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Khedraoui M, Abchir O, Nour H, Yamari I, Errougui A, Samadi A, Chtita S. An In Silico Study Based on QSAR and Molecular Docking and Molecular Dynamics Simulation for the Discovery of Novel Potent Inhibitor against AChE. Pharmaceuticals (Basel) 2024; 17:830. [PMID: 39065681 PMCID: PMC11280381 DOI: 10.3390/ph17070830] [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: 05/10/2024] [Revised: 06/09/2024] [Accepted: 06/17/2024] [Indexed: 07/28/2024] Open
Abstract
Acetylcholinesterase (AChE) is one of the main drug targets for treating Alzheimer's disease. This current study relies on multiple molecular modeling approaches to develop new potent inhibitors of AChE. We explored a 2D QSAR study using the statistical method of multiple linear regression based on a set of substituted 5-phenyl-1,3,4-oxadiazole and N-benzylpiperidine analogs, which were recently synthesized and proved their inhibitory activities against acetylcholinesterase (AChE). The molecular descriptors, polar surface area, dipole moment, and molecular weight are the key structural properties governing AChE inhibition activity. The MLR model was selected based on its statistical parameters: R2 = 0.701, R2test = 0.76, Q2CV = 0.638, and RMSE = 0.336, demonstrating its predictive reliability. Randomization tests, VIF tests, and applicability domain tests were adopted to verify the model's robustness. As a result, 11 new molecules were designed with higher anti-Alzheimer's activities than the model molecule. We demonstrated their improved pharmacokinetic properties through an in silico ADMET study. A molecular docking study was conducted to explore their AChE inhibition mechanisms and binding affinities in the active site. The binding scores of compounds M1, M2, and M6 were (-12.6 kcal/mol), (-13 kcal/mol), and (-12.4 kcal/mol), respectively, which are higher than the standard inhibitor Donepezil with a binding score of (-10.8 kcal/mol). Molecular dynamics simulations over 100 ns were used to validate the molecular docking results, indicating that compounds M1 and M2 remain stable in the active site, confirming their potential as promising anti-AChE inhibitors.
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Affiliation(s)
- Meriem Khedraoui
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 20670, Morocco; (M.K.); (O.A.); (H.N.); (I.Y.); (A.E.)
| | - Oussama Abchir
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 20670, Morocco; (M.K.); (O.A.); (H.N.); (I.Y.); (A.E.)
| | - Hassan Nour
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 20670, Morocco; (M.K.); (O.A.); (H.N.); (I.Y.); (A.E.)
| | - Imane Yamari
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 20670, Morocco; (M.K.); (O.A.); (H.N.); (I.Y.); (A.E.)
| | - Abdelkbir Errougui
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 20670, Morocco; (M.K.); (O.A.); (H.N.); (I.Y.); (A.E.)
| | - Abdelouahid Samadi
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 20670, Morocco; (M.K.); (O.A.); (H.N.); (I.Y.); (A.E.)
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Identify promising IKK-β inhibitors: A docking-based 3D-QSAR study combining molecular design and molecular dynamics simulation. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.103786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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3
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Chen W, Li A, Wang J, Zhong H, Yuan J, Luo Y, Ou J, Chen J, Li L. A Combined approach of QSAR study, molecular docking and pharmacokinetics prediction of promising Amide-Ac6-aminoacetonitriles Cathepsin K inhibitors. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Huang L, Wu X, Fu X, Wang H, Tang B, Xiao Y, Zhou C, Zhao Z, Wan Y, Chen H, Tang Z, Yao H, Shan Z, Bu T. Ligand based 3D-QSAR model, pharmacophore, molecular docking and ADME to identify potential fibroblast growth factor receptor 1 inhibitors. J Biomol Struct Dyn 2021; 40:7584-7597. [PMID: 33734039 DOI: 10.1080/07391102.2021.1899049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The FGF/FGFR system may affect tumor cells and stromal microenvironment through autocrine and paracrine stimulation, thereby significantly promoting oncogene transformation and tumor growth. Abnormal expression of FGFR1 in cells is considered to be the main cause of tumorigenesis and a potential target for the treatment of cancer. In this study, a combination of structure-based drug carriers and molecular docking-based virtual screening was used to screen new potential FGFR1 inhibitors. Forty eight known inhibitors were collected to establish 3 D-QSAR models and pharmacophore models, investigate the relationship between the activity and conformation of compounds, and verify the efficiency of pharmacophore. In Accelrys Discovery Studio 2016, the ZINC database was filtered by Lipinski's Rule of Five and SMART's filtration. Then, Hypo01 was used for virtual screening of ZINC database. Compounds with predicted activity values less than 1 μM were molecularly docked with FGFR1 protein crystals, the docking results were observed, and the interaction between compounds and targets was studied. The absorption, distribution, metabolism and excretion (ADME) and toxicity of potential inhibitors were studied, and a compound with new structural scaffolds were obtained. It could be further studied to explore their better therapeutic effects.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lu Huang
- College of Life Sciences, Sichuan Agricultural University, Ya'an, China
| | - Xulong Wu
- Chengdu Agricultural College, Chengdu, China
| | - Xiaoli Fu
- College of Life Sciences, Sichuan Agricultural University, Ya'an, China
| | - Haoxiang Wang
- College of Life Sciences, Sichuan Agricultural University, Ya'an, China
| | - Biao Tang
- College of Life Sciences, Sichuan Agricultural University, Ya'an, China
| | - Yirong Xiao
- Sichuan Agricultural University Hospital, Ya'an, China
| | - Caixia Zhou
- College of Life Sciences, Sichuan Agricultural University, Ya'an, China
| | - Zhiqiao Zhao
- College of Life Sciences, Sichuan Agricultural University, Ya'an, China
| | - Yujun Wan
- Sichuan Food Fermentation Industry Research and Design Institute, Chengdu, China
| | - Hui Chen
- College of Life Sciences, Sichuan Agricultural University, Ya'an, China
| | - Zizhong Tang
- College of Life Sciences, Sichuan Agricultural University, Ya'an, China
| | - Huipeng Yao
- College of Life Sciences, Sichuan Agricultural University, Ya'an, China
| | - Zhi Shan
- College of Life Sciences, Sichuan Agricultural University, Ya'an, China
| | - Tongliang Bu
- College of Life Sciences, Sichuan Agricultural University, Ya'an, China
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Wang J, Chen W, Zhong H, Luo Y, Zhang L, He L, Wu C, Li L. Identify of promising isoquinolone JNK1 inhibitors by combined application of 3D-QSAR, molecular docking and molecular dynamics simulation approaches. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chen DH, Zheng G, Zhong XY, Lin ZH, Yang SW, Liu HX, Shang P. Oroxylin A attenuates osteoarthritis progression by dual inhibition of cell inflammation and hypertrophy. Food Funct 2020; 12:328-339. [PMID: 33300913 DOI: 10.1039/d0fo02159h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The imbalance between the anabolism and catabolism of the extracellular matrix (ECM) is of great importance to osteoarthritis (OA) development. Aberrant inflammatory responses and hypertrophic changes of chondrocytes are the main contributors to these metabolic disorders. In the present study, we found that Oroxylin A (ORA), a flavonoid compound derived from Oroxylum indicum, maintained ECM hemostasis of chondrocytes by Interleukin-1β (IL-1β) stimulation. Besides, it was demonstrated that IL-1β induced over-production of inflammatory mediators was attenuated by ORA treatment. Moreover, ORA could rescue IL-1β mediated hypertrophic alterations of chondrocytes. Mechanistically, ORA's protective effects were found to be associated with both NF-κB and Wnt/β-catenin signaling inhibition. Meanwhile, molecular docking analysis revealed that ORA could strongly bind to the inhibitor kappa B kinaseβ (IKKβ) and dishevelled, Dsh Homolog 2 (Dvl2), the upstream molecules of the NF-κB axis and β-catenin axis, respectively. In addition, ORA driven chondroprotective effects were also affirmed in a surgically induced OA mouse model. Taken together, the current study suggested that ORA might be a promising therapeutic option for the treatment of OA.
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Affiliation(s)
- De-Heng Chen
- Department of Orthopaedic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109, Xueyuanxi road, 325027 Wenzhou, China.
| | - Gang Zheng
- Department of Orthopaedic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109, Xueyuanxi road, 325027 Wenzhou, China.
| | - Xin-Yang Zhong
- The Second School of Medicine, Wenzhou Medical University, China
| | - Zi-Hao Lin
- The Second School of Medicine, Wenzhou Medical University, China
| | - Shi-Wei Yang
- The Second School of Medicine, Wenzhou Medical University, China
| | - Hai-Xiao Liu
- Department of Orthopaedic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109, Xueyuanxi road, 325027 Wenzhou, China.
| | - Ping Shang
- Department of Rehabilitation, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109, Xueyuanxi road, 325027 Wenzhou, China.
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Taslimi P, Türkan F, Güngördü Solğun D, Aras A, Erden Y, Celebioglu HU, Tuzun B, Ağırtaş MS, Günay S, Gulcin I. Metal contained Phthalocyanines with 3,4-Dimethoxyphenethoxy substituents: their anticancer, antibacterial activities and their inhibitory effects on some metabolic enzymes with molecular docking studies. J Biomol Struct Dyn 2020; 40:2991-3002. [PMID: 33234029 DOI: 10.1080/07391102.2020.1844051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The compounds (3-6) used in this study were re-synthesized in accordance with our previous study. The inhibitory effect of the complexes on some metabolic enzymes was examined and it was demonstrated that the enzymes inhibited by ligands and their complex molecules at micromolar level. The best Ki value for α-glycosidase enzyme was absorved 1.01±0.08 µM for compound 6. The biological activity of ligand and metal complexes against enzymes was compared with molecular docking method. The enzymes used against ligand and metal complexes respectively: Achethylcholinesterase for ID 4M0E (AChE), butyrylcholinesterase for ID 5NN0 (BChE), α-glycosidase for ID 1XSI (α-Gly). ADME analysis was performed to examine the drug properties of the compounds (3-6). Besides, the anticancer properties of the complexes were studied. The doses of all compounds caused significant reductions in MCF-7 cell viability. The 3 and 5 compounds administered to PC-3 cells exhibited a more pronounced cytotoxic effect than the other two compounds (4 and 6). Furthermore, antibacterial activities of these compounds against Escherichia coli and Staphylococcus aureus were examined.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Turkey
| | - Fikret Türkan
- Health Services Vocational School, Igdır University, Igdır, Turkey
| | - Derya Güngördü Solğun
- Department of Chemistry, Faculty of Science, Van Yuzuncu Yıl University, Van, Turkey
| | - Abdülmelik Aras
- Department of Biochemistry, Faculty of Science and Arts, Iğdır University, Iğdır, Turkey
| | - Yavuz Erden
- Department of Molecular Biology and Genetics, Faculty of Science, Bartin University, Bartin, Turkey
| | | | - Burak Tuzun
- Department of Chemistry, Faculty of Science, Cumhuriyet University, Sivas, Turkey
| | - Mehmet Salih Ağırtaş
- Department of Chemistry, Faculty of Science, Van Yuzuncu Yıl University, Van, Turkey
| | - Sevilay Günay
- Department of Molecular Biology and Genetics, Faculty of Science, Bartin University, Bartin, Turkey
| | - Ilhami Gulcin
- Department of Chemistry, Faculty of Science, Ataturk University, Erzurum, Turkey
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Hammoudi NEH, Benguerba Y, Attoui A, Hognon C, Lemaoui T, Sobhi W, Benaicha M, Badawi M, Monari A. In silico drug discovery of IKK-β inhibitors from 2-amino-3-cyano-4-alkyl-6-(2-hydroxyphenyl) pyridine derivatives based on QSAR, docking, molecular dynamics and drug-likeness evaluation studies. J Biomol Struct Dyn 2020; 40:886-902. [PMID: 32948119 DOI: 10.1080/07391102.2020.1819878] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The Inhibitor of IKK-β (nuclear factor kappa B kinase subunit beta), a specific modulator of NF-κB (nuclear factor-κB), is considered a valid target to discover new active compounds for various cancers and rheumatoid arthritis treatment. In this study a series of thirty 2-amino-3-cyano-4-alkyl-6-(2-hydroxyphenyl) pyridine derivatives was involved for a quantitative structure activity relationship model (QSAR) elaboration which allows the prediction of the pIC50 values of new designed compounds. The model can be used to predict the activity of new compounds within its applicability domain. Then a molecular docking study was carried out to identify the interactions between the compounds and the amino acids of the active site. After that, golden triangle, Veber's rule, and Lipinski's rule properties were calculated to identify the drug-likeness properties of the investigated compounds. Finally, in-silico-toxicity studies were performed to predict the toxicity of the new designed compounds. The analysis of the results of QSAR model and molecular docking succeeded to screen 21 interesting compounds with better inhibitory concentration having a good affinity to IKK-β. All compounds were within the range set by Veber's rule and Lipinski's rule. the analysis of golden triangle showed that the thirty 2-amino-3-cyano-4-alkyl-6-(2-hydroxyphenyl) pyridine derivatives would not have clearance and cell membrane permeability problems except comp6 comp12,comp20, comp21, and comp26.As for the new designed compounds, their properties may have these problems, except two compounds which are: A8m, A8p. The A1m, A1p, A3p and A11m compounds were predicted to be nontoxic. These findings indicate that the novel potent candidate drugs have promising potential to IKK-β enzyme inhibition and should motivate future experimental investigations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nour-El-Houda Hammoudi
- Laboratoire des Matériaux Polymères Multiphasiques, LMPMP, Université Ferhat ABBAS Sétif-1, Sétif, Algeria.,Energetics and Solid-State Electrochemistry Laboratory (LEES), Processes Engineering Department, Faculty of Technology, Ferhat Abbas-Setif1 University, Setif, Algeria
| | - Yacine Benguerba
- Laboratoire des Matériaux Polymères Multiphasiques, LMPMP, Université Ferhat ABBAS Sétif-1, Sétif, Algeria
| | - Ayoub Attoui
- Laboratoire des Matériaux Polymères Multiphasiques, LMPMP, Université Ferhat ABBAS Sétif-1, Sétif, Algeria.,Laboratoire de Biochimie Appliquée, Université Ferhat ABBAS Sétif-1, Sétif, Algeria
| | - Cecilia Hognon
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, Université de Lorraine, Nancy, France
| | - Tarek Lemaoui
- Laboratoire des Matériaux Polymères Multiphasiques, LMPMP, Université Ferhat ABBAS Sétif-1, Sétif, Algeria
| | - Widad Sobhi
- Laboratoire de Biochimie Appliquée, Université Ferhat ABBAS Sétif-1, Sétif, Algeria
| | - Mohamed Benaicha
- Energetics and Solid-State Electrochemistry Laboratory (LEES), Processes Engineering Department, Faculty of Technology, Ferhat Abbas-Setif1 University, Setif, Algeria
| | - Michael Badawi
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, Université de Lorraine, Nancy, France
| | - Antonio Monari
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, Université de Lorraine, Nancy, France
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Huseynova A, Kaya R, Taslimi P, Farzaliyev V, Mammadyarova X, Sujayev A, Tüzün B, Kocyigit UM, Alwasel S, Gulçin İ. Design, synthesis, characterization, biological evaluation, and molecular docking studies of novel 1,2-aminopropanthiols substituted derivatives as selective carbonic anhydrase, acetylcholinesterase and α-glycosidase enzymes inhibitors. J Biomol Struct Dyn 2020; 40:236-248. [DOI: 10.1080/07391102.2020.1811772] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Afat Huseynova
- Laboratory of ‘Fine Organic Synthesis’ of Baku State University, Baku, Azerbaijan
| | - Ruya Kaya
- Agri Ibrahim Cecen University Central Research and Application Laboratory, Agri, Turkey
- Faculty of Science, Department of Chemistry, Atatürk University, Erzurum, Turkey
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Turkey
| | - Vagif Farzaliyev
- Laboratory of Theoretical Bases of Synthesis and Action Mechanism of Additives, Institute of Chemistry of Additives, Azerbaijan National Academy of Sciences, Baku, Azerbaijan
| | - Xadija Mammadyarova
- Laboratory of Theoretical Bases of Synthesis and Action Mechanism of Additives, Institute of Chemistry of Additives, Azerbaijan National Academy of Sciences, Baku, Azerbaijan
| | - Afsun Sujayev
- Laboratory of Theoretical Bases of Synthesis and Action Mechanism of Additives, Institute of Chemistry of Additives, Azerbaijan National Academy of Sciences, Baku, Azerbaijan
| | - Burak Tüzün
- Department of Chemistry, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Umit M. Kocyigit
- Department of Basic Pharmaceutical Sciences, Division of Biochemistry, Faculty of Pharmacy, Sivas Cumhuriyet University, Sivas, Turkey
| | - Saleh Alwasel
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - İlhami Gulçin
- Faculty of Science, Department of Chemistry, Atatürk University, Erzurum, Turkey
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Demir Y, Taslimi P, Koçyiğit ÜM, Akkuş M, Özaslan MS, Duran HE, Budak Y, Tüzün B, Gürdere MB, Ceylan M, Taysi S, Gülçin İ, Beydemir Ş. Determination of the inhibition profiles of pyrazolyl-thiazole derivatives against aldose reductase and α-glycosidase and molecular docking studies. Arch Pharm (Weinheim) 2020; 353:e2000118. [PMID: 32761859 DOI: 10.1002/ardp.202000118] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/08/2020] [Accepted: 07/11/2020] [Indexed: 12/14/2022]
Abstract
Aldose reductase (AR) is the first and rate-limiting enzyme of the polyol pathway, which converts glucose to sorbitol in an NADPH-dependent reaction. α-Glycosidase breaks down starch and disaccharides to glucose. Hence, inhibition of these enzymes can be regarded a considerable approach in the treatment of diabetic complications. AR was purified from sheep liver using simple chromatographic methods. The inhibitory effects of pyrazolyl-thiazoles ((3aR,4S,7R,7aS)-2-(4-{1-[4-(4-bromophenyl)thiazol-2-yl]-5-(aryl)-4,5-dihydro-1H-pyrazol-3-yl}phenyl)-3a,4,7,7a-tetrahydro-1H-4,7-methanoisoindole-1,3(2H)-dione derivatives; 3a-i) on AR and α-glycosidase enzymes were investigated. All compounds showed a good inhibitory action against AR and α-glycosidase. Among these compounds, compound 3d exhibited the best inhibition profiles against AR, with a Ki value of 7.09 ± 0.19 µM, whereas compound 3e showed the lowest inhibition effects, with a Ki value of 21.89 ± 1.87 µM. Also, all compounds showed efficient inhibition profiles against α-glycosidase, with Ki values in the range of 0.43 ± 0.06 to 2.30 ± 0.48 µM, whereas the Ki value of acarbose was 12.60 ± 0.78 µM. Lastly, molecular modeling approaches were implemented to predict the binding affinities of compounds against AR and α-glycosidase. In addition, the ADME analysis of the molecules was performed.
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Affiliation(s)
- Yeliz Demir
- Department of Pharmacy Services, Nihat Delibalta Göle Vocational High School, Ardahan University, Ardahan, Turkey
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Turkey
| | - Ümit M Koçyiğit
- Department of Basic Pharmaceutical Sciences, Division of Biochemistry, Faculty of Pharmacy, Cumhuriyet University, Sivas, Turkey
| | - Musa Akkuş
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - Muhammet Serhat Özaslan
- Department of Pharmacy Services, Nihat Delibalta Göle Vocational High School, Ardahan University, Ardahan, Turkey
| | - Hatice Esra Duran
- Department of Biochemistry, Medical School, Kafkas University, Kars, Turkey
| | - Yakup Budak
- Department of Chemistry, Faculty of Arts and Sciences, Gaziosmanpasa University, Tokat, Turkey
| | - Burak Tüzün
- Department of Chemistry, Faculty of Science, Cumhuriyet University, Sivas, Turkey
| | - Meliha B Gürdere
- Department of Chemistry, Faculty of Arts and Sciences, Gaziosmanpasa University, Tokat, Turkey
| | - Mustafa Ceylan
- Department of Chemistry, Faculty of Arts and Sciences, Gaziosmanpasa University, Tokat, Turkey
| | - Seyithan Taysi
- Department of Biochemistry and Clinical Biochemistry, Medical School, Gaziantep University, Gaziantep, Turkey
| | - İlhami Gülçin
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - Şükrü Beydemir
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey.,The Rectorate of Bilecik Şeyh Edebali University, Bilecik, Turkey
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Türkan F, Taslimi P, Abdalrazaq SM, Aras A, Erden Y, Celebioglu HU, Tuzun B, Ağırtaş MS, Gülçin İ. Determination of anticancer properties and inhibitory effects of some metabolic enzymes including acetylcholinesterase, butyrylcholinesterase, alpha-glycosidase of some compounds with molecular docking study. J Biomol Struct Dyn 2020; 39:3693-3702. [DOI: 10.1080/07391102.2020.1768901] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Fikret Türkan
- Health Services Vocational School, Igdır University, Igdır, Turkey
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Turkey
| | | | - Abdülmelik Aras
- Department of Biochemistry, Faculty of Science and Arts, Iğdır University, Iğdır, Turkey
| | - Yavuz Erden
- Department of Molecular Biology and Genetics, Faculty of Science, Bartin University, Bartin, Turkey
| | | | - Burak Tuzun
- Department of Chemistry, Faculty of Science, Cumhuriyet University, Sivas, Turkey
| | - Mehmet Salih Ağırtaş
- Department of Chemistry, Faculty of Science, Van Yuzuncu Yıl University, Van, Turkey
| | - İlhami Gülçin
- Department of Chemistry, Faculty of Science, Ataturk University, Erzurum, Turkey
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12
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Ul-Haq Z, Khan A, Ashraf S, Morales-Bayuelo A. Quantum mechanics and 3D-QSAR studies on thienopyridine analogues: inhibitors of IKKβ. Heliyon 2020; 6:e04125. [PMID: 32566780 PMCID: PMC7298411 DOI: 10.1016/j.heliyon.2020.e04125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/11/2020] [Accepted: 05/29/2020] [Indexed: 01/23/2023] Open
Abstract
Inhibitor of kappa B kinase subunit β (IKKβ) is a main regulator of nuclear factor kappa B (NF-κB) and has received considerable attention as an attractive therapeutic target for the treatment of lung cancer or other inflammatory disease. A group of diversified thienopyridine derivatives exhibited a wide range of biological activity was used to investigate its structural requirements by using DFT and 3D-Quantitative structure activity relationship. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were established using the experimental activity of thienopyridine derivatives. The cross-validation coefficient (q2) values for CoMFA and CoMSIA are 0.671 and 0.647 respectively, were achieved, demonstrating high predictive capability of the model. The contour analysis indicate that presence of hydrophobic and electrostatic field is highly desirable for biological activity. The results indicate that substitution of hydrophobic group with electron withdrawing effect at R4 and R6 position have more possibility to increase the biological activity of thienopyridine derivatives. Subsequently molecular docking and DFT calculation were performed to assess the potency of the compounds.
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Affiliation(s)
- Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Alamgir Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Sajda Ashraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Alejandro Morales-Bayuelo
- Grupo de Investigaciones Básicas y Clínicas de la Universidad del Sinú (GIBACUS), Escuela de Medicina, Universidad del Sinú, Seccional Cartagena de Indias, Colombia
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Jain Pancholi N, Sonker N, Bajpai J, Bajpai AK. Predictions of Drug-Protein Interactions and Study of Magnetically Assisted Release Dynamics of 5-Fluorouracil from Soya Protein-Coated Iron Oxide Core-Shell Nanoparticles. ACS APPLIED BIO MATERIALS 2020; 3:3170-3186. [PMID: 35025360 DOI: 10.1021/acsabm.0c00178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In silico studies were performed using 5-fluorouracil (5-FU) to explore the efficacy of template docking and facilitate designing of drug nanocarrier systems. The binding of human uridine phosphorylase (huPP1) with 5-FU was found to show the following interactions: (1) hydrogen bonds were alleviated by a network of GLN217 and ARG219, (2) hydrophobic interactions were shown by PHE213, THR141, LEU272, and ILE281 (3) positive electrostatic interactions were shown by PHE213, THR141, LEU272, SER142, GLU248, and GLY143. As an experimental supplementation and validation to the adopted computational approach, 5- FU-loaded soya protein-coated iron oxide (SPCIO) core-shell nanoparticles were prepared following microemulsion and co-precipitation techniques and subsequently characterized by FTIR, particle size and zeta potential studies, TEM, XRD, and DSC techniques. Whereas the FTIR spectra confirm the presence of the soya protein and drug 5-FU in the nanoparticles, the zeta potential was found to be suppressed due to the loading of 5-FU. The XRD study confirmed the crystalline nature of the drug-loaded nanoparticles. TEM analysis suggested that the nanoparticles have sizes up to 200 nm and the morphology and size remain almost the same even after loading of the drug 5-FU onto nanoparticles. The soya protein-coated iron oxide nanoparticles demonstrated zero cytotoxicity against fibroblast cells. The controlled release of 5-FU was studied in vitro, and the effects of pH, chemical composition of nanoparticles, extent of drug loading, and simulated biofluids on the controlled release of 5-FU were studied. The swelling of nanoparticles and release of 5-FU were found to increase with increasing strength of the externally applied magnetic field.
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Affiliation(s)
- Nilanjana Jain Pancholi
- Bose Memorial Research Lab Department of Chemistry Government Autonomous Science College, Jabalpur, M.P. 482001, India
| | - Neha Sonker
- Bose Memorial Research Lab Department of Chemistry Government Autonomous Science College, Jabalpur, M.P. 482001, India
| | - Jaya Bajpai
- Bose Memorial Research Lab Department of Chemistry Government Autonomous Science College, Jabalpur, M.P. 482001, India
| | - Anil Kumar Bajpai
- Bose Memorial Research Lab Department of Chemistry Government Autonomous Science College, Jabalpur, M.P. 482001, India
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Biofilm inhibition and DNA binding studies of isoxazole-triazole conjugates in the development of effective anti-bacterial agents. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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15
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Gagic Z, Ruzic D, Djokovic N, Djikic T, Nikolic K. In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs. Front Chem 2020; 7:873. [PMID: 31970149 PMCID: PMC6960140 DOI: 10.3389/fchem.2019.00873] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Rational drug design implies usage of molecular modeling techniques such as pharmacophore modeling, molecular dynamics, virtual screening, and molecular docking to explain the activity of biomolecules, define molecular determinants for interaction with the drug target, and design more efficient drug candidates. Kinases play an essential role in cell function and therefore are extensively studied targets in drug design and discovery. Kinase inhibitors are clinically very important and widely used antineoplastic drugs. In this review, computational methods used in rational drug design of kinase inhibitors are discussed and compared, considering some representative case studies.
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Affiliation(s)
- Zarko Gagic
- Department of Pharmaceutical Chemistry, Faculty of Medicine, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Nemanja Djokovic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Teodora Djikic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
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16
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Zhou P, Hua F, Wang X, Huang JL. Therapeutic potential of IKK-β inhibitors from natural phenolics for inflammation in cardiovascular diseases. Inflammopharmacology 2020; 28:19-37. [PMID: 31894515 DOI: 10.1007/s10787-019-00680-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022]
Abstract
Cardiovascular disease (CVDs) is a chronic disease with the highest morbidity and mortality in the world. Previous studies have suggested that preventing inflammation serves an efficient role in protection against cardiovascular diseases. Modulation of IKK-β activity can be used to treat and control CVDs associated with chronic inflammation, which targets the phosphorylation of IκB following the release of the RelA complex, and then translocates to the nucleus, eventually triggering the transcription of several genes that induce chemokines, cytokines, and adhesion molecules. Most importantly, the IκB kinase (IKK) complex is involved in transcriptional activation by phosphorylating the inhibitory molecule IkBα, enabling activation of NF-κB. Phenolic compounds possess cardioprotective potential that may be related to modulating inflammatory responses involved in CVDs. The SystemsDock analysis was used to explore whether 38 active compounds inhibit IKK-β activity based on literature. Docking results showed that the top docking score of three chemical compounds were icariin, salvianolic acid B, and plantainoside D in all compounds. Icariin, salvianolic acid B, and plantainoside D are the most promising IKKβ inhibitors. These phytochemicals could be helpful to find the lead compounds on designing and developing novel cardioprotective agents.
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Affiliation(s)
- Peng Zhou
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, People's Republic of China. .,Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, 230012, People's Republic of China. .,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, People's Republic of China.
| | - Fang Hua
- Pharmacy School, Anhui Xinhua University, Hefei, 230088, People's Republic of China.,Natural Products Laboratory, International Joint Lab of Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Xiang Wang
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, People's Republic of China.,Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, 230012, People's Republic of China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, People's Republic of China
| | - Jin-Ling Huang
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, People's Republic of China. .,Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, 230012, People's Republic of China. .,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, People's Republic of China.
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Tüzün B, Saripinar E. Molecular docking and 4D-QSAR model of methanone derivatives by electron conformational-genetic algorithm method. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2019. [DOI: 10.1007/s13738-019-01835-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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18
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Wang J, Peng W, Li X, Fan W, Wei D, Wu B, Fan L, Wu C, Li L. Towards to potential 2-cyano-pyrimidines cathepsin-K inhibitors: An in silico design and screening research based on comprehensive application of quantitative structure–activity relationships, molecular docking and ADMET prediction. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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19
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Phytochemicals as potential IKK-β inhibitor for the treatment of cardiovascular diseases in plant preservation: terpenoids, alkaloids, and quinones. Inflammopharmacology 2019; 28:83-93. [DOI: 10.1007/s10787-019-00640-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/27/2019] [Indexed: 12/11/2022]
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