2,4]triazin-3-yl)thio]-N-[4-(trifluoromethyl)phenyl]acetamide, demonstrated IC50 values of 31.87 and 24.64 nM against α-glucosidase and α-amylase enzymes, respectively. To study their mechanism of action, kinetic studies were also done, which determined the mode of inhibition of both enzymes. Molecular docking was used to confirm the binding interactions of the most active compounds.
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Affiliation(s)
- Soheila Seyfi
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Salarinejad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Setareh Moghimi
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsa Toolabi
- Department of Medicinal Chemistry, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Nastaran Sadeghian
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Turkey
| | - Burak Tüzün
- Plant and Animal Production Department, Technical Sciences Vocational School of Sivas, Sivas Cumhuriyet University, Sivas, Turkey
| | - Loghman Firoozpour
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Shima H M E Ketabforoosh
- Department of Medicinal Chemistry, School of Pharmacy, Alborz University of Medical Science, Karaj, Iran
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Turkey
| | - Alireza Foroumadi
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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Poustforoosh A, Faramarz S, Negahdaripour M, Tüzün B, Hashemipour H. Investigation on the mechanisms by which the herbal remedies induce anti-prostate cancer activity: uncovering the most practical natural compound. J Biomol Struct Dyn 2024; 42:3349-3362. [PMID: 37194430 DOI: 10.1080/07391102.2023.2213344] [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: 12/21/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023]
Abstract
Prostate cancer (PCa) is one of the most reported cancers among men worldwide. Targeting the essential proteins associated with PCa could be a promising method for cancer treatment. Traditional and herbal remedies (HRs) are the most practical approaches for PCa treatment. Here, the proteins and enzymes associated with PCa were determined based on the information obtained from the DisGeNET database. The proteins with a gene-disease association (GDA) score greater than 0.7 and the genes that have a disease specificity index (DSI) = 1 were selected as the target proteins. 28 HRs with anti-PCa activity as a traditional treatment for PCa were chosen as potential bioactive compounds. More than 500 compound-protein complexes were screened to find the top-ranked bioactives. The results were further evaluated using the molecular dynamics (MD) simulation and binding free energy calculations. The outcomes revealed that procyanidin B2 3,3'-di-O-gallate (B2G2), the most active ingredient of grape seed extract (GSE), can act as an agonist for PTEN. PTEN has a key role in suppressing PCa cells by applying phosphatase activity and inhibiting cell proliferation. B2G2 exhibited a considerable binding affinity to PTEN (11.643 kcal/mol). The MD results indicated that B2G2 could stabilize the key residues of the phosphatase domain of PTEN and increase its activity. Based on the obtained results, the active ingredient of GSE, B2G2, could play an agonist role and effectively increase the phosphatase activity of PTEN. The grape seed extract is a useful nutrition that can be used in men's diets to inhibit PCa in their bodies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alireza Poustforoosh
- Department of Chemical Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sanaz Faramarz
- Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Burak Tüzün
- Plant and Animal Production Department, Technical Sciences Vocational School of Sivas, Sivas Cumhuriyet University, Sivas, Turkey
| | - Hassan Hashemipour
- Chemical Engineering Department, Faculty of Engineering, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
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Poustforoosh A, Faramarz S, Nematollahi MH, Mahmoodi M, Azadpour M. Structure-Based Drug Design for Targeting IRE1: An in Silico Approach for Treatment of Cancer. Drug Res (Stuttg) 2024; 74:81-88. [PMID: 38134918 DOI: 10.1055/a-2211-2218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
BACKGROUND Endoplasmic Reticulum (ER) stress and Unfolded Protein Response (UPR) play a key role in cancer progression. The aggregation of incorrectly folded proteins in the ER generates ER stress, which in turn activates the UPR as an adaptive mechanism to fix ER proteostasis. Inositol-requiring enzyme 1 (IRE1) is the most evolutionary conserved ER stress sensor, which plays a pro-tumoral role in various cancers. Targeting its' active sites is one of the most practical approaches for the treatment of cancers. OBJECTIVE In this study, we aimed to use the structure of 4μ8C as a template to produce newly designed compounds as IRE1 inhibitors. METHODS Various functional groups were added to the 4μ8C, and their binding affinity to the target sites was assessed by conducting a covalent molecular docking study. The potential of the designed compound for further in vitro and in vivo studies was evaluated using ADMET analysis. RESULTS Based on the obtained results, the addition of hydroxyl groups to 4μ8C enhanced the binding affinity of the designed compound to the target efficiently. Compound 17, which was constructed by the addition of one hydroxyl group to the structure of 4μ8C, can construct a strong covalent bond with Lys907. The outcomes of ADMET analysis indicated that compound 17 could be considered a drug-like molecule. CONCLUSION Our results revealed that designed compound 17 could inhibit IRE1 activity. Therefore, this designed compound is a remarkable inhibitor of IRE1 and introduces a promising therapeutic strategy for cancer treatment.
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Affiliation(s)
- Alireza Poustforoosh
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sanaz Faramarz
- Applied Cellular and Molecular Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hadi Nematollahi
- Applied Cellular and Molecular Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Mahmoodi
- Applied Cellular and Molecular Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Mahdiyeh Azadpour
- Department of Chemical Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
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Firouzi M, Haghighijoo Z, Eskandari M, Mohabbati M, Miri R, Jamei MH, Poustforoosh A, Nazari S, Firuzi O, Khoshneviszadeh M, Edraki N. Synthesis and cytotoxic activity evaluation of novel imidazopyridine carbohydrazide derivatives. BMC Chem 2024; 18:6. [PMID: 38184605 PMCID: PMC10770970 DOI: 10.1186/s13065-023-01073-3] [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: 07/08/2022] [Accepted: 10/30/2023] [Indexed: 01/08/2024] Open
Abstract
Two series of novel imidazo[1,2-a]pyridine-2-carbohydrazide derivatives have been designed, synthesized, and evaluated for cytotoxic activity. Target compounds were designed in two series: aryl hydrazone derivatives that were devoid of triazole moiety (7a-e) and aryl triazole bearing group (11a-e). In vitro cytotoxicity screening was carried out using MTT assay against three human cancer cells including breast cancer (MCF-7), colon cancer (HT-29), and leukemia (K562) cell lines as well as a non-cancer cell line (Vero). Compound 7d bearing 4-bromophenyl pendant from aryl hydrazone series exhibited the highest cytotoxic potential with IC50 values of 22.6 µM and 13.4 µM against MCF-7 and HT-29 cells, respectively, while it was not toxic towards non-cancer cells up to the concentration of 100 µM. Cell cycle analysis revealed that 7d increased the number of MCF-7 cells in the G0/G1 phase and also induced apoptosis in these cells as revealed by Hoechst 33,258 staining. The molecular mechanism contributing to the anti-proliferative effect of the most potent compound was investigated in silico using Super Pred software and introduced PDGFRA as a plausible target for 7d. Molecular docking and molecular dynamic studies demonstrated Lys627 and Asp836 as key residues interacting with the active compound. Overall, 7d could serve as a suitable candidate for further modifications as a lead anticancer structure.
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Affiliation(s)
- Maryam Firouzi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Haghighijoo
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Masoomeh Eskandari
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Mohabbati
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ramin Miri
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hasan Jamei
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Alireza Poustforoosh
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Somayeh Nazari
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Omidreza Firuzi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Khoshneviszadeh
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Najmeh Edraki
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Taysi MR, Kirici M, Kirici M, Tuzun B, Poustforoosh A. Antioxidant enzyme activities, molecular docking studies, MM-GBSA, and molecular dynamic of chlorpyrifos in freshwater fish Capoeta umbla. J Biomol Struct Dyn 2024; 42:163-176. [PMID: 36974945 DOI: 10.1080/07391102.2023.2192807] [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: 10/15/2022] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
Abstract
Chlorpyrifos (CPF), which was started to be used in 1965, is a broad spectrum organophosphate insecticide that is used more and more day by day. Commonly used to control pests in farmland and homes, CPF is more toxic to fish than organochlorine compounds. CPF poses a serious threat to the health of humans and aquatic organisms. This paper studies the relationship between CPF exposure and antioxidant enzyme activities in gill, kidney and liver tissues of Capoeta umbla. Different time intervals (12, 24, 48, 72, and 96 h) and CPF doses (55 and 110 µg L-1) were used in the study. Spectrophotometrical measures were taken in all tissues for antioxidant enzyme activities and malondialdehyde (MDA) levels, as indices of the lipid peroxidation (LPO). A positive relationship between CPF and MDA levels was found in the study at a statistically significant level (p < 0.05). The study also found a negative relationship between CPF levels and catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), and glutathione reductase (GR) activity. Independent variables in the study can act as biomarkers of CPF exposure. The study recommends employing proper ecotoxicological risk evaluations in cases of CPF usage as a pesticide. The activities of the studied molecules against various proteins that are crystal structure of human peroxiredoxin 5 (PDB ID: 1HD2) has docking score value is -2.67, crystal structure of Bovine Xanthine Oxidase (PDB ID: 3NRZ) has docking score value is -3.76, and crystal structure of antibacterial FabH (PDB ID: 4Z8D) has docking score value is -3.16, were compared. Molecular dynamic (MD) calculations were made in 100 ns. MM/GBSA methods are calculated binding free energy. Afterwards, ADME/T analysis was performed to examine the some properties of the molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mehmet Reşit Taysi
- Department of Fisheries, Faculty of Agriculture, Bingol University, Bingöl, Turkey
| | - Muammer Kirici
- Department of Veterinary Health, Food Agriculture and Livestock Vocational School, Bingöl University, Bingöl, Turkey
| | - Mahinur Kirici
- Department of Chemistry, Faculty of Arts and Science, Bingöl University, Bingöl, Turkey
| | - Burak Tuzun
- Plant and Animal Production Department, Technical Sciences Vocational School of Sivas, Sivas Cumhuriyet University, Sivas, Turkey
| | - Alireza Poustforoosh
- Chemical Engineering Department, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
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Yin Q, Zhang H, Huang T, Liu B, Negm S, El-Kott AF. Anti-collagenase, Anti-elastase, Anti-urease, and Anti-cancer Potentials of Isokaempferide as Natural Compound: In vitro and in silico Study. J Oleo Sci 2024; 73:187-199. [PMID: 38311409 DOI: 10.5650/jos.ess23176] [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] [Indexed: 02/10/2024] Open
Abstract
One of the main goals of medicinal chemistry in recent years has been the development of new enzyme inhibitors and anti-cancer medicines. The isokaempferide' ability to inhibit the enzymes urease, elastase, and collagenase were also studied. The results showed that isokaempferide was the most effective compound against the assigned enzymes, with IC 50 values of 23.05 µM for elastase, 12.83 µM for urease, and 33.62 µM for collagenase respectively. It should be emphasized that natural compound was more effective at inhibiting some enzymes. Additionally, the compound was tested for their anti-cancer properties using colon, lung, breast cancer cell lines. The chemical activities of isokaempferide against urease, collagenase, and elastase were investigated utilizing the molecular docking study. The anti-cancer activities of the compound were evaluated against lung cancer cells such as SPC-A-1, SK-LU-1, 95D, breast cancer cells like MCF7, Hs 578Bst, Hs 319.T, and UACC-3133 cell lines, and colon cancer cell lines like CL40, SW1417, LS1034, and SW480. The chemical activities of isokaempferide against some of the expressed surface receptor proteins (EGFR, estrogen receptor, CD47, progesterone receptor, folate receptor, CD44, HER2, CD155, CXCR4, CD97, and endothelin receptor) in the mentioned cell lines were assessed using the molecular docking calculations. The results showed the probable interactions and their characteristics at an atomic level. The docking scores revealed that isokaempferide has a strong binding affinity to the enzymes and proteins. In addition, the compound formed powerful contact with the enzymes and receptors. Thus, isokaempferide could be potential inhibitor for enzymes and cancer cells.
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Affiliation(s)
- Qian Yin
- Department of Pathology, The Third Clinical Medical College of China Three Gorges University·Gezhouba Central Hospital of Sinopharm
| | - Hao Zhang
- Department of Endocrinology, The Third Clinical Medical College of China Three Gorges University·Gezhouba Central Hospital of Sinopharm
| | - Ting Huang
- Department of Oncology, No. 215 Hospital of Shaanxi Nuclear Industry
| | - Bin Liu
- Department of General Surgery, Dalian University Affiliated Xinhua Hospital
| | - Sally Negm
- Department of Life Sciences, College of Science and Art Mahyel Aseer, King Khalid University
| | - Attalla F El-Kott
- Department of Biology, College of Science, King Khalid University
- Department of Zoology, Faculty of Science, Damanhour University
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Li L, Zhu Y, Huang YG, Hou DZ, Ahmed Zaki MS, Sideeg AM, Mohammed H, El-Kott AF, Al-Saeed FA, Ling P. Therapeutic properties, biological effects, antiliver cancer, and anticolon cancer effects of some natural compounds: A biochemical approach. J Biochem Mol Toxicol 2024; 38:e23573. [PMID: 37934567 DOI: 10.1002/jbt.23573] [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: 04/18/2023] [Revised: 08/19/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
Natural compounds, such as carotenoids, flavonoids, anthocyanins, or terpenoids, are physiologically active components found in plants (pigments), often known as phytochemicals or phytonutrients. The in vitro cytotoxic and anticolon cancer effects of biologically bavachin, bavachinin, artepillin C, and aromadendrin compounds against SW48, SNU-C1, COLO 205, RKO, LS411N, and SW1417 cancer cell lines were assessed. Results of enzymes and antibacterial, antifungal were in level of micromolar that is good impacts. These natural compounds may be antidiabetic, anticancer, and antibacterial candidates for drug design. IC50 results were obtained between 14-19 and 5-119 µM for α-amylase and α-glucosidase, respectively. Good inhibitor Bavachinin was detected for both enzymes (IC50 for α-amylase: 14.37 µM and IC50 for α-glucosidase: 5.27 µM). The chemical activities of aromadendrin, artepillin C, bavachin, and bavachinin against pancreatic α-amylase and α-glucosidase were assessed by conducting the molecular docking study. The chemical activities of aromadendrin, artepillin C, bavachin, and bavachinin against some of the expressed surface receptor proteins (CD44, CD47, CXCR4, EGFR, folate receptor, HER2, and endothelin receptor) in the mentioned cell lines were investigated using the molecular docking calculations. The results illustrated the atomic-level properties and potential interactions. These chemicals have high binding affinities to the enzymes and proteins, according to the docking scores. In addition, the compounds formed strong contacts with the enzymes and receptors. Thus, these compounds could be potential inhibitors for enzymes and cancer cells.
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Affiliation(s)
- Long Li
- Department of General Surgery I, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yu Zhu
- Department of General Surgery I, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Ying-Guang Huang
- Department of General Surgery I, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - De-Zhi Hou
- Department of General Surgery I, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | | | - Abulqasim M Sideeg
- Department of Anatomy, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Heitham Mohammed
- Department of Anatomy, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Attalla F El-Kott
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
- Department of Zoology, College of Science, Damanhour University, Damanhour, Egypt
| | - Fatimah A Al-Saeed
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Ping Ling
- Department of General Surgery I, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
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Poustforoosh A, Faramarz S, Negahdaripour M, Tüzün B, Hashemipour H. Tracing the pathways and mechanisms involved in the anti-breast cancer activity of glycyrrhizin using bioinformatics tools and computational methods. J Biomol Struct Dyn 2024; 42:819-833. [PMID: 37042955 DOI: 10.1080/07391102.2023.2196347] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/22/2023] [Indexed: 04/13/2023]
Abstract
A complete investigation to understand the pathways that could be affected by glycyrrhizin (licorice), as anti-breast cancer (BC) agent, has not been performed to date. This study aims to investigate the pathways involved in the anti-cancer activity of glycyrrhizin against BC. For this purpose, the target genes of glycyrrhizin were obtained from the ChEMBL database. The BC-associated genes for three types of BC (breast carcinoma, malignant neoplasm of breast, and triple-negative breast neoplasms) were retrieved from DisGeNET. The target genes of glycyrrhizin and the BC-associated genes were compared, and the genes with disease specificity index (DSI) > 0.6 were selected for further evaluation using in silico methods. The protein-protein interaction (PPI) network was constructed, and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed. The potential complexes were further evaluated using molecular dynamics (MD) simulation. The results revealed that among 80 common genes, ten genes had DSI greater than 0.6, which included POLK, TACR2, MC3R, TBXAS1, HH1R, SLCO4A1, NPY2R, ADRA2C, ADRA1A, and SLCO2B1. The binding affinity of glycyrrhizin to the cognate proteins and binding characteristics were assessed using molecular docking and binding free energy calculations (MM/GBSA). POLK, TBXAS1, and ADRA1A showed the highest binding affinity with -8.9, -9.3, and -9.6 kcal/mol, respectively. The final targets had an association with BC at several stages of tumor growth. By affecting these targets, glycyrrhizin could influence and control BC efficiently. MD simulation suggested the pathways triggered by the complex glycyrrhizin-ADRA1A were more likely to happen.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alireza Poustforoosh
- Department of Chemical Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sanaz Faramarz
- Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Burak Tüzün
- Plant and Animal Production Department, Technical Sciences Vocational School of Sivas, Sivas Cumhuriyet University, Sivas, Turkey
| | - Hassan Hashemipour
- Chemical Engineering Department, Faculty of Engineering, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
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Safarova AS, Khalilov AN, Akkurt M, Brito I, Bhattarai A, Naghiyev FN, Mamedov IG. Crystal structure and Hirshfeld surface analysis of (2 Z)-3-oxo- N-phenyl-2-[(1 H-pyrrol-2-yl)methylidene]butanamide monohydrate. Acta Crystallogr E Crystallogr Commun 2023; 79:1142-1146. [PMID: 38313126 PMCID: PMC10833397 DOI: 10.1107/s2056989023009799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 02/06/2024]
Abstract
In the title compound, C15H14N2O2·H2O, the 1H-pyrrole ring makes a dihedral angle of 59.95 (13)° with the phenyl ring. In the crystal, the mol-ecules are connected by C-H⋯O hydrogen bonds into layers parallel to the (020) plane, while two mol-ecules are connected to the water mol-ecule by two N-H⋯O hydrogen bonds and one mol-ecule by an O-H⋯O hydrogen bond. C-H⋯π and π-π inter-actions further link the mol-ecules into chains extending in the [01] direction and stabilize the mol-ecular packing. According to a Hirshfeld surface study, H⋯H (49.4%), C⋯H/H⋯C (23.2%) and O⋯H/H⋯O (20.0%) inter-actions are the most significant contributors to the crystal packing.
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Affiliation(s)
- Ayten S. Safarova
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, AZ1148 Baku, Azerbaijan
| | - Ali N. Khalilov
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, AZ1148 Baku, Azerbaijan
- "Composite Materials’ Scientific Research Center, Azerbaijan State Economic University (UNEC), H. Aliyev str. 135, AZ1063, Baku, Azerbaijan
| | - Mehmet Akkurt
- Department of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Türkiye
| | - Ivan Brito
- Departamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta, Avenida Angamos 601, Casilla 170, Antofagasta 1240000, Chile
| | - Ajaya Bhattarai
- Department of Chemistry, M.M.A.M.C (Tribhuvan University) Biratnagar, Nepal
| | - Farid N. Naghiyev
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, AZ1148 Baku, Azerbaijan
| | - Ibrahim G. Mamedov
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, AZ1148 Baku, Azerbaijan
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Tokalı FS, Taslimi P, Tuzun B, Karakuş A, Sadeghian N, Gulçin İ. Novel Quinazolinone Derivatives: Potential Synthetic Analogs for the Treatment of Glaucoma, Alzheimer's Disease and Diabetes Mellitus. Chem Biodivers 2023; 20:e202301134. [PMID: 37695993 DOI: 10.1002/cbdv.202301134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023]
Abstract
Quinazolinones, which represent an important part of nitrogen-containing six-membered heterocyclic compounds, are frequently used in drug design due to their wide biological activity properties. Therefore, the novel quinazolinones were synthesized from the reaction of acylated derivatives of 4-hydroxy benzaldehyde with 3-amino-2-alkylquinazolin-4(3H)-ones with good yields (85-94 %) and their structures were characterized using Fourier-transform Infrared (FT-IR), Nuclear Magnetic Resonance (1 H-NMR, 13 C-NMR), and High-Resolution Mass Spectroscopy (HR-MS). As the application of the synthesized compounds, their inhibition properties of the synthesized compounds on α-Glucosidase (α-Glu), Acetylcholinesterase (AChE), Butyrylcholinesterase (BChE), and Carbonic anhydrase I-II (hCA I-II) metabolic enzymes were investigated. All compounds showed inhibition at nanomolar level with the Ki values in the range of 12.73±1.26-93.42±9.44 nM for AChE, 8.48±0.92-25.84±2.59 nM for BChE, 66.17±5.16-818.06±44.41 for α-Glu, 2.56±0.26-88.23±9.72 nM for hCA I, and 1.68±0.14-85.43±7.41 nM for hCA II. Molecular docking study was performed to understand the interactions of the most potent compounds with corresponding enzymes. Also, absorption, distribution, metabolism, excretion, and toxicity (ADME/T) properties of the compounds were investigated.
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Affiliation(s)
- Feyzi Sinan Tokalı
- Department of Material and Material Processing Technologies, Kars Vocational School, Kafkas University, Kars, 36100, Turkiye
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, 74100, Turkiye
| | - Burak Tuzun
- Departmentof Plant and Animal Production, Sivas Technical Sciences Vocational School, Sivas Cumhuriyet University, 58140, Sivas, Turkiye
| | - Ahmet Karakuş
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, 74100, Turkiye
| | - Nastaran Sadeghian
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, 74100, Turkiye
| | - İlhami Gulçin
- Department of Chemistry, Faculty of Sciences, Atatürk University, 25240-, Erzurum, Turkiye
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12
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Akkurt M, Naghiyev FN, Khrustalev VN, Asadov KA, Khalilov AN, Bhattarai A, Mamedov İG. Crystal structure and Hirshfeld surface analysis of (2 E)-1-(4-bromo-phen-yl)-3-(2-methyl-phen-yl)prop-2-en-1-one. Acta Crystallogr E Crystallogr Commun 2023; 79:847-851. [PMID: 37693662 PMCID: PMC10483568 DOI: 10.1107/s2056989023007387] [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: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023]
Abstract
In the title com-pound, C16H13BrO, the planes of the aromatic rings are inclined at an angle of 23.49 (15)°, and the configuration about the C=C bond is E. In the crystal, the mol-ecules are linked into chains by weak C-H⋯O inter-actions along the b axis. Successive chains form a zigzag structure along the c axis, and these chains are connected to each other by face-to-face π-π stacking inter-actions along the a axis. These layers, parallel to the (001) plane, are linked by van der Waals inter-actions, thus consolidating the crystal structure. Hirshfeld surface analysis showed that the most significant contacts in the structure are H⋯H (43.1%), C⋯H/H⋯C (17.4%), Br⋯H/H⋯Br (14.9%), C⋯C (11.9%) and O⋯H/H⋯O (9.8%).
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Affiliation(s)
- Mehmet Akkurt
- Department of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Türkiye
| | - Farid N. Naghiyev
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, AZ1148, Baku, Azerbaijan
| | - Victor N. Khrustalev
- Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklay St. 6, Moscow 117198, Russian Federation
- N. D. Zelinsky Institute of Organic Chemistry RAS, Leninsky Prosp. 47, Moscow, 119991, Russian Federation
| | - Khammed A. Asadov
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, AZ1148, Baku, Azerbaijan
| | - Ali N. Khalilov
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, AZ1148, Baku, Azerbaijan
- ‘Composite Materials’ Scientific Research Center, Azerbaijan State Economic University (UNEC), H. Aliyev str. 135, AZ1063, Baku, Azerbaijan
| | - Ajaya Bhattarai
- Department of Chemistry, M.M.A.M.C. (Tribhuvan University) Biratnagar, Nepal
| | - İbrahim G. Mamedov
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, AZ1148, Baku, Azerbaijan
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13
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Lefin N, Herrera-Belén L, Farias JG, Beltrán JF. Review and perspective on bioinformatics tools using machine learning and deep learning for predicting antiviral peptides. Mol Divers 2023:10.1007/s11030-023-10718-3. [PMID: 37626205 DOI: 10.1007/s11030-023-10718-3] [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: 05/02/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023]
Abstract
Viruses constitute a constant threat to global health and have caused millions of human and animal deaths throughout human history. Despite advances in the discovery of antiviral compounds that help fight these pathogens, finding a solution to this problem continues to be a task that consumes time and financial resources. Currently, artificial intelligence (AI) has revolutionized many areas of the biological sciences, making it possible to decipher patterns in amino acid sequences that encode different functions and activities. Within the field of AI, machine learning, and deep learning algorithms have been used to discover antimicrobial peptides. Due to their effectiveness and specificity, antimicrobial peptides (AMPs) hold excellent promise for treating various infections caused by pathogens. Antiviral peptides (AVPs) are a specific type of AMPs that have activity against certain viruses. Unlike the research focused on the development of tools and methods for the prediction of antimicrobial peptides, those related to the prediction of AVPs are still scarce. Given the significance of AVPs as potential pharmaceutical options for human and animal health and the ongoing AI revolution, we have reviewed and summarized the current machine learning and deep learning-based tools and methods available for predicting these types of peptides.
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Affiliation(s)
- Nicolás Lefin
- Department of Chemical Engineering, Faculty of Engineering and Science, University of La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Lisandra Herrera-Belén
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Temuco, Chile
| | - Jorge G Farias
- Department of Chemical Engineering, Faculty of Engineering and Science, University of La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Jorge F Beltrán
- Department of Chemical Engineering, Faculty of Engineering and Science, University of La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
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14
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Rashedinia M, Rasti Arbabi Z, Sabet R, Emami L, Poustforoosh A, Sabahi Z. Comparison of Protective Effects of Phenolic Acids on Protein Glycation of BSA Supported by In Vitro and Docking Studies. Biochem Res Int 2023; 2023:9984618. [PMID: 37496561 PMCID: PMC10368515 DOI: 10.1155/2023/9984618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/18/2023] [Accepted: 07/04/2023] [Indexed: 07/28/2023] Open
Abstract
Several diabetic complications are associated with forming advanced glycation end products (AGEs). Different chemical and natural compounds are able to prevent the development of these products. In this study, glycosylation was induced as a model by incubating bovine serum albumin (BSA) with glucose. Consequently, BSA was treated with glucose and different concentrations (1.25, 2.5, and 5 μM) of syringic acid, gallic acid, ellagic acid, ferulic acid, paracoumaric acid, and caffeic acid for 4 and 6 weeks. Biochemical experiments comprise measurements of fluorescent AGEs, protein carbonyl contents, total thiol, hemolysis tests, and also malondialdehyde (MDA) levels in RBC. These demonstrated the antiglycating mechanism of these phenolic acids. Most of the phenolic acids used in this study reduced MDA levels and protected thiol residues in protein structures. They also inhibited the formation of fluorescent AGEs and RBC lysis, except gallic acid. Moreover, ferulic acid, paracoumaric acid, and caffeic acid proteins significantly prevent carbonylation. Molecular docking and simulation studies showed that ellagic, caffeic, gallic, and syringic acids could interact with lysine and arginine residues in the active site of BSA and stabilize its structure to inhibit the formation of AGEs. Our results suggest that phenolic acid could be used as a potential phytochemical against protein glycation and related diabetic complications.
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Affiliation(s)
- Marzieh Rashedinia
- Food and Supplements Safety Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Medicinal Plants Processing Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmacology and Toxicology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Rasti Arbabi
- Department of Pharmacology and Toxicology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Razieh Sabet
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Leila Emami
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Alireza Poustforoosh
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Sabahi
- Food and Supplements Safety Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Medicinal Plants Processing Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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15
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Khalilov AN, Khrustalev VN, Samigullina AI, Akkurt M, Rzayev RM, Bhattarai A, Mamedov İG. Crystal structure and Hirshfeld surface analysis of ( E)-1-(2,4-di-methyl-furan-3-yl)-3-phenyl-prop-2-en-1-one. Acta Crystallogr E Crystallogr Commun 2023; 79:736-740. [PMID: 37601402 PMCID: PMC10439413 DOI: 10.1107/s2056989023006084] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
The title compound, C15H14O2, adopts an E configuration about the C=C double bond. The furan ring is inclined to the phenyl ring by 12.03 (9)°. In the crystal, pairs of mol-ecules are linked by C-H⋯O hydrogen bonds, forming dimers with R 2 2(14) ring motifs. The mol-ecules are connected via C-H⋯π inter-actions, forming a three dimensional network. No π-π inter-actions are observed.
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Affiliation(s)
- Ali N. Khalilov
- "Composite Materials" Scientific Research Center, Azerbaijan State Economic University (UNEC), H. Aliyev str. 135, Az 1063, Baku, Azerbaijan
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, Az, 1148, Baku, Azerbaijan
| | - Victor N. Khrustalev
- Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklay St.6, Moscow, 117198, Russian Federation
- N. D. Zelinsky Institute of Organic Chemistry RAS, Leninsky Prosp. 47, Moscow, 119991, Russian Federation
| | - Aida I. Samigullina
- N. D. Zelinsky Institute of Organic Chemistry RAS, Leninsky Prosp. 47, Moscow, 119991, Russian Federation
| | - Mehmet Akkurt
- Department of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Türkiye
| | - Rovnag M. Rzayev
- "Composite Materials" Scientific Research Center, Azerbaijan State Economic University (UNEC), H. Aliyev str. 135, Az 1063, Baku, Azerbaijan
| | - Ajaya Bhattarai
- Department of Chemistry, M.M.A.M.C (Tribhuvan University) Biratnagar, Nepal
| | - İbrahim G. Mamedov
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, Az, 1148, Baku, Azerbaijan
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16
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Naghiyev FN, Khrustalev VN, Mamedov HM, Akkurt M, Khalilov AN, Bhattarai A, Mamedov İG. Crystal structure and Hirshfeld surface analysis of 5-oxo-7-phenyl-2-(phenyl-amino)-1 H-[1,2,4]triazolo[1,5- a]pyridine-6,8-dicarbo-nitrile dimethyl sulfoxide monosolvate. Acta Crystallogr E Crystallogr Commun 2023; 79:567-570. [PMID: 37288458 PMCID: PMC10242740 DOI: 10.1107/s2056989023004383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 05/20/2023] [Indexed: 06/09/2023]
Abstract
In the title compound, C20H12N6O·C2H6OS, the [1,2,4]triazolo[1,5-a]pyridine ring system is almost planar and makes dihedral angles of 16.33 (7) and 46.80 (7)°, respectively, with the phenyl-amino and phenyl rings. In the crystal, mol-ecules are linked by inter-molecular N-H⋯O and C-H⋯O hydrogen bonds into chains along the b-axis direction through the dimethyl sulfoxide solvent mol-ecule, forming C(10)R 2 1(6) motifs. These chains are connected via S-O⋯π inter-actions, π-π stacking inter-actions between the pyridine rings [centroid-to-centroid distance = 3.6662 (9) Å] and van der Waals inter-actions. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯H (28.1%), C⋯H/H⋯C (27.2%), N⋯H/H⋯N (19.4%) and O⋯H/H⋯O (9.8%) inter-actions.
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Affiliation(s)
- Farid N. Naghiyev
- Faculty of Chemistry, Baku State University, Z. Khalilov str. 23, Az, 1148, Baku, Azerbaijan
| | - Victor N. Khrustalev
- Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklay St. 6, Moscow, 117198, Russian Federation
- N. D. Zelinsky Institute of Organic Chemistry RAS, Leninsky Prosp. 47, Moscow, 119991, Russian Federation
| | - Huseyn M. Mamedov
- Faculty of Physics, Baku State University, Z. Khalilov str. 23, Az, 1148 Baku, Azerbaijan
| | - Mehmet Akkurt
- Department of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Türkiye
| | - Ali N. Khalilov
- Faculty of Chemistry, Baku State University, Z. Khalilov str. 23, Az, 1148, Baku, Azerbaijan
| | - Ajaya Bhattarai
- Department of Chemistry, M.M.A.M.C (Tribhuvan University) Biratnagar, Nepal
| | - İbrahim G. Mamedov
- Faculty of Chemistry, Baku State University, Z. Khalilov str. 23, Az, 1148, Baku, Azerbaijan
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17
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Naghiyev FN, Khrustalev VN, Asadov KA, Akkurt M, Khalilov AN, Bhattarai A, Mamedov İG. Crystal structure and Hirshfeld surface analysis of 2-amino-6-[(1-phenyl-eth-yl)amino]-4-(thio-phen-2-yl)pyridine-3,5-dicarbo-nitrile. Acta Crystallogr E Crystallogr Commun 2023; 79:526-530. [PMID: 37288460 PMCID: PMC10242736 DOI: 10.1107/s2056989023003845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 06/09/2023]
Abstract
In the title compound, C19H15N5S, the thio-phene ring is disordered in a 0.6:0.4 ratio by an approximate 180° rotation of the ring around the C-C bond linking it to the pyridine ring. In the crystal, the mol-ecules are linked by N-H⋯N hydrogen bonds into dimers with an R 2 2(12) motif, forming chains along the b-axis direction. These chains are connected to each other by further N-H⋯N hydrogen bonds, forming a three-dimensional network. Furthermore, N-H⋯π and π-π [centroid-centroid separations = 3.899 (8) and 3.7938 (12) Å] inter-actions also contribute to the crystal cohesion. A Hirshfeld surface analysis indicated that the most important contributions to the surface contacts are from H⋯H (46.1%), N⋯H/H⋯N (20.4%) and C⋯H/H⋯C (17.4%) inter-actions.
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Affiliation(s)
- Farid N. Naghiyev
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, Az, 1148, Baku, Azerbaijan
| | - Victor N. Khrustalev
- Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklay St. 6, Moscow, 117198, Russian Federation
- N. D. Zelinsky Institute of Organic Chemistry RAS, Leninsky Prosp. 47, Moscow, 119991, Russian Federation
| | - Khammed A. Asadov
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, Az, 1148, Baku, Azerbaijan
| | - Mehmet Akkurt
- Department of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Türkiye
| | - Ali N. Khalilov
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, Az, 1148, Baku, Azerbaijan
- "Composite Materials" Scientific Research Center, Azerbaijan State Economic University (UNEC), H. Aliyev str. 135, Az 1063, Baku, Azerbaijan
| | - Ajaya Bhattarai
- Department of Chemistry, M.M.A.M.C (Tribhuvan University) Biratnagar, Nepal
| | - İbrahim G. Mamedov
- Department of Chemistry, Baku State University, Z. Khalilov str. 23, Az, 1148, Baku, Azerbaijan
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18
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Modeling and affinity maturation of an anti-CD20 nanobody: a comprehensive in-silico investigation. Sci Rep 2023; 13:582. [PMID: 36631511 PMCID: PMC9834265 DOI: 10.1038/s41598-023-27926-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023] Open
Abstract
B-cell Non-Hodgkin lymphomas are the malignancies of lymphocytes. CD20 is a membrane protein, which is highly expressed on the cell surface of the B-cells in NHL. Treatments using monoclonal antibodies (mAbs) have resulted in failure in some cases. Nanobodies (NBs), single-domain antibodies with low molecular weights and a high specificity in antigen recognition, could be practical alternatives for traditional mAbs with superior characteristics. To design an optimized NB as a candidate CD20 inhibitor with raised binding affinity to CD20, the structure of anti-CD20 NB was optimized to selectively target CD20. The 3D structure of the NB was constructed based on the optimal templates (6C5W and 5JQH), and the key residues were determined by applying a molecular docking study. After identifying the key residues, some mutations were introduced using a rational protocol to improve the binding affinity of the NB to CD20. The rational mutations were conducted using the experimental design (Taguchi method). Six residues (Ser27, Thr28, Phe29, Ile31, Asp99, and Asn100) were selected as the key residues, and five residues were targeted for rational mutation (Trp, Phe, His, Asp, and Tyr). Based on the mutations suggested by the experimental design, two optimized NB structures were constructed. NB2 showed a remarkable binding affinity to CD20 in docking studies with a binding energy of - 853 kcal/mol. The optimized NB was further evaluated using molecular dynamics simulation. The results revealed that CDR1 (complementarity determining regions1) and CDR3 are essential loops for recognizing the antigen. NB2 could be considered as a potential inhibitor of CD20, though experimental evaluations are needed to confirm it.
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Shahzadi I, Zahoor AF, Tüzün B, Mansha A, Anjum MN, Rasul A, Irfan A, Kotwica-Mojzych K, Mojzych M. Repositioning of acefylline as anti-cancer drug: Synthesis, anticancer and computational studies of azomethines derived from acefylline tethered 4-amino-3-mercapto-1,2,4-triazole. PLoS One 2022; 17:e0278027. [PMID: 36520942 PMCID: PMC9754256 DOI: 10.1371/journal.pone.0278027] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/08/2022] [Indexed: 12/23/2022] Open
Abstract
Novel azomethines derived from acefylline tethered triazole hybrids (7a-k) have been synthesized and evaluated against human liver cancer cell line (Hep G2) using MTT assay. The synthesized series of azomethines exhibited promising efficacy against liver cancer cell line. Screening of the synthesized series identified compound 7d with the least cell viability value (11.71 ± 0.39%) as the most potent anticancer agent in contrast to the reference drug acefylline (cell viability = 80 ± 3.87%). In this study, the potentials of the novel agents (7a-k) to inhibit liver cancer proteins were assessed. Subsequently, the structure-activity relationship of the potential drug candidates was assessed via ADME/T molecular screening. The cytotoxic potential of these derivatives was also investigated by hemolysis and thrombolysis. Their hemolytic and thrombolytic studies showed that all of these drugs had very low cytotoxicity and moderate clot lysis activity. Compound 7g (0.26% hemolysis) and 7k (52.1% clot lysis) were the least toxic and moderate thrombolytic agents respectively.
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Affiliation(s)
- Irum Shahzadi
- Department of Chemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Burak Tüzün
- Plant and Animal Production Department, Technical Sciences Vocational School of Sivas, Sivas Cumhuriyet University, Sivas, Turkey
| | - Asim Mansha
- Department of Chemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Naveed Anjum
- Department of Applied Chemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Azhar Rasul
- Department of Zoology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ali Irfan
- Department of Chemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, Siedlce, Poland
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Poustforoosh A, Farmarz S, Nematollahi MH, Hashemipour H, Pardakhty A. Construction of Bio-conjugated nano-vesicles using non-ionic surfactants for targeted drug delivery: A computational supported experimental study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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