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Mettai M, Daoud I, Mesli F, Kenouche S, Melkemi N, Kherachi R, Belkadi A. Molecular docking/dynamics simulations, MEP analysis, bioisosteric replacement and ADME/T prediction for identification of dual targets inhibitors of Parkinson's disease with novel scaffold. In Silico Pharmacol 2023; 11:3. [PMID: 36687301 PMCID: PMC9852416 DOI: 10.1007/s40203-023-00139-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Monoamine oxidase B and Adenosine A2A receptors are used as key targets for Parkinson's disease. Recently, hMAO-B and hA2AR Dual-targets inhibitory potential of a novel series of Phenylxanthine derivatives has been established in experimental findings. Hence, the current study examines the interactions between 38 compounds of this series with hMAO-B and hA2AR targets using different molecular modeling techniques to investigate the binding mode and stability of the formed complexes. A molecular docking study revealed that the compounds L24 ((E)-3-(3-Chlorophenyl)-N-(4-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl) phenyl) acrylamide and L32 ((E)-3-(3-Chlorophenyl)-N-(3-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)phenyl)acrylamide) had a high affinity (S-score: -10.160 and -7.344 kcal/mol) with the pocket of hMAO-B and hA2AR targets respectively, and the stability of the studied complexes was confirmed during MD simulations. Also, the MEP maps of compounds 24 and 32 were used to identify the nucleophilic and electrophilic attack regions. Moreover, the bioisosteric replacement approach was successfully applied to design two new analogs of each compound with similar biological activities and low energy scores. Furthermore, ADME-T and Drug-likeness results revealed the promising pharmacokinetic properties and oral bioavailability of these compounds. Thus, compounds L24, L32, and their analogs can undergo further analysis and optimization in order to design new lead compounds with higher efficacy toward Parkinson's disease. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00139-3.
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Affiliation(s)
- Merzaka Mettai
- Group of Computational and Pharmaceutical Chemistry LMCE Laboratory, University of Biskra, 07000 Biskra, Algeria
| | - Ismail Daoud
- Department of Matter Sciences, University Mohamed Khider, BP 145 RP, 07000 Biskra, Algeria
- Laboratory of Natural and Bio-actives Substances, Faculty of Science, Tlemcen University, P.O. Box 119, Tlemcen, Algeria
| | - Fouzia Mesli
- Laboratory of Natural and Bio-actives Substances, Faculty of Science, Tlemcen University, P.O. Box 119, Tlemcen, Algeria
| | - Samir Kenouche
- Group of Modeling of Chemical Systems using Quantum Calculations, Applied Chemistry Laboratory, University of Mohamed Khider, 07000 Biskra, Algeria
| | - Nadjib Melkemi
- Group of Computational and Pharmaceutical Chemistry LMCE Laboratory, University of Biskra, 07000 Biskra, Algeria
| | - Rania Kherachi
- Group of Computational and Pharmaceutical Chemistry LMCE Laboratory, University of Biskra, 07000 Biskra, Algeria
| | - Ahlem Belkadi
- Group of Computational and Pharmaceutical Chemistry LMCE Laboratory, University of Biskra, 07000 Biskra, Algeria
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Investigation of [3H]diazepam derivatives as allosteric modulators of GABAA receptor α1β2γ2 subtypes: combination of molecular docking/dynamic simulations, pharmacokinetics/drug-likeness prediction, and QSAR analysis. Struct Chem 2022; 34:791-823. [PMID: 35971551 PMCID: PMC9365687 DOI: 10.1007/s11224-022-02029-4] [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: 03/09/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022]
Abstract
In this paper, a data set of [3H] diazepam derivatives was analyzed using various computational methods: molecular docking/dynamic simulations, and QSAR analysis. The main aims of these studies are to understand the binding mechanisms by which benzodiazepines allosterically modulate GABAA receptor α1β2γ2 subtypes, from inducing neuronal inhibition at lower doses to the anesthetic effect at higher doses, and also, to define the structural requirements that contribute to improving the response of GABAA/α1β2γ2 receptor to benzodiazepine drugs. The results of the molecular docking study allowed selecting Ro12-6377 and proflazepam as the best modulators for the four binding sites simultaneously. Subsequently, the stability of the selected complexes was investigated by performing molecular dynamics simulation. The latter confirmed the features of both modulators to exert direct effects on the chloride-channel lining residues. Pharmacokinetics and drug-likeness profile were assessed through in silico tool. Furthermore, a QSAR analysis was conducted using an improved vemolecular dynamics simulations proposed byrsion of PLS regression. The goodness of fit and the predictive power of the resulting PLS model were estimated according to internal and external validation parameters: R2 = 0.632, R2adj = 0.584, F = 12.806; p-value = 6.2050e − 07, Q2loo = 0.639, and Q2F3 = 0.813. Clearly, the obtained results ensure the predictive ability of the developed QSAR model for the design of new high-potency benzodiazepine drugs.
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Kibou Z, Aissaoui N, Daoud I, Seijas JA, Vázquez-Tato MP, Klouche Khelil N, Choukchou-Braham N. Efficient Synthesis of 2-Aminopyridine Derivatives: Antibacterial Activity Assessment and Molecular Docking Studies. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113439. [PMID: 35684377 PMCID: PMC9182143 DOI: 10.3390/molecules27113439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022]
Abstract
A new and suitable multicomponent one-pot reaction was developed for the synthesis of 2-amino-3-cyanopyridine derivatives. BACKGROUND This synthesis was demonstrated by the efficient and easy access to a variety of substituted 2-aminopyridines using enaminones as key precursors under solvent-free conditions. METHODS A range of spectroscopic techniques was used to determine and confirm the chemical structures (FTIR, 1H NMR, 13C NMR). The antimicrobial potency of synthesized compounds (2a-d) was tested using disk diffusion assays, and the Minimum Inhibitory Concentration (MIC) for the active compounds was determined against a panel of microorganisms, including Gram-positive and Gram-negative bacteria and yeasts. Moreover, a docking analysis was conducted by Molecular Operating Environment (MOE) software to provide supplementary information about the potential, as well as an ADME-T prediction to describe the pharmacokinetic properties of the best compound and its toxicity. RESULTS The results of the antimicrobial activity indicated that compound 2c showed the highest activity against Gram-positive bacteria, particularly S. aureus and B. subtilis whose MIC values were 0.039 ± 0.000 µg·mL-1. The results of the theoretical study of compound 2c were in line with the experimental data and exhibited excellent antibacterial potential. CONCLUSIONS On the basis of the obtained results, compound 2c can be used as an antibacterial agent model with high antibacterial potency.
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Affiliation(s)
- Zahira Kibou
- Laboratoire de Catalyse et Synthèse en Chimie Organique, Faculté des Sciences, Université de Tlemcen, BP 119, Tlemcen 13000, Algeria;
- Faculté des Sciences et de la Technologie, Université de Ain Témouchent, BP 284, Ain Témouchent 46000, Algeria
- Correspondence: (Z.K.); (J.A.S.)
| | - Nadia Aissaoui
- Laboratory of the Sustainable Management of Natural Resources in Arid and Semi Aridareas, University Center Salhi Ahmed Naama, BP 66, Naama 45000, Algeria;
- Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, Tlemcen 13000, Algeria
| | - Ismail Daoud
- Département des Sciences de la Matière, Université de Mohamed Khider, BP 145 RP, Biskra 07000, Algerie;
- Laboratory of Natural and Bio-Active Substances, Faculty of Sciences, University of Tlemcen, BP 119, Tlemcen 13000, Algeria
| | - Julio A. Seijas
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Santiago de Compostela, A da, Alfonso X El Sabio s/n, 27002 Lugo, Spain;
- Correspondence: (Z.K.); (J.A.S.)
| | - María Pilar Vázquez-Tato
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Santiago de Compostela, A da, Alfonso X El Sabio s/n, 27002 Lugo, Spain;
| | - Nihel Klouche Khelil
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE), Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, Tlemcen 13000, Algeria;
- Laboratory of Experimental Surgery, Medical Faculty, University of Tlemcen, Tlemcen 13000, Algeria
| | - Noureddine Choukchou-Braham
- Laboratoire de Catalyse et Synthèse en Chimie Organique, Faculté des Sciences, Université de Tlemcen, BP 119, Tlemcen 13000, Algeria;
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El-Hawary SS, Mohammed R, Taher MA, AbouZid SF, Mansour MA, Almahmoud SA, Huwaimel B, Amin E. Characterization of Promising Cytotoxic Metabolites from Tabebuia guayacan Hemsl.: Computational Prediction and In Vitro Testing. PLANTS (BASEL, SWITZERLAND) 2022; 11:888. [PMID: 35406868 PMCID: PMC9002841 DOI: 10.3390/plants11070888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022]
Abstract
Genus Tabebuia is famous for its traditional uses and valuable phytoconstituents. Our previous investigation of Tabebuia species noted the promising anticancer activity of T. guayacan Hemsl. leaves extract, however, the mechanism underlying the observed anticancer activity is still unexplored. The current research was designed to explore the phytochemical content as well as to address the phytoconstituent(s) responsible for the recorded anticancer activity. Accordingly, sixteen compounds were isolated, and their structures were elucidated using different spectroscopic techniques. The drug-likeness of the isolated compounds, as well as their binding affinity with four anticancer drug target receptors: CDK-2/6, topoisomerase-1, and VEGFR-2, were evaluated. Additionally, the most promising compounds were in vitro evaluated for inhibitory activities against CDK-2/6 and VEGFR-2 enzymes using kinase assays method. Corosolic acid (3) and luteolin-7-O-β-glucoside (16) were the most active inhibitors against CDK-2 (-13.44 kcal/mol) and topoisomerase 1 (-13.83 kcal/mol), respectively. Meanwhile, quercetin 3-O-β-xyloside (10) scored the highest binding free energies against both CDK-6 (-16.23 kcal/mol) as well as against VEGFR-2 protein targets (-10.39 kcal/mol). Molecular dynamic simulation indicated that quercetin 3-O-β-xyloside (10) exhibited the least fluctuations and deviations from the starting binding pose with RMSD (2.6 Å). Interestingly, in vitro testing results confirmed the potent activity of 10 (IC50 = 0.154 µg/mL) compared to IC50 = 0.159 µg/mL of the reference drug ribociclib. These findings suggest the three noted compounds (3, 10, and 16) for further in vivo anticancer studies.
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Affiliation(s)
- Seham S. El-Hawary
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Giza 12613, Egypt;
| | - Rabab Mohammed
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt; (R.M.); (S.F.A.)
| | - Marwa A. Taher
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62521, Egypt;
| | - Sameh Fekry AbouZid
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt; (R.M.); (S.F.A.)
- Department of Pharmacognosy, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Mostafa A. Mansour
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Nahda University, Beni-Suef 62521, Egypt;
| | - Suliman A. Almahmoud
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraidah 51452, Saudi Arabia;
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia;
| | - Elham Amin
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt; (R.M.); (S.F.A.)
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraidah 51452, Saudi Arabia;
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Multitarget-Based Virtual Screening for Identification of Herbal Substances toward Potential Osteoclastic Targets. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Osteoporosis is a complex bone disease indicating porous bone with low bone mass density and fragility. Cathepsin K, V-ATPase, and αVβ3 integrin are exhibited as novel targets for osteoporosis treatment. Our preliminary study uses a state-of-the-art method, including target-based virtual screening and clustering methods to determine promising candidates with multitarget properties. Phytochemicals with osteoprotective properties from the literature are used to elucidate the molecular interactions toward three targets. The binding scores of compounds are normalized and rescored. The K-means and hierarchical clustering methods are applied to filter and define the promising compounds, and the silhouette analysis is supposed to validate the clustering method. We explore 108 herbal compounds by virtual screening and the cluster approach, and find that rutin, sagittatoside A, icariin, and kaempferitrin showed strong binding affinities against Cathepsin K, V-ATPase, and αVβ3 integrin. Dockings of candidates toward three targets also provide the protein-ligand interactions and crucial amino acids for binding. Our study provides a straightforward and less time-consuming approach to exploring the new multitarget candidates for further investigations, using a combination of in silico methods.
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Belkadi A, Kenouche S, Melkemi N, Daoud I, Djebaili R. Molecular docking/dynamic simulations, MEP, ADME-TOX-based analysis of xanthone derivatives as CHK1 inhibitors. Struct Chem 2022. [DOI: 10.1007/s11224-022-01898-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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