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Yenigün S, Başar Y, İpek Y, Behçet L, Özen T, Demirtaş İ. Determination of antioxidant, DNA protection, enzyme inhibition potential and molecular docking studies of a biomarker ursolic acid in Nepeta species. J Biomol Struct Dyn 2024; 42:5799-5816. [PMID: 37394807 DOI: 10.1080/07391102.2023.2229440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/17/2023] [Indexed: 07/04/2023]
Abstract
Ursolic acid (UA), which has many biological properties such as anti-cancer, anti-inflammatory and antioxidant, and regulates some pharmacological processes, has been isolated from the flowers, leaves, berries and fruits of many plant species. In this work, UA was purified from the methanol-chloroform crude extract of Nepeta species (N. aristata, N. baytopii, N. italica, N. trachonitica, N. stenantha) using a silica gel column with chloroform or ethyl acetate solvents via bioactivity-guided isolation. The most active sub-fractions were determined under bioactivities using antioxidant and DNA protection activities and enzyme inhibitions. UA was purified from these fractions and its structure was elucidated by NMR spectroscopy techniques. The highest amount of UA was found in N. stenantha (8.53 mg UA/g), while the lowest amount of UA was found in N. trachonitica (1.92 mg UA/g). The bioactivities of UA were evaluated with antioxidant and DNA protection activities, enzyme inhibitions, kinetics and interactions. The inhibition values (IC50) of α-amylase, α-glucosidase, urease, CA, tyrosinase, lipase, AChE, and BChE were determined between 5.08 and 181.96 µM. In contrast, Ki values of enzyme inhibition kinetics were observed between 0.04 and 0.20 mM. In addition, Ki values of these enzymes for enzyme-UA interactions were calculated as 0.38, 0.86, 0.45, 1.01, 0.23, 0.41, 0.01 and 2.24 µM, respectively. It is supported that UA can be widely used as a good antioxidant against oxidative damage, an effective DNA protector against genetic diseases, and a suitable inhibitor for metabolizing enzymes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Semiha Yenigün
- Faculty of Science, Department of Chemistry, Ondokuz Mayıs University, Samsun, Turkey
| | - Yunus Başar
- Faculty of Arts and Sciences, Department of Biochemistry, Iğdır University, Iğdır, Turkey
| | - Yaşar İpek
- Faculty of Science, Department of Chemistry, Çankırı Karatekin University, Çankırı, Turkey
| | - Lütfi Behçet
- Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, Bingöl University, Bingöl, Turkey
| | - Tevfik Özen
- Faculty of Science, Department of Chemistry, Ondokuz Mayıs University, Samsun, Turkey
| | - İbrahim Demirtaş
- Faculty of Arts and Sciences, Department of Biochemistry, Iğdır University, Iğdır, Turkey
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ondokuz Mayıs University, Samsun, Turkey
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N Hegde V, J S S, B S C, Benedict Leoma M, N K L. Structural, computational and in silico studies of 4-bromo-3-flurobenzonitrile as anti-Alzheimer and anti-Parkinson agents. J Biomol Struct Dyn 2024; 42:4619-4643. [PMID: 37418246 DOI: 10.1080/07391102.2023.2226755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 05/29/2023] [Indexed: 07/08/2023]
Abstract
A novel dimer of the 4-bromo-3-fluorobenzonitrile was crystallized and studied using a spectroscopic method such as the scanning electron microscope method. The computational simulations substantiated the structural analysis findings. The Hirshfeld surface analysis has been performed for visualizing, exploring and quantifying the intra and inter-molecular interactions that stabilize the crystal packing of the compound. The NBO and QTAIM analyses were applied to study the nature and origin of the attractive forces involved in the crystal structure. Further, the pharmacokinetic properties of the compound were evaluated, indicating good brain-blood barrier and central nervous system penetration capability. Hence, in silico studies was carried out to explore the binding pattern of the titled compound against acetylcholinesterase and butyrylcholinesterase, and tumor necrosis factor-alpha converting enzyme proteins using molecular docking and molecular dynamics simulations approach. Further, the titled compound is compared with standard drugs through molecular docking studies. The in silico studies finally predicts that the compound under investigation may act as a good inhibitor for treating Alzheimer's disease and further in vitro and in vivo studies may provide its therapeutic potential.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Shyambhargav J S
- Department of Studies in Physics, University of Mysore, Mysuru, India
| | - Chethan B S
- Department of Studies in Physics, University of Mysore, Mysuru, India
| | | | - Lokanath N K
- Department of Studies in Physics, University of Mysore, Mysuru, India
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Yenigun S, Ipek Y, Marah S, Demirtas I, Ozen T. DNA protection, molecular docking, antioxidant, antibacterial, enzyme inhibition, and enzyme kinetic studies for parietin, isolated from Xanthoria parietina (L.) Th. Fr. J Biomol Struct Dyn 2024; 42:848-862. [PMID: 37021462 DOI: 10.1080/07391102.2023.2196693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023]
Abstract
Parietin was isolated from Xanthoria parietina (L.) Th. Fr.' (methanol:chloroform) extract, using a silica column. 13 C NMR and 1H NMR were used to confirm the structure of the isolated parietin. For the first time, parietin was investigated for its antioxidant, antibacterial and DNA protective activities. Molecular docking was carried out to determine the binding affinity and interactions between the enzymes and our molecule. Inhibition and kinetic mechanism studies for the action of the enzymes were performed too. Parietin exhibited high metal chelating activity. The MIC values of parietin were sufficient to inhibit different bacterial strains; E. coli, P. aeruginosa, K. pneumoniae and S. aureus. Molecular docking applications exhibited that acetylcholinesterase (AChE), butyrylcholinesterase (BChE), lipase, and tyrosinase have high potential for binding with the parietin. Especially, the parietin's highest binding affinity was recorded with AChE and tyrosinase. These results were confirmed by the inhibition and kinetics results, where, parietin observed a potent inhibition with an IC50 values between 0.013-0.003 µM. Moreover, parietin acts' as a non-competitive inhibitor against AChE, BChE, and lipase, and as a competitive inhibitor against tyrosinase with a high rate of inhibition stability. The promising biological properties of parietin revealed its effectiveness in terms of suitability in the food and pharmaceutical industries.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Semiha Yenigun
- Department of Chemistry, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
| | - Yasar Ipek
- Department of Biochemistry, Faculty of Science and Art, Cankiri Karatekin University, Cankiri, Turkey
| | - Sarmad Marah
- Department of Chemistry, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
| | - Ibrahim Demirtas
- Department of Biochemistry, Faculty of Science and Art, Igdir University, Igdir, Turkey
| | - Tevfik Ozen
- Department of Chemistry, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
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Haroon F, Farwa U, Arif M, Raza MA, Sandhu ZA, El Oirdi M, Farhan M, Alhasawi MAI. Novel Para-Aminobenzoic Acid Analogs and Their Potential Therapeutic Applications. Biomedicines 2023; 11:2686. [PMID: 37893060 PMCID: PMC10604881 DOI: 10.3390/biomedicines11102686] [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: 08/23/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
A "building block" is a key component that plays a substantial and critical function in the pharmaceutical research and development industry. Given its structural versatility and ability to undergo substitutions at both the amino and carboxyl groups, para-aminobenzoic acid (PABA) is a commonly used building block in pharmaceuticals. Therefore, it is great for the development of a wide range of novel molecules with potential medical applications. Anticancer, anti-Alzheimer's, antibacterial, antiviral, antioxidant, and anti-inflammatory properties have been observed in PABA compounds, suggesting their potential as therapeutic agents in future clinical trials. PABA-based therapeutic chemicals as molecular targets and their usage in biological processes are the primary focus of this review study. PABA's unique features make it a strong candidate for inclusion in a massive chemical database of molecules having drug-like effects. Based on the current literature, further investigation is needed to evaluate the safety and efficacy of PABA derivatives in clinical investigations and better understand the specific mechanism of action revealed by these compounds.
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Affiliation(s)
- Faisal Haroon
- Department of Basic Sciences, Preparatory Year Deanship, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Umme Farwa
- Department of Chemistry, Hafiz Hayat Campus, University of Gujrat, Gujrat 50700, Pakistan
| | - Maimoona Arif
- Department of Chemistry, Hafiz Hayat Campus, University of Gujrat, Gujrat 50700, Pakistan
| | - Muhammad Asam Raza
- Department of Chemistry, Hafiz Hayat Campus, University of Gujrat, Gujrat 50700, Pakistan
| | - Zeshan Ali Sandhu
- Department of Chemistry, Hafiz Hayat Campus, University of Gujrat, Gujrat 50700, Pakistan
| | - Mohamed El Oirdi
- Department of Basic Sciences, Preparatory Year Deanship, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Mohd Farhan
- Department of Basic Sciences, Preparatory Year Deanship, King Faisal University, Al-Ahsa 31982, Saudi Arabia
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Almaz Z. Investigation of biological activities of various 1,2,3-triazole compounds: Their effects on cholinesterase enzymes, determination of antioxidant capacity and antimicrobial activity. J Biochem Mol Toxicol 2023; 37:e23277. [PMID: 36514839 DOI: 10.1002/jbt.23277] [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: 01/16/2022] [Revised: 09/14/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
1,2,3-triazoles are pharmaceutically significant compounds that have attracted recent interest from medicinal chemists because of their important biological activities. Addressed herein, some 1,2,3-triazoles were synthesized to investigate the inhibitory activities against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes, antioxidant capacity, and antimicrobial effect. The antioxidant profile of 1,2,3-triazoles determined by varied bioanalytical antioxidant methods, including 2,2'-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid) (ABTS.+ ), 1,1-diphenyl-2-picrylhydrazil (DPPH·), cupric ion (Cu2+ ) and ferric ion (Fe3+ ) ascorbic acid, butylated hydroxyanisole (BHA), and butylated hydroxytoluene (BHT) were used as the standard compounds. In addition, the antibacterial and antifungal activities of these compounds were investigated against seven bacteria and three fungal species using the hollow agar method. As a result of these studies, it was determined that compound 4 showed the best antimicrobial activity and antioxidant activity close to the standards. Inhibitory effects and kinetic studies of these molecules on cholinesterase enzymes were performed. According to the results obtained, compound 4 showed stronger AChE inhibition and compound 3 stronger BChE inhibition compared to other compounds. In kinetic studies, it was found that AChE showed noncompetitive inhibition by compound 4, and BChE showed competitive inhibition by compound 3.
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Affiliation(s)
- Züleyha Almaz
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Mus Alparslan University, Mus, Turkey
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A Review on Recent Approaches on Molecular Docking Studies of Novel Compounds Targeting Acetylcholinesterase in Alzheimer Disease. Molecules 2023; 28:molecules28031084. [PMID: 36770750 PMCID: PMC9921523 DOI: 10.3390/molecules28031084] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Alzheimer's disease (AD), a neurodegenerative brain disorder that affects millions of people worldwide, is characterized by memory loss and cognitive decline. Low levels of acetylcholine and abnormal levels of beta-amyloid, T protein aggregation, inflammation, and oxidative stress, have been associated with AD, and therefore, research has been oriented towards the cholinergic system and primarily on acetylcholinesterase (AChE) inhibitors. In this review, we are focusing on the discovery of AChE inhibitors using computer-based modeling and simulation techniques, covering the recent literature from 2018-2022. More specifically, the review discusses the structures of novel, potent acetylcholinesterase inhibitors and their binding mode to AChE, as well as the physicochemical requirements for the design of potential AChE inhibitors.
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A series of 1,2,3-triazole compounds: Synthesis, characterization, and investigation of the cholinesterase inhibitory properties via in vitro and in silico studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Novel Morpholine-Bearing Quinoline Derivatives as Potential Cholinesterase Inhibitors: The Influence of Amine, Carbon Linkers and Phenylamino Groups. Int J Mol Sci 2022; 23:ijms231911231. [PMID: 36232533 PMCID: PMC9570490 DOI: 10.3390/ijms231911231] [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: 07/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/24/2022] Open
Abstract
A series of novel 4-N-phenylaminoquinoline derivatives containing a morpholine group were designed and synthesized, and their anti-cholinesterase activities and ABTS radical-scavenging activities were tested. Among them, compounds 11a, 11g, 11h, 11j, 11l, and 12a had comparable inhibition activities to reference galantamine in AChE. Especially, compound 11g revealed the most potent inhibition on AChE and BChE with IC50 values of 1.94 ± 0.13 μM and 28.37 ± 1.85 μM, respectively. The kinetic analysis demonstrated that both the compounds 11a and 11g acted as mixed-type AChE inhibitors. A further docking comparison between the 11a- and 12a-AChE complexes agreed with the different inhibitory potency observed in experiments. Besides, compounds 11f and 11l showed excellent ABTS radical-scavenging activities, with IC50 values of 9.07 ± 1.34 μM and 6.05 ± 1.17 μM, respectively, which were superior to the control, Trolox (IC50 = 11.03 ± 0.76 μM). It is worth noting that 3-aminoquinoline derivatives 12a–12d exhibited better drug-like properties.
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Tan A. Synthesis, spectroscopic characterization of novel phthalimides derivatives bearing a 1,2,3-triazole unit and examination as potential SARS-CoV-2 inhibitors via in silico studies. J Mol Struct 2022; 1261:132915. [PMID: 35345413 PMCID: PMC8942404 DOI: 10.1016/j.molstruc.2022.132915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 12/16/2022]
Abstract
In the present study, novel phthalimide derivatives 8(a-f) and 9(a-f) bearing a 1,2,3-triazole subunit were synthesized via CuAAC reactions and characterized by 1H, 13C NMR, HR-MS, and FT-IR analyses. To support the fight against SARS-CoV-2, in silico molecular docking studies were carried out to examine their interactions with the proteins of SARS-CoV-2 (Mpro and PLpro) and the protein-protein interactions (PPI) between the ACE2-spike (S1) in comparison with various inhibitors reported to be active by in vitro experiments. The ligand-protein stabilities of compounds 8a-Mpro, 8b-PLpro, and 9a-'ACE2-S1' showing the best binding energy and predicted inhibition constant values (Ki) were examined by molecular dynamics simulation studies. Finally, in silico ADMET properties of the target compounds were investigated using the Swiss ADME and ProTox-II web tools. According to in silico results, all phthalimide analogs may block the PPI between S1 and ACE2. The compounds may also inhibit the progression of the Mpro, and PLpro proteins of SARS-CoV-2. Additionally, it has been estimated that the compounds are suitable for oral administration and exhibit low levels of toxicity.
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Affiliation(s)
- Ayse Tan
- Vocational School of Technical Sciences, Mus Alparslan University, Mus 49250, Turkey
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Novel diamide derivatives: Synthesis, characterization, urease inhibition, antioxidant, antibacterial, and molecular docking studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132932] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Synthesis, investigation of the cholinesterase inhibitory activities and in silico studies of some novel N-substituted phthalimide derivatives. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-022-02492-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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