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Article ; Online: Computer-Aided Strategy on 5-(Substituted benzylidene) Thiazolidine-2,4-Diones to Develop New and Potent PTP1B Inhibitors: QSAR Modeling, Molecular Docking, Molecular Dynamics, PASS Predictions, and DFT Investigations.

Derki, Nour-El Houda / Kerassa, Aicha / Belaidi, Salah / Derki, Maroua / Yamari, Imane / Samadi, Abdelouahid / Chtita, Samir

Molecules (Basel, Switzerland)

2024 Volume 29, Issue 4

Abstract: A set of 5-(substituted benzylidene) thiazolidine-2,4-dione derivatives was explored to study the main structural requirement for the design of protein tyrosine phosphatase 1B (PTP1B) inhibitors. Utilizing multiple linear regression (MLR) analysis, we ... ...

Abstract	A set of 5-(substituted benzylidene) thiazolidine-2,4-dione derivatives was explored to study the main structural requirement for the design of protein tyrosine phosphatase 1B (PTP1B) inhibitors. Utilizing multiple linear regression (MLR) analysis, we constructed a robust quantitative structure-activity relationship (QSAR) model to predict inhibitory activity, resulting in a noteworthy correlation coefficient (R
MeSH term(s)	Humans ; Molecular Docking Simulation ; Quantitative Structure-Activity Relationship ; Thiazolidines/pharmacology ; Thiazolidines/chemistry ; Reproducibility of Results ; Molecular Dynamics Simulation ; Enzyme Inhibitors/chemistry ; Diabetes Mellitus/drug therapy
Chemical Substances	Thiazolidines ; Enzyme Inhibitors
Language	English
Publishing date	2024-02-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules29040822
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Article ; Online: Identification of Potent Acetylcholinesterase Inhibitors as New Candidates for Alzheimer Disease via Virtual Screening, Molecular Docking, Dynamic Simulation, and Molecular Mechanics-Poisson-Boltzmann Surface Area Calculations.

Chennai, Hind Yassmine / Belaidi, Salah / Bourougaa, Lotfi / Ouassaf, Mebarka / Sinha, Leena / Samadi, Abdelouahid / Chtita, Samir

Molecules (Basel, Switzerland)

2024 Volume 29, Issue 6

Abstract: Huperzine A (HUP) plays a crucial role in Alzheimer's therapy by enhancing cognitive function through increased cholinergic activity as a reversible acetylcholinesterase (AChE) inhibitor. Despite some limitations being seen in AChE inhibitors, ongoing ... ...

Abstract	Huperzine A (HUP) plays a crucial role in Alzheimer's therapy by enhancing cognitive function through increased cholinergic activity as a reversible acetylcholinesterase (AChE) inhibitor. Despite some limitations being seen in AChE inhibitors, ongoing research remains dedicated to finding innovative and more effective treatments for Alzheimer's disease. To achieve the goal of the discovery of potential HUP analogues with improved physicochemical properties, less toxic properties, and high biological activity, many in silico methods were applied. Based on the acetylcholinesterase-ligand complex, an e-pharmacophore model was developed. Subsequently, a virtual screening involving a collection of 1762 natural compounds, sourced from the PubChem database, was performed. This screening yielded 131 compounds that exhibited compatibility with the established pharmacophoric hypothesis. These selected ligands were then subjected to molecular docking within the active site of the 4EY5 receptor. As a result, we identified four compounds that displayed remarkable docking scores and exhibited low free binding energy to the target. These top four compounds, CID_162895946, CID_44461278, CID_44285285, and CID_81108419, were submitted to ADMET prediction and molecular dynamic simulations, yielding encouraging findings in terms of their pharmacokinetic characteristics and stability. Finally, the molecular dynamic simulation, cross-dynamic correlation matrix, free energy landscape, and MM-PBSA calculations demonstrated that two ligands from the selected ligands formed very resilient complexes with the enzyme acetylcholinesterase, with significant binding affinity. Therefore, these two compounds are recommended for further experimental research as possible (AChE) inhibitors.
MeSH term(s)	Humans ; Cholinesterase Inhibitors/chemistry ; Alzheimer Disease/drug therapy ; Molecular Dynamics Simulation ; Molecular Docking Simulation ; Acetylcholinesterase/metabolism ; Ligands ; Alkaloids ; Sesquiterpenes
Chemical Substances	Cholinesterase Inhibitors ; Acetylcholinesterase (EC 3.1.1.7) ; huperzine A (0111871I23) ; Ligands ; Alkaloids ; Sesquiterpenes
Language	English
Publishing date	2024-03-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules29061232
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Article ; Online: Identification of novel curcumin derivatives against pancreatic cancer: a comprehensive approach integrating 3D-QSAR pharmacophore modeling, virtual screening, and molecular dynamics simulations.

Chahbaoui, Narimene / Khamouli, Saida / Alaqarbeh, Marwa / Belaidi, Salah / Sinha, Leena / Chtita, Samir / Bouachrine, Mohammed

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–19

Abstract: Pancreatic cancer, known as the "silent killer," poses a daunting challenge in cancer therapy. The dysregulation of the PI3Kα signaling pathway in pancreatic cancer has attracted considerable interest as a promising target for therapeutic intervention. ... ...

Abstract	Pancreatic cancer, known as the "silent killer," poses a daunting challenge in cancer therapy. The dysregulation of the PI3Kα signaling pathway in pancreatic cancer has attracted considerable interest as a promising target for therapeutic intervention. In this regard, the use of curcumin derivatives as inhibitors of PI3Kα has emerged, providing a novel and promising avenue for developing effective treatments for this devastating disease. Computational approaches were employed to explore this potential and investigate 58 curcumin derivatives with cytotoxic activity against the Panc-1 cell line. Our approach involved ligand-based pharmacophore modeling and atom-based 3D-QSAR analysis. The resulting QSAR model derived from the best-fitted pharmacophore hypothesis (AAHRR_1) demonstrated remarkable performance with high correlation coefficients (R
Language	English
Publishing date	2023-10-09
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2266502
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Article ; Online: Combined computational approaches for developing new anti-Alzheimer drug candidates: 3D-QSAR, molecular docking and molecular dynamics studies of liquiritigenin derivatives

Nour, Hassan / Daoui, Ossama / Abchir, Oussama / ElKhattabi, Souad / Belaidi, Salah / Chtita, Samir

Heliyon. 2022 Dec., v. 8, no. 12 p.e11991-

2022

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 ... ...

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, R²ₚᵣₑd = 0.85; CoMISA model: R² = 0.92, Q² = 0.59, R²ₚᵣₑd = 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.
Keywords	Alzheimer disease ; active sites ; cholinesterase ; drugs ; models ; molecular dynamics ; pharmacokinetics ; structure-activity relationships ; Alzheimer's disease ; Butyrylcholinesterase ; Liquiritigenin ; CoMFA ; CoMISA ; Molecular docking
Language	English
Dates of publication	2022-12
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2022.e11991
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Combined 3D-{QSAR} and Molecular Docking Analysis of Thienopyrimidine Derivatives as Staphylococcus aureus Inhibitors.

Ouassaf, Mebarka / Belaidi, Salah / Khamouli, Saida / Belaidi, Houmam / Chtita, Samir

Acta chimica Slovenica

2021 Volume 68, Issue 2, Page(s) 289–303

Abstract: The discovery of antibacterials is considered one of the greatest medical achievements of all time. In this work, a combination of three computational analyzes: 3D-QSAR, molecular docking and ADME evaluation were applied in thienopyrimidine derivatives ... ...

Abstract	The discovery of antibacterials is considered one of the greatest medical achievements of all time. In this work, a combination of three computational analyzes: 3D-QSAR, molecular docking and ADME evaluation were applied in thienopyrimidine derivatives intended toward gram-positive bacterium Staphylococcus aureus. The validity of 3D-QSAR model was tested with a set of data which is divided into a training and a test set. The two models constructed (CoMFA and CoMSIA) show good statistical reliability (q2 = 0.758; r2 = 0.96; r2pred = 0.783) and (q2 = 0.744; r2 = 0.97; r2pred = 0.625) respectively. In addition, docking methods were applied to understand the structural features responsible for the affinity of the ligands in the binding of S. aureus DNA gyrase. Drug likeness and ADME analysis applied in this series of new proposed compounds, have shown that the five lead molecules would have the potential to be effective drugs and could be used as a starting point for designing compounds against Staphylococcus aureus.
MeSH term(s)	Anti-Bacterial Agents/analysis ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Molecular Structure ; Pyrimidines/analysis ; Pyrimidines/pharmacology ; Quantitative Structure-Activity Relationship ; Staphylococcus aureus/drug effects
Chemical Substances	Anti-Bacterial Agents ; Pyrimidines ; thienopyrimidine
Language	English
Publishing date	2021-10-19
Publishing country	Slovenia
Document type	Journal Article
ZDB-ID	2029709-9
ISSN	1580-3155 ; 1318-0207
ISSN (online)	1580-3155
ISSN	1318-0207
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Article ; Online: Combined Pharmacophore Modeling, 3D-QSAR, Molecular Docking and Molecular Dynamics Study on Indolyl-aryl-sulfone Derivatives as New HIV1 Inhibitors.

Ouassaf, Mebarka / Abul Qais, Faizan / Belaidi, Salah / Bakhouch, Mohamed / Mohamed, Ahmed Said / Chtita, Samir

Acta chimica Slovenica

2022 Volume 69, Issue 2, Page(s) 489–506

Abstract: The present study deals with the in silico of 45 indolyl-aryl-sulfones known as anti-HIV1. The data were collected from recent previously reported inhibitors and divided into a sub-set of 33 compounds as the training set and the remaining 12 compounds ... ...

Abstract	The present study deals with the in silico of 45 indolyl-aryl-sulfones known as anti-HIV1. The data were collected from recent previously reported inhibitors and divided into a sub-set of 33 compounds as the training set and the remaining 12 compounds were kept in the test set. The selected pharmacophore-ADRRR-yielded a statistically significant 3D-QSAR model containing high confidence scores (R2 = 0.930, Q2 = 0.848, and RMSE = 0.460). The predictive power of the established pharmacophore model was validated with an external test (r2 = 0.848). A systematic virtual screening workflow shows an enrichment factor and has revealed a high predictive power. Then the model was used to screen the filtered PubChem database mapping all chemical features of model pharmacophore. The recognized hits were further assessed by in silico ADMET studies. Molecular dynamics also used to explore the stability of obtained complexes. Finally, these selected compounds are probably to become a good lead molecule for the development of effective anti-HIV-1 drugs.
MeSH term(s)	Molecular Docking Simulation ; Molecular Dynamics Simulation ; Quantitative Structure-Activity Relationship ; Sulfones
Chemical Substances	Sulfones
Language	English
Publishing date	2022-06-14
Publishing country	Slovenia
Document type	Journal Article
ZDB-ID	2029709-9
ISSN	1580-3155 ; 1318-0207
ISSN (online)	1580-3155
ISSN	1318-0207
DOI	10.17344/acsi.2022.7427
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Article ; Online: Pharmacophore-based virtual screening, molecular docking, and molecular dynamics studies for the discovery of novel FLT3 inhibitors.

Ouassaf, Mebarka / Daoui, Ossama / Alam, Sarfaraz / Elkhattabi, Souad / Belaidi, Salah / Chtita, Samir

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 16, Page(s) 7712–7724

Abstract: FLT3 is considered a potential target of acute myeloid leukemia therapy. In this study, we applied a computer-aided methodology unifying molecular docking and pharmacophore screening to identify potent inhibitors against FLT3. To investigate the ... ...

Abstract	FLT3 is considered a potential target of acute myeloid leukemia therapy. In this study, we applied a computer-aided methodology unifying molecular docking and pharmacophore screening to identify potent inhibitors against FLT3. To investigate the pharmacophore area and binding mechanism of FLT3, the reported co-crystallized Gilteritinib ligand was docked into the active site using Glide XP. Based on the docking results, we identified structure-based pharmacophore characteristics resistant to potent FLT3 inhibitors. The best hypothesis was corroborated using test and decoy sets, and the verified hypo was utilized to screen the chemical database. The hits from the pharmacophore-based screening were then screened again using a structure-based method that included molecular docking at various precisions; the selected molecules were further examined and refined using drug-like filters and ADMET analysis. Finally, two hits were picked out for molecular dynamic simulation. The results showed two hits were expected to have potent inhibitory activity and excellent ADMET characteristics, and they might be used as new leads in the development of FLT3 inhibitors.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2022-09-15
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2123403
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Article ; Online: Cyclohexane-1,3-dione Derivatives as Future Therapeutic Agents for NSCLC: QSAR Modeling, In Silico ADME-Tox Properties, and Structure-Based Drug Designing Approach.

Daoui, Ossama / Elkhattabi, Souad / Bakhouch, Mohamed / Belaidi, Salah / Bhandare, Richie R / Shaik, Afzal B / Mali, Suraj N / Chtita, Samir

ACS omega

2023 Volume 8, Issue 4, Page(s) 4294–4319

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 ... ...

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
Language	English
Publishing date	2023-01-19
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.2c07585
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Article ; Online: Combined molecular docking and dynamics simulations studies of natural compounds as potent inhibitors against SARS-CoV-2 main protease.

Ouassaf, Mebarka / Belaidi, Salah / Chtita, Samir / Lanez, Touhami / Abul Qais, Faizan / Md Amiruddin, Hashmi

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 21, Page(s) 11264–11273

Abstract: Main protease (Mpro) of SARS-CoV-2 is a key CoV enzyme that plays a pivotal role in mediating viral replication and transcription, making it an attractive drug target for SARS-CoV-2 the new strain of coronavirus. In this study, we evaluated biologically ... ...

Abstract	Main protease (Mpro) of SARS-CoV-2 is a key CoV enzyme that plays a pivotal role in mediating viral replication and transcription, making it an attractive drug target for SARS-CoV-2 the new strain of coronavirus. In this study, we evaluated biologically active compounds present in medicinal plants as potential SARS-CoV-2 Mpro inhibitors, using a molecular docking study with Autodock Vina software. Top seven compounds
MeSH term(s)	Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protease Inhibitors/pharmacology ; SARS-CoV-2/drug effects ; Silybin/pharmacology
Chemical Substances	3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Protease Inhibitors ; Silybin (4RKY41TBTF)
Language	English
Publishing date	2021-07-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1957712
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Article ; Online: QSAR Studies and Structure Property/Activity Relationships Applied in Pyrazine Derivatives as Antiproliferative Agents Against the BGC823.

Soualmia, Fatima / Belaidi, Salah / Tchouar, Noureddine / Lanez, Touhami / Boudergua, Samia

Acta chimica Slovenica

2021 Volume 68, Issue 4, Page(s) 882–895

Abstract: Electronic structures, the effect of the substitution, structure physicochemical property/activity relationships and drug-likeness applied in pyrazine derivatives, have been studied at ab initio (HF, MP2) and B3LYP/DFT (density functional theory) levels. ...

Abstract	Electronic structures, the effect of the substitution, structure physicochemical property/activity relationships and drug-likeness applied in pyrazine derivatives, have been studied at ab initio (HF, MP2) and B3LYP/DFT (density functional theory) levels. In the paper, the calculated values, i.e., NBO (natural bond orbitals) charges, bond lengths, dipole moments, electron affinities, heats of formation and quantitative structure-activity relationships (QSAR) properties are presented. For the QSAR studies, we used multiple linear regression (MLR) and artificial neural network (ANN) statistical modeling. The results show a high correlation between experimental and predicted activity values, indicating the validation and the good quality of the derived QSAR models. In addition, statistical analysis reveals that the ANN technique with (9-4-1) architecture is more significant than the MLR model. The virtual screening based on the molecular similarity method and applicability domain of QSAR allowed the discovery of novel anti-proliferative activity candidates with improved activity.
MeSH term(s)	Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Density Functional Theory ; Humans ; Linear Models ; Neural Networks, Computer ; Pyrazines/chemistry ; Pyrazines/pharmacology ; Quantitative Structure-Activity Relationship
Chemical Substances	Antineoplastic Agents ; Pyrazines
Language	English
Publishing date	2021-12-15
Publishing country	Slovenia
Document type	Journal Article
ZDB-ID	2029709-9
ISSN	1580-3155 ; 1318-0207
ISSN (online)	1580-3155
ISSN	1318-0207
DOI	10.17344/acsi.2021.6875
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