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Ja'afaru SC, Uzairu A, Chandra A, Sallau MS, Ndukwe GI, Ibrahim MT, Qamar I. Ligand based-design of potential schistosomiasis inhibitors through QSAR, homology modeling, molecular dynamics, pharmacokinetics, and DFT studies. J Taibah Univ Med Sci 2024; 19:429-446. [PMID: 38440085 PMCID: PMC10909894 DOI: 10.1016/j.jtumed.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/03/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
Objectives Schistosomiasis, a neglected tropical disease, is a leading cause of mortality in affected geographic areas. Currently, because no vaccine for schistosomiasis is available, control measures rely on widespread administration of the drug praziquantel (PZQ). The mass administration of PZQ has prompted concerns regarding the emergence of drug resistance. Therefore, new therapeutic targets and potential compounds are necessary to combat schistosomiasis. Methods Twenty-four potent derivatives of PZQ were optimized via density functional theory (DFT) at the B3LYP/6-31G∗ level. Quantitative structureactivity relationship (QSAR) models were generated and statistically validated, and a lead candidate was selected to develop therapeutic options with improved efficacy against schistosomiasis. The biological and binding energies of the designed compounds were evaluated. In addition, molecular dynamics; drug-likeness; absorption, distribution, metabolism, excretion, and toxicity (ADMET); and DFT studies were performed on the newly designed compounds. Results Five QSAR models were generated, among which model 1 had favorable validation parameters (R2train: 0.957, R2adj: 0.941, LOF: 0.101, Q2cv: 0.906, and R2test: 0.783) and was chosen to identify a lead candidate. Other statistical parameters for the chosen model included variance inflation factor values ranging from 1.242 to 1.678, and a Y-scrambling coefficient (cRp2) of 0.747. Five new compounds were designed with improved predicted activity (ranging from 5.081 to 7.022) surpassing those of both the lead compound and PZQ (predicted pEC50 of 5.545). Molecular dynamics simulation revealed high binding affinity of the proposed compounds toward the target receptor. ADMET and drug-likeness assessments indicated adherence to Lipinski's rule of five criteria, thereby suggesting pharmacological and oral safety. In addition, DFT analysis indicated resistance to electronic alteration during chemical reactions. Conclusion The proposed compounds exhibited potential drug characteristics, thus indicating their suitability for further investigation to enhance schistosomiasis treatment options.
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Affiliation(s)
- Saudatu C. Ja'afaru
- Department of Chemistry, Ahmadu Bello University Zaria, Nigeria
- Department of Chemistry, Aliko Dangote University of Science and Technology, Wudil, Kano, Nigeria
| | - Adamu Uzairu
- Department of Chemistry, Ahmadu Bello University Zaria, Nigeria
| | - Anshuman Chandra
- School of Physical Sciences, JawaharLal Nehru University, New Delhi, India
| | | | | | | | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
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Abchir O, Khedraoui M, Nour H, Yamari I, Errougui A, Samadi A, Chtita S. Integrative Approach for Designing Novel Triazole Derivatives as α-Glucosidase Inhibitors: QSAR, Molecular Docking, ADMET, and Molecular Dynamics Investigations. Pharmaceuticals (Basel) 2024; 17:261. [PMID: 38399476 PMCID: PMC10892212 DOI: 10.3390/ph17020261] [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: 01/17/2024] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
In response to the increasing prevalence of diabetes mellitus and the limitations associated with the current treatments, there is a growing need to develop novel medications for this disease. This study is focused on creating new compounds that exhibit a strong inhibition of alpha-glucosidase, which is a pivotal enzyme in diabetes control. A set of 33 triazole derivatives underwent an extensive QSAR analysis, aiming to identify the key factors influencing their inhibitory activity against α-glucosidase. Using the multiple linear regression (MLR) model, seven promising compounds were designed as potential drugs. Molecular docking and dynamics simulations were employed to shed light on the mode of interaction between the ligands and the target, and the stability of the obtained complexes. Furthermore, the pharmacokinetic properties of the designed compounds were assessed to predict their behavior in the human body. The binding free energy was also calculated using MMGBSA method and revealed favorable thermodynamic properties. The results highlighted three novel compounds with high biological activity, strong binding affinity to the target enzyme, and suitability for oral administration. These results offer interesting prospects for the development of effective and well-tolerated medications against diabetes mellitus.
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Affiliation(s)
- Oussama Abchir
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Meriem Khedraoui
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Hassan Nour
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Imane Yamari
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Abdelkbir Errougui
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Abdelouahid Samadi
- Department of Chemistry, College of Science, United Arab Emirates University (UAEU), 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 7955, Morocco; (O.A.); (M.K.); (A.E.)
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Abchir O, Yamari I, Shtaiwi AM, Nour H, Kouali ME, Talbi M, Errougui A, Chtita S. Insights into the inhibitory potential of novel hydrazinyl thiazole-linked indenoquinoxaline against alpha-amylase: a comprehensive QSAR, pharmacokinetic, and molecular modeling study. J Biomol Struct Dyn 2024:1-18. [PMID: 38305802 DOI: 10.1080/07391102.2024.2310778] [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: 10/23/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024]
Abstract
The rising prevalence of diabetes necessitates the development of novel drugs, especially given the side effects associated with current medications like Acarbose and Voglibose. A series of 36 Hydrazinyl thiazole-linked indenoquinoxaline derivatives with notable activity against alpha-amylase were studied. To create a molecular model predicting alpha-amylase activity, a QSAR study was performed on these compounds. Molecular descriptors were calculated using Chem3D and Gaussian software and then correlated with their IC50 biological activities to form a dataset. This model data was refined using PCA and modeled with MLR. The model's performance was statistically verified (R2 =0.800; R adj 2 = 0.767; R cv 2 = 0.651) and its applicability domain was defined. It was predicted to possess high predictive power (R test 2 = 0.872). Based on this, new compounds were proposed, and their activities were predicted using the developed model. Additionally, their binding ability to the biological target was studied through molecular docking and dynamics. Their pharmacokinetics were also evaluated using ADMET predictions. Two designed compounds named AE and AB emerged as particularly promising, displaying properties that suggest substantial therapeutic potential and they can form stable complexes into the binding pocket of alpha-amylase enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Oussama Abchir
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Imane Yamari
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | | | - Hassan Nour
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mhammed El Kouali
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mohammed Talbi
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Abdelkbir Errougui
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
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Bouhadi M, Abchir O, Yamari I, El Hamsas El Youbi A, Azgaoui A, Chtita S, El Hajjouji H, El Kouali M, Talbi M, Fougrach H. Genotoxic effects and mitosis aberrations of chromium (VI) on root cells of Vicia faba and its molecular docking analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108361. [PMID: 38237423 DOI: 10.1016/j.plaphy.2024.108361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 03/16/2024]
Abstract
Like other heavy metals, Cr (VI) is a powerful carcinogen and mutagen agent. Its toxic effects on plants are well considered. In order to elucidate its adverse effects, the present work aims to study the mitosis aberrations of Cr (VI) on the Vicia faba root-cells and its molecular docking analysis to understand the genotoxicity mechanisms. In-vivo, Vicia faba plants were exposed to 50 and 100 μM Cr (VI) for 48 h. In-silico, molecular docking and molecular dynamics simulation were used to study the interactions between dichromate and tubulin tyrosine ligase T2R-TTL (PDBID: 5XIW) with reference to Colchicine (microtubule inhibitor). According to our results, Cr (VI) affects growth and cell division and also induces many mitosis aberrations such as chromosome sticking, anaphase/telophase bridges, lagging chromosomes and fragmentation during all phases of mitosis. On the one hand, Cr (VI) reduces mitotic index and promotes micronuclei induction. The in-silico results showed that dichromate establishes very strong bonds at the binding site of the tubulin tyrosine ligase T2R-TTL, with a binding affinity of -5.17 Kcal/Mol and an inhibition constant of 163.59 μM. These interactions are similar to those of colchicine with this protein, so dichromate could be a very potent inhibitor of this protein's activity. TTL plays a fundamental role in the tyrosination/detyrosination of tubulin, which is crucial to the regulation of the microtubule cytoskeleton. Its inhibition leads to the appearance of many morphogenic abnormalities such as mitosis aberrations. In conclusion, our data confirm the highest genotoxicity effects of Cr (VI) on Vicia faba root-cells.
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Affiliation(s)
- Mohammed Bouhadi
- Laboratory of Ecology and Environment, Faculty of Sciences Ben M'sick, Hassan II University of Casablanca, B.P 7955, Casablanca, Morocco; Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'sick, Hassan II University of Casablanca, B.P 7955, Casablanca, Morocco.
| | - Oussama Abchir
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'sick, Hassan II University of Casablanca, B.P 7955, Casablanca, Morocco
| | - Imane Yamari
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'sick, Hassan II University of Casablanca, B.P 7955, Casablanca, Morocco
| | - Amal El Hamsas El Youbi
- Laboratory of Biology and Health, Faculty of Sciences Ben M'sick, Hassan II University of Casablanca, B.P 7955, Casablanca, Morocco
| | - Anas Azgaoui
- Ibn Sina University Hospital Center, Faculty of Medicine and Pharmacy of Rabat, Mohammed V University, Rabat, Morocco
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'sick, Hassan II University of Casablanca, B.P 7955, Casablanca, Morocco
| | - Houda El Hajjouji
- Laboratory of Ecology and Environment, Faculty of Sciences Ben M'sick, Hassan II University of Casablanca, B.P 7955, Casablanca, Morocco
| | - M'hammed El Kouali
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'sick, Hassan II University of Casablanca, B.P 7955, Casablanca, Morocco
| | - Mohammed Talbi
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'sick, Hassan II University of Casablanca, B.P 7955, Casablanca, Morocco
| | - Hassan Fougrach
- Laboratory of Ecology and Environment, Faculty of Sciences Ben M'sick, Hassan II University of Casablanca, B.P 7955, Casablanca, Morocco
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Riaz S, Siddiqui S, Abul Qais F, Mateen S, Moin S. Inhibitory effect of baicalein against glycation in HSA: an in vitro approach. J Biomol Struct Dyn 2024; 42:935-947. [PMID: 37098813 DOI: 10.1080/07391102.2023.2201856] [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: 01/25/2023] [Accepted: 03/22/2023] [Indexed: 04/27/2023]
Abstract
Hyperglycaemia accelerates the aging process significantly. Diabetes problems can be mitigated by inhibiting glycation. To learn more about glycation and antiglycation mediated by methyl glyoxal and baicalein, we studied human serum albumin as a model protein. A Methylglyoxal (MGO) incubation period of seven days at 37 degrees Celsius induced glycation of Human Serum Albumin.s Hyperchromicity, decreased tryptophan and intrinsic fluorescence, increased AGE-specific fluorescence, and reduced mobility were all seen in glycated human serum albumin (MGO-HSA) in sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). Fourier transform infrared spectroscopy (FT-IR) and then far ultraviolet dichroism were used to detect secondary and tertiary structural perturbations (CD). The Congo red assay (CR), scanning electron microscopy (SEM), and transmission electron microscopy (TEM) all verified the presence of amyloid-like clumps. Structure (carbonyl groups on ketoamine moieties) (CO), physiological problems including diabetes mellitus, and cardiovascular disease, etc. are linked to the structural and functional changes in glycated HSA, as proven by these studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sana Riaz
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, India
| | - Sana Siddiqui
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, India
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
| | - Somaiya Mateen
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, India
| | - Shagufta Moin
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, India
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Asen ND, Udenigwe CC, Aluko RE. Quantitative Structure-Activity Relationship Modeling of Pea Protein-Derived Acetylcholinesterase and Butyrylcholinesterase Inhibitory Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16323-16330. [PMID: 37856319 DOI: 10.1021/acs.jafc.3c04880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
The aim of this work was to determine the structural requirements for peptides that inhibit acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) activities. The data set used consisted of 19 oligopeptides that had been identified through mass spectrometry analysis of enzymatic digests of yellow field pea protein. The structure-function relationship was analyzed by partial least squares regression using the 5z scores. A nine-component model was created from 16 peptides for AChE inhibitory peptides (Q2 = 67.2% and R2 = 0.9974), while three data sets were prepared for BuChE inhibitory peptides to improve the quality of the models (Q2 = 26.7-46.4% and R2 = 0.9577-0.9958). The most active peptides from the PLS models have threonine, leucine, alanine, and valine at the N terminal, asparagine, histidine, proline, and arginine at the second position, with aspartic acid and serine at the third, and arginine at the C terminal.
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Affiliation(s)
- Nancy D Asen
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Chibuike C Udenigwe
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Rotimi E Aluko
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- Richardson Centre for Food Technology and Research, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Nguyen HD. In silico identification of novel heterocyclic compounds combats Alzheimer's disease through inhibition of butyrylcholinesterase enzymatic activity. J Biomol Struct Dyn 2023:1-21. [PMID: 37723904 DOI: 10.1080/07391102.2023.2259482] [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: 03/31/2023] [Accepted: 09/09/2023] [Indexed: 09/20/2023]
Abstract
Increasing evidence indicates that heterocyclic molecules possess properties against butyrylcholinesterase (BChE) enzymatic activity, which is a potential therapeutic target for Alzheimer's disease (AD). Thus, this study aimed to further evaluate the relationship between heterocyclic molecules and their biological activities. A dataset of 38 selective and potent heterocyclic compounds (-log[the half‑maximal inhibitory concentration (pIC50)]) values ranging from 8.02 to 10.05) was applied to construct a quantitative structure-activity relationship (QSAR) study, including Bayesian model average (BMA), artificial neural network (ANN), multiple nonlinear regression (MNLR), and multiple linear regression (MLR) models. Four models met statistical acceptance in internal and external validation. The ANN model was superior to other models in predicting the pIC50 of the outcome. The descriptors put into the models were found to be comparable with the target-ligand complex X-ray structures, making these models interpretable. Three selected molecules possess drug-like properties (pIC50 values ranged from 9.19 to 9.54). The docking score between candidates and the BChE receptor (RCSB ID 6EYF) ranged from -8.4 to -9.0 kcal/mol. Remarkably, the pharmacokinetics, biological activities, molecular dynamics, and physicochemical properties of compound 18 (C20H22N4O, pIC50 value = 9.33, oxadiazole derivative group) support its protective effects on AD treatment due to its non-toxic nature, non-carcinogen, cholinergic nature, capability to penetrate the blood-brain barrier, and high gastrointestinal absorption.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hai Duc Nguyen
- Department of Pharmacy, College of Pharmacy, Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, South Korea
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Daoui O, Nour H, Abchir O, Elkhattabi S, Bakhouch M, Chtita S. A computer-aided drug design approach to explore novel type II inhibitors of c-Met receptor tyrosine kinase for cancer therapy: QSAR, molecular docking, ADMET and molecular dynamics simulations. J Biomol Struct Dyn 2023; 41:7768-7785. [PMID: 36120976 DOI: 10.1080/07391102.2022.2124456] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/09/2022] [Indexed: 10/14/2022]
Abstract
Small molecules such as 4-phenoxypyridine derivatives have remarkable inhibitory activity against c-Met enzymatic activity and proliferation of cancer cell lines. Since there is a relationship between structure and biological activity of these molecules, these little compounds may have great potential for clinical pharmaceutical use against various types of cancer caused by c-Met activity. The purpose of this study was to remodel the structures of 4-phenoxypyridine derivatives to achieve strong inhibitory activity against c-Met and provide favorable pharmacokinetic properties for drug design and discovery. Therefore, this paper describes the structure-activity relationship and the rationalization of appropriate pharmacophore sites to improve the biological activity of the investigated molecules, based on bioinformatics techniques represented by a computer-aided drug design approach. Accordingly, robust and reliable 3D-QSAR models were developed based on CoMFA and CoMSIA techniques. As a result, 46 lead molecules were designed and their biological and pharmacokinetic activities were predicted in silico. Screening filters by 3D-QSAR, Molecular Docking, drug-like and ADME-Tox identified the computer-designed compounds P54 and P55 as the best candidates to achieve high inhibition of c-Met enzymatic activity compared to the synthesized template compound T14. Finally, through molecular dynamics simulations, the structural properties and dynamics of c-Met free and complex (PDB code: 3LQ8) in the presence of 4-phenoxypyridine-derived compounds in an aqueous environment are discussed. Overall, the rectosynthesis of the designed drug inhibitors (P54 and P55) and their in vitro and in vivo bioactivity evaluation may be attractive for design and discovery of novel drug effective to inhibit c-Met enzymatic activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ossama Daoui
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez, Morocco
| | - Hassan Nour
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Oussama Abchir
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Souad Elkhattabi
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez, Morocco
| | - Mohamed Bakhouch
- Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
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Moulishankar A, Thirugnanasambandam S. Quantitative structure activity relationship (QSAR) modeling study of some novel thiazolidine 4-one derivatives as potent anti-tubercular agents. J Recept Signal Transduct Res 2023; 43:83-92. [PMID: 37990804 DOI: 10.1080/10799893.2023.2281671] [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: 05/15/2023] [Accepted: 09/03/2023] [Indexed: 11/23/2023]
Abstract
This study aims to develop a QSAR model for Antitubercular activity. The quantitative structure-activity relationship (QSAR) approach predicted the thiazolidine-4-ones derivative's Antitubercular activity. For the QSAR study, 53 molecules with Antitubercular activity on H37Rv were collected from the literature. Compound structures were drawn by ACD/Labs ChemSketch. The energy minimization of the 2D structure was done using the MM2 force field in Chem3D pro. PaDEL Descriptor software was used to construct the molecular descriptors. QSARINS software was used in this work to develop the 2D QSAR model. A series of thiazolidine 4-one with MIC data were taken from the literature to develop the QSAR model. These compounds were split into a training set (43 compounds) and a test set (10 compounds). The PaDEL software calculated 2300 descriptors for this series of thiazolidine 4-one derivatives. The best predictive Model 4, which has R2 of 0.9092, R2adj of 0.8950 and LOF parameter of 0.0289 identify a preferred fit. The QSAR study resulted in a stable, predictive, and robust model representing the original dataset. In the QSAR equation, the molecular descriptor of MLFER_S, GATSe2, Shal, and EstateVSA 6 positively correlated with Antitubercular activity. While the SpMAD_Dzs 6 is negatively correlated with Antitubercular activity. The high polarizability, Electronegativities, Surface area contributions and number of Halogen atoms in the thiazolidine 4-one derivatives will increase the Antitubercular activity.
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Affiliation(s)
- Anguraj Moulishankar
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu 603203, India
| | - Sundarrajan Thirugnanasambandam
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu 603203, India
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Moussaoui M, Baassi M, Baammi S, Soufi H, Salah M, Daoud R, El Allali A, Belghiti ME, Belaaouad S. In silico design of novel CDK2 inhibitors through QSAR, ADMET, molecular docking and molecular dynamics simulation studies. J Biomol Struct Dyn 2023; 41:13646-13662. [PMID: 37203327 DOI: 10.1080/07391102.2023.2212304] [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: 08/23/2022] [Accepted: 02/04/2023] [Indexed: 05/20/2023]
Abstract
The present study aims to investigate about the quantitative structure-activity relationship (QSAR) of a series of Thiazole derivatives reported as anticancer agents (hepatocellular carcinoma), using principally the electronic descriptors calculated by the DFT method and by applying the multiple linear regression method. The developed model showed good statistical parameters (R2 = 0.725, R2adj = 0.653, MSE = 0.060, R2test = 0.827, Q2cv = 0.536). The energy EHOMO orbital, electronic energy (TE), shape coefficient (I), number of rotatable bonds (NROT), and index of refraction (n) were revealed to be the main descriptors influencing the anti-cancer activity. Further, new Thiazole derivatives have been designed and their activities and pharmacokinetic properties have been predicted using the validated QSAR model. The designed molecules were then assessed to molecular docking (MD), and molecular dynamic (MDs) simulation accompanied by the calculation of the binding affinity using MMPBSA script according to 100 ns a simulation trajectory, to study both their affinity and their stability towards CDK2 as a target protein for the cancer disease treatment. This research concluded with the identification of four new CDK2 inhibitors which are A1, A3, A5, and A6 showing good pharmacokinetic properties. The MDs results revealed that the newly designed compound A5 remained stable in the active center of the discovered CDK2 protein, indicating its potential as a novel inhibitor for the treatment of hepatocellular carcinoma. The current findings may eventually contribute to the development of robust CDK2 inhibitors in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed Moussaoui
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mouna Baassi
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Hatim Soufi
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mohammed Salah
- Team of Chemoinformatics Research and Spectroscopy and Quantum Chemistry, Department of chemistry, Faculty of Science, University Chouaib Doukkali, El Jadida, Morocco
| | - Rachid Daoud
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Achraf El Allali
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - M E Belghiti
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
- Laboratory of Nernest Technology, Sherbrook, Quebec, Canada
| | - Said Belaaouad
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
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Alomar SY. Studying the Mechanism of Interaction of Doxofylline with Human Lysozyme: A Biophysical and In Silico Approach. Molecules 2023; 28:molecules28083462. [PMID: 37110695 PMCID: PMC10146846 DOI: 10.3390/molecules28083462] [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: 12/29/2022] [Revised: 03/29/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023] Open
Abstract
In this study, multiple spectroscopic and computational methods were utilized to investigate the binding mechanism of doxofylline with lysozyme. The in vitro methods were used to obtain the binding kinetics and thermodynamics. UV-vis spectroscopy indicated the formation of complex between doxofylline and lysozyme. The Gibb's free energy and binding constant from UV-vis data was obtained as -7.20 kcal M-1 and 1.929 × 105 M-1, respectively. Doxofylline successfully quenched the fluorescence of lysozyme, confirming the formation of complex. The kq and Ksv values for the quenching of lysozyme's fluorescence by doxofylline were 5.74 × 1011 M-1 s-1 and 3.32 × 103 M-1, respectively. These values signified a moderate binding affinity between doxofylline and lysozyme. In synchronous spectroscopy, red shifts were observed for indicating the changes in microenvironment of lysozyme following the binding of doxofylline. The secondary structural analysis was determined using circular dichroism (CD) which revealed an increase in % α-helical as a result of doxofylline interaction. The binding affinity and flexibility of lysozyme upon complexation have been revealed via molecular docking and molecular dynamic (MD) simulations, respectively. According to the many parameters of the MD simulation, the lysozyme-doxofylline complex was stable under physiological conditions. All during the simulation time, hydrogen bonds were continuously present. The MM-PBSA binding energy for lysozyme and doxofylline binding was found to be -30.55 kcal mol-1.
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Affiliation(s)
- Suliman Yousef Alomar
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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12
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Daoui O, Elkhattabi S, Bakhouch M, Belaidi S, Bhandare RR, Shaik AB, Mali SN, Chtita S. Cyclohexane-1,3-dione Derivatives as Future Therapeutic Agents for NSCLC: QSAR Modeling, In Silico ADME-Tox Properties, and Structure-Based Drug Designing Approach. ACS OMEGA 2023; 8:4294-4319. [PMID: 36743017 PMCID: PMC9893467 DOI: 10.1021/acsomega.2c07585] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 12/29/2022] [Indexed: 05/20/2023]
Abstract
The abnormal expression of the c-Met tyrosine kinase has been linked to the proliferation of several human cancer cell lines, including non-small-cell lung cancer (NSCLC). In this context, the identification of new c-Met inhibitors based on heterocyclic small molecules could pave the way for the development of a new cancer therapeutic pathway. Using multiple linear regression (MLR)-quantitative structure-activity relationship (QSAR) and artificial neural network (ANN)-QSAR modeling techniques, we look at the quantitative relationship between the biological inhibitory activity of 40 small molecules derived from cyclohexane-1,3-dione and their topological, physicochemical, and electronic properties against NSCLC cells. In this regard, screening methods based on QSAR modeling with density-functional theory (DFT) computations, in silico pharmacokinetic/pharmacodynamic (ADME-Tox) modeling, and molecular docking with molecular electrostatic potential (MEP) and molecular mechanics-generalized Born surface area (MM-GBSA) computations were used. Using physicochemical (stretch-bend, hydrogen bond acceptor, Connolly molecular area, polar surface area, total connectivity) and electronic (total energy, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels) molecular descriptors, compound 6d is identified as the optimal scaffold for drug design based on in silico screening tests. The computer-aided modeling developed in this study allowed us to design, optimize, and screen a new class of 36 small molecules based on cyclohexane-1,3-dione as potential c-Met inhibitors against NSCLC cell growth. The in silico rational drug design approach used in this study led to the identification of nine lead compounds for NSCLC therapy via c-Met protein targeting. Finally, the findings are validated using a 100 ns series of molecular dynamics simulations in an aqueous environment on c-Met free and complexed with samples of the proposed lead compounds and Foretinib drug.
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Affiliation(s)
- Ossama Daoui
- Laboratory
of Engineering, Systems and Applications, National School of Applied
Sciences, Sidi Mohamed Ben Abdellah-Fez
University, BP Box 72, Fez30000, Morocco
| | - Souad Elkhattabi
- Laboratory
of Engineering, Systems and Applications, National School of Applied
Sciences, Sidi Mohamed Ben Abdellah-Fez
University, BP Box 72, Fez30000, Morocco
| | - Mohamed Bakhouch
- Laboratory
of Bioorganic Chemistry, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, P.O. Box 24, 24000El Jadida, Morocco
| | - Salah Belaidi
- Group
of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra,
BP 145, Biskra707000, Algeria
| | - Richie R. Bhandare
- Department
of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Ajman University, Ajman346, United Arab Emirates
- Center of Medical and Bio-allied
Health Sciences Research, Ajman University, Ajman P.O. Box 340, 346, United Arab Emirates
| | - Afzal B. Shaik
- St. Mary’s
College of Pharmacy, St. Mary’s Group
of Institutions Guntur, Affiliated to Jawaharlal Nehru Technological
University Kakinada, Chebrolu, Guntur, Andhra Pradesh522212, India
| | - Suraj N. Mali
- Department
of Pharmacy, Government College of Pharmacy, Karad, Affiliated to Shivaji University, Kolhapur, Maharashtra415124, India
| | - Samir Chtita
- Laboratory
of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca7955, Morocco
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13
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Chalkha M, Nour H, Chebbac K, Nakkabi A, Bahsis L, Bakhouch M, Akhazzane M, Bourass M, Chtita S, Bin Jardan YA, Augustyniak M, Bourhia M, Aboul-Soud MA, El Yazidi M. Synthesis, Characterization, DFT Mechanistic Study, Antimicrobial Activity, Molecular Modeling, and ADMET Properties of Novel Pyrazole-isoxazoline Hybrids. ACS OMEGA 2022; 7:46731-46744. [PMID: 36570248 PMCID: PMC9773794 DOI: 10.1021/acsomega.2c05788] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
A series of new heterocycle hybrids incorporating pyrazole and isoxazoline rings was successfully synthesized, characterized, and evaluated for their antimicrobial responses. The synthesized compounds were obtained utilizing N-alkylation and 1,3-dipolar cycloaddition reactions, as well as their structures were established through spectroscopic methods and confirmed by mass spectrometry. To get more light on the regioselective synthesis of new hybrid compounds, mechanistic studies were performed using DFT calculations with B3LYP/6-31G(d,p) basis set. Additionally, the results of the preliminary screening indicate that some of the examined hybrids showed potent antimicrobial activity, compared to standard drugs. The results confirm that the antimicrobial activity is strongly dependent on the nature of the substituents linked pyrazole and isoxazoline rings. Furthermore, molecular docking studies were conducted to highlight the interaction modes between the investigated hybrid compounds and the Escherichia coli and Candida albicans receptors. Notably, the results demonstrate that the investigated compounds have strong protein binding affinities. The stability of the formed complexes by the binding between the hybrid compound 6c, and the target proteins was also confirmed using a 100 ns molecular dynamics simulation. Finally, the prediction of ADMET properties suggests that almost all hybrid compounds possess good pharmacokinetic profiles and no signs of observed toxicity, except for compounds 6e, 6f, and 6g.
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Affiliation(s)
- Mohammed Chalkha
- Engineering
Laboratory of Organometallic, Molecular, Materials and Environment,
Faculty of Sciences Dhar EL Mahraz, Sidi
Mohamed Ben Abdellah University, P.O. Box 1796, 30000 Fez, Morocco
| | - Hassan Nour
- Laboratory
of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, P.O. Box 7955, Casablanca, Morocco
| | - Khalid Chebbac
- Laboratory
of Biotechnology Conservation and Valorisation of Natural Resources,
Faculty of Sciences Dhar El Mahraz, Sidi
Mohammed Ben Abdallah University, P.O.
Box 1796, Fez 30000, Morocco
| | - Asmae Nakkabi
- Engineering
Laboratory of Organometallic, Molecular, Materials and Environment,
Faculty of Sciences Dhar EL Mahraz, Sidi
Mohamed Ben Abdellah University, P.O. Box 1796, 30000 Fez, Morocco
| | - Lahoucine Bahsis
- Laboratory
of Analytical and Molecular Chemistry, Polydisciplinary Faculty, Cadi Ayyad University, P.O. Box 4162, Safi 46000, Morocco
- Department
of Chemistry, Faculty of Sciences of El Jadida, Chouaïb Doukkali University,
P.O. Box 20, El Jadida 24000, Morocco
| | - Mohamed Bakhouch
- Laboratory
of Bioorganic Chemistry, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, P.O. Box 24, El Jadida 24000, Morocco
| | - Mohamed Akhazzane
- Engineering
Laboratory of Organometallic, Molecular, Materials and Environment,
Faculty of Sciences Dhar EL Mahraz, Sidi
Mohamed Ben Abdellah University, P.O. Box 1796, 30000 Fez, Morocco
- Cité
de l’innovation, Université
Sidi Mohamed Ben Abdellah, Route Immouzer, P.O. Box 2626, 30000 Fez, Morocco
| | - Mohamed Bourass
- Université
de Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, 351 Cours de la Libération, F-33405 Talence, Cédex France
| | - Samir Chtita
- Laboratory
of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, P.O. Box 7955, Casablanca, Morocco
| | - Yousef A. Bin Jardan
- Department
of Pharmaceutics, College of Pharmacy, King
Saud University, 11451 Riyadh, Saudi Arabia
| | - Maria Augustyniak
- Institute
of Biology, Biotechnology and Environmental Protection, Faculty of
Natural Sciences, University of Silesia
in Katowice, Bankowa 9, 40-007 Katowice, Poland
| | - Mohammed Bourhia
- Higher
Institute of Nursing Professions and Technical Health, Laayoune 70000, Morocco
| | - Mourad A.M. Aboul-Soud
- Department
of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University,
P.O. Box 10219, Riyadh 11433, Saudi Arabia
| | - Mohamed El Yazidi
- Engineering
Laboratory of Organometallic, Molecular, Materials and Environment,
Faculty of Sciences Dhar EL Mahraz, Sidi
Mohamed Ben Abdellah University, P.O. Box 1796, 30000 Fez, Morocco
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14
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Nour H, Daoui O, Abchir O, ElKhattabi S, Belaidi S, Chtita S. Combined computational approaches for developing new anti-Alzheimer drug candidates: 3D-QSAR, molecular docking and molecular dynamics studies of liquiritigenin derivatives. Heliyon 2022; 8:e11991. [PMID: 36544815 PMCID: PMC9761610 DOI: 10.1016/j.heliyon.2022.e11991] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
Butyrylcholinesterase is an acetylcholine-degrading enzyme involved in the memorization process, which is becoming an interesting target for the symptomatic treatment of Alzheimer's disease. In the present investigation, the structure-activity relationship of a set of Liquiritigenin derivatives recently revealed to be Butyrylcholinesterase inhibitors was studied basing on comparative field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMISA). As a result, performant models with high predictive capability have been developed (CoMFA model: R2 = 0.91, Q2 = 0.62, R2 pred = 0.85; CoMISA model: R2 = 0.92, Q2 = 0.59, R2 pred = 0.83) and implemented to design new Liquiritigenin derivatives with improved activity. Besides, the affinity of the designed derivatives towards the active site of Butyrylcholinesterase, was confirmed by molecular docking and molecular dynamics studies. Moreover, they exhibited good pharmacokinetics properties. Accordingly, the outcomes of the present investigations can provide important direction for the development of new anti-Alzheimer's drug candidates.
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Affiliation(s)
- Hassan Nour
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, 7955, Morocco
| | - Ossama Daoui
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, BP 72, Fez, Morocco
| | - Oussama Abchir
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, 7955, Morocco
| | - Souad ElKhattabi
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, BP 72, Fez, Morocco
| | - Salah Belaidi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, BP 145, Biskra 707000, Algeria
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, 7955, Morocco,Corresponding author.
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15
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Nour H, Abdou A, Belaidi S, Jamal J, Elmakssoudi A, Dakir M, Chtita S. Discovery of promising cholinesterase inhibitors for Alzheimer's disease treatment through DFT, docking, and molecular dynamics studies of eugenol derivatives. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Hassan Nour
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik Hassan II University of Casablanca Casablanca Morocco
| | - Achraf Abdou
- Laboratory of Organic Synthesis, Extraction and Valorization, Department of Chemistry, Faculty of Sciences Ain Chock Hassan II University of Casablanca Casablanca Morocco
| | - Salah Belaidi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory University of Biskra Biskra Algeria
| | - JamalEddine Jamal
- Laboratory of Organic Synthesis, Extraction and Valorization, Department of Chemistry, Faculty of Sciences Ain Chock Hassan II University of Casablanca Casablanca Morocco
| | - Abdelhakim Elmakssoudi
- Laboratory of Organic Synthesis, Extraction and Valorization, Department of Chemistry, Faculty of Sciences Ain Chock Hassan II University of Casablanca Casablanca Morocco
| | - Mohamed Dakir
- Laboratory of Organic Synthesis, Extraction and Valorization, Department of Chemistry, Faculty of Sciences Ain Chock Hassan II University of Casablanca Casablanca Morocco
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik Hassan II University of Casablanca Casablanca Morocco
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