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Article: Design of new molecules against cervical cancer using DFT, theoretical spectroscopy, 2D/3D-QSAR, molecular docking, pharmacophore and ADMET investigations.

El Rhabori, Said / El Aissouq, Abdellah / Daoui, Ossama / Elkhattabi, Souad / Chtita, Samir / Khalil, Fouad

2024 Volume 10, Issue 3, Page(s) e24551

Abstract: Cervical cancer is a major health problem of women. Hormone therapy, via aromatase inhibition, has been proposed as a promising way of blocking estrogen production as well as treating the progression of estrogen-dependent cancer. To overcome the ... ...

Abstract	Cervical cancer is a major health problem of women. Hormone therapy, via aromatase inhibition, has been proposed as a promising way of blocking estrogen production as well as treating the progression of estrogen-dependent cancer. To overcome the challenging complexities of costly drug design, in-silico strategy, integrating Structure-Based Drug Design (SBDD) and Ligand-Based Drug Design (LBDD), was applied to large representative databases of 39 quinazoline and thioquinazolinone compound derivatives. Quantum chemical and physicochemical descriptors have been investigated using density functional theory (DFT) and MM2 force fields, respectively, to develop 2D-QSAR models, while CoMSIA and CoMFA descriptors were used to build 3D-QSAR models. The robustness and predictive power of the reliable models were verified, via several validation methods, leading to the design of 6 new drug-candidates. Afterwards, 2 ligands were carefully selected using virtual screening methods, taking into account the applicability domain, synthetic accessibility, and Lipinski's criteria. Molecular docking and pharmacophore modelling studies were performed to examine potential interactions with aromatase (PDB ID: 3EQM). Finally, the ADMET properties were investigated in order to select potential drug-candidates against cervical cancer for experimental in vitro and in vivo testing.
Language	English
Publishing date	2024-01-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e24551
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Article: Integrative Approach for Designing Novel Triazole Derivatives as α-Glucosidase Inhibitors: QSAR, Molecular Docking, ADMET, and Molecular Dynamics Investigations.

Abchir, Oussama / Khedraoui, Meriem / Nour, Hassan / Yamari, Imane / Errougui, Abdelkbir / Samadi, Abdelouahid / Chtita, Samir

Pharmaceuticals (Basel, Switzerland)

2024 Volume 17, Issue 2

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 ... ...

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.
Language	English
Publishing date	2024-02-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph17020261
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Article ; Online: A comprehensive computational study to explore promising natural bioactive compounds targeting glycosyltransferase MurG in Escherichia coli for potential drug development.

Shtaiwi, Amneh / Khan, Shafi Ullah / Khedraoui, Meriem / Alaraj, Mohd / Samadi, Abdelouahid / Chtita, Samir

Scientific reports

2024 Volume 14, Issue 1, Page(s) 7098

Abstract: Peptidoglycan is a carbohydrate with a cross-linked structure that protects the cytoplasmic membrane of bacterial cells from damage. The mechanism of peptidoglycan biosynthesis involves the main synthesizing enzyme glycosyltransferase MurG, which is ... ...

Abstract	Peptidoglycan is a carbohydrate with a cross-linked structure that protects the cytoplasmic membrane of bacterial cells from damage. The mechanism of peptidoglycan biosynthesis involves the main synthesizing enzyme glycosyltransferase MurG, which is known as a potential target for antibiotic therapy. Many MurG inhibitors have been recognized as MurG targets, but high toxicity and drug-resistant Escherichia coli strains remain the most important problems for further development. In addition, the discovery of selective MurG inhibitors has been limited to the synthesis of peptidoglycan-mimicking compounds. The present study employed drug discovery, such as virtual screening using molecular docking, drug likeness ADMET proprieties predictions, and molecular dynamics (MD) simulation, to identify potential natural products (NPs) for Escherichia coli. We conducted a screening of 30,926 NPs from the NPASS database. Subsequently, 20 of these compounds successfully passed the potency, pharmacokinetic, ADMET screening assays, and their validation was further confirmed through molecular docking. The best three hits and the standard were chosen for further MD simulations up to 400 ns and energy calculations to investigate the stability of the NPs-MurG complexes. The analyses of MD simulations and total binding energies suggested the higher stability of NPC272174. The potential compounds can be further explored in vivo and in vitro for promising novel antibacterial drug discovery.
MeSH term(s)	Glycosyltransferases/metabolism ; Escherichia coli/metabolism ; Bacterial Outer Membrane Proteins/metabolism ; Molecular Docking Simulation ; Peptidoglycan ; Anti-Bacterial Agents/pharmacology ; Molecular Dynamics Simulation ; Drug Development
Chemical Substances	Glycosyltransferases (EC 2.4.-) ; Bacterial Outer Membrane Proteins ; Peptidoglycan ; Anti-Bacterial Agents
Language	English
Publishing date	2024-03-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-57702-x
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Article: Rational identification of small molecules derived from 9,10-dihydrophenanthrene as potential inhibitors of 3CL

Daoui, Ossama / Elkhattabi, Souad / Chtita, Samir

Structural chemistry

2022 Volume 33, Issue 5, Page(s) 1667–1690

Abstract: Small molecules such as 9,10-dihydrophenanthrene derivatives have remarkable activity toward inhibition of SARS-CoV-2 3CL: Supplementary information: The online version contains supplementary material available at 10.1007/s11224-022-02004-z. ...

Abstract	Small molecules such as 9,10-dihydrophenanthrene derivatives have remarkable activity toward inhibition of SARS-CoV-2 3CL Supplementary information: The online version contains supplementary material available at 10.1007/s11224-022-02004-z.
Language	English
Publishing date	2022-07-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2018832-8
ISSN	1572-9001 ; 1040-0400
ISSN (online)	1572-9001
ISSN	1040-0400
DOI	10.1007/s11224-022-02004-z
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Article ; Online: Repositioning Cannabinoids and Terpenes as Novel EGFR-TKIs Candidates for Targeted Therapy Against Cancer: A virtual screening model using CADD and biophysical simulations

Daoui, Ossama / Mali, Suraj N. / Elkhattabi, Kaouakeb / Elkhattabi, Souad / Chtita, Samir

Heliyon. 2023 Apr., v. 9, no. 4 p.e15545-

2023

Abstract: This study examines the potential of Cannabis sativa L. plants to be repurposed as therapeutic agents for cancer treatment through designing of hybrid Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs). A set of 50 phytochemicals was ...

Abstract	This study examines the potential of Cannabis sativa L. plants to be repurposed as therapeutic agents for cancer treatment through designing of hybrid Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs). A set of 50 phytochemicals was taken from Cannabinoids and Terpenes and subjected for screening using Semi-flexible and Flexible Molecular Docking methods, MM-GBSA free binding energy computations, and pharmacokinetic/pharmacodynamic (ADME-Tox) predictions. Nine promising phytochemicals, Cannabidiolic acid (CBDA), Cannabidiol (CBD), Tetrahydrocannabivarin (THCV), Dronabinol (Δ-9-THC), Delta-8-Tetrahydrocannabinol (Δ-8-THC), Cannabicyclol (CBL), Delta9-tetrahydrocannabinolic acid (THCA), Beta-Caryophyllene (BCP), and Gamma-Elemene (γ-Ele) were identified as potential EGFR-TKIs natural product candidates for cancer therapy. To further validate these findings, a set of Molecular Dynamics simulations were conducted over a 200 ns trajectory. This hybrid early drug discovery screening strategy has the potential to yield a new generation of EGFR-TKIs based on natural cannabis products, suitable for cancer therapy. In addition, the application of this computational strategy in the virtual screening of both natural and synthetic chemical libraries could support the discovery of a wide range of lead drug agents to address numerous diseases.
Keywords	Cannabis sativa ; beta-caryophyllene ; cancer therapy ; cannabidiol ; drugs ; energy ; epidermal growth factor receptors ; molecular dynamics ; pharmacodynamics ; pharmacokinetics ; phytochemicals ; Cannabis sativa L. ; Virtual Screening ; CADD ; Semi-flexible & Flexible Molecular Docking ; MM-GBSA free Binding energy ; The inhibition constant (Ki) ; EGFR-TKIs ; Breast & Lung Cancer ; Cannabinoids & Terpenes
Language	English
Dates of publication	2023-04
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.2023.e15545
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Design of novel quinoline derivatives as antibreast cancer using 3D-QSAR, molecular docking and pharmacokinetic investigation.

El Rhabori, Said / El Aissouq, Abdellah / Chtita, Samir / Khalil, Fouad

Anti-cancer drugs

2022 Volume 33, Issue 9, Page(s) 789–802

Abstract: Breast cancer has been one of the most challenging women's cancers and leading cause of mortality for decades. There are several studies being conducted all the time to find a cure for breast cancer. Quinoline derivatives have shown their potential as ... ...

Abstract	Breast cancer has been one of the most challenging women's cancers and leading cause of mortality for decades. There are several studies being conducted all the time to find a cure for breast cancer. Quinoline derivatives have shown their potential as antitumor agents in breast cancer therapy. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR) and molecular docking with aromatase enzyme (Protein Data Bank: 3S7S) studies were performed to suggest the current scenario of quinoline derivatives as antitumor agents and to refine the path of these derivatives to discover and develop new drugs against breast cancer. For developing the 3D-QSAR model, comparative molecular similarity indices analysis (CoMSIA) and comparative molecular field analysis (CoMFA) were included. To attain the high level of predictability, the best CoMSIA model was applied. External validation utilizing a test set has been used in order to validate the predictive capabilities of the built model. According to the findings, electrostatic, hydrophobic and hydrogen bond donor, and acceptor fields had a significant impact on antibreast cancer activity. Thus, we generated a variety of novel effective aromatase inhibitors based on prior findings and we predicted their inhibitory activity using the built model. In addition, absorption, distribution, metabolism, elimination and toxicity properties were employed to explore the effectiveness of new drug candidates.
MeSH term(s)	Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology ; Aromatase ; Aromatase Inhibitors/pharmacology ; Breast Neoplasms/drug therapy ; Drug Design ; Female ; Humans ; Models, Molecular ; Molecular Docking Simulation ; Quantitative Structure-Activity Relationship
Chemical Substances	Antineoplastic Agents ; Aromatase Inhibitors ; Aromatase (EC 1.14.14.1)
Language	English
Publishing date	2022-09-14
Publishing country	England
Document type	Journal Article
ZDB-ID	1065301-6
ISSN	1473-5741 ; 0959-4973
ISSN (online)	1473-5741
ISSN	0959-4973
DOI	10.1097/CAD.0000000000001318
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Ligand-Based Design of Novel Quinoline Derivatives as Potential Anticancer Agents: An In-Silico Virtual Screening Approach.

Mkhayar, Khaoula / Daoui, Ossama / Haloui, Rachid / Elkhattabi, Kaouakeb / Elabbouchi, Abdelmoula / Chtita, Samir / Samadi, Abdelouahid / Elkhattabi, Souad

Molecules (Basel, Switzerland)

2024 Volume 29, Issue 2

Abstract: In this study, using the Comparative Molecular Field Analysis (CoMFA) approach, the structure-activity relationship of 33 small quinoline-based compounds with biological anti-gastric cancer activity in vitro was analyzed in 3D space. Once the 3D ... ...

Abstract	In this study, using the Comparative Molecular Field Analysis (CoMFA) approach, the structure-activity relationship of 33 small quinoline-based compounds with biological anti-gastric cancer activity in vitro was analyzed in 3D space. Once the 3D geometric and energy structure of the target chemical library has been optimized and their steric and electrostatic molecular field descriptions computed, the ideal 3D-QSAR model is generated and matched using the Partial Least Squares regression (PLS) algorithm. The accuracy, statistical precision, and predictive power of the developed 3D-QSAR model were confirmed by a range of internal and external validations, which were interpreted by robust correlation coefficients (RTrain2=0.931; Qcv2=0.625; RTest2=0.875). After carefully analyzing the contour maps produced by the trained 3D-QSAR model, it was discovered that certain structural characteristics are beneficial for enhancing the anti-gastric cancer properties of Quinoline derivatives. Based on this information, a total of five new quinoline compounds were developed, with their biological activity improved and their drug-like bioavailability measured using POM calculations. To further explore the potential of these compounds, molecular docking and molecular dynamics simulations were performed in an aqueous environment for 100 nanoseconds, specifically targeting serine/threonine protein kinase. Overall, the new findings of this study can serve as a starting point for further experiments with a view to the identification and design of a potential next-generation drug for target therapy against cancer.
MeSH term(s)	Humans ; Ligands ; Molecular Docking Simulation ; Antineoplastic Agents/pharmacology ; Quinolines/pharmacology ; Quantitative Structure-Activity Relationship ; Stomach Neoplasms/drug therapy
Chemical Substances	Ligands ; Antineoplastic Agents ; Quinolines
Language	English
Publishing date	2024-01-15
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/molecules29020426
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Article ; Online: Design of new small molecules derived from indolin-2-one as potent TRKs inhibitors using a computer-aided drug design approach.

Haloui, Rachid / Mkhayar, Khaoula / Daoui, Ossama / El Khattabi, Kaouakeb / El Abbouchi, Abdelmoula / Chtita, Samir / Elkhattabi, Souad

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–18

Abstract: Tropomyosin receptor kinase (TRKs) enzymes are responsible for cancers associated with the neurotrophic tyrosine kinase receptor gene fusion and are identified as effective targets for anticancer drug discovery. A series of small-molecule indolin-2-one ... ...

Abstract	Tropomyosin receptor kinase (TRKs) enzymes are responsible for cancers associated with the neurotrophic tyrosine kinase receptor gene fusion and are identified as effective targets for anticancer drug discovery. A series of small-molecule indolin-2-one derivatives showed remarkable biological activity against TRKs enzymatic activity. These small molecules could have an excellent profile for pharmaceutical application in the treatment of cancers caused by TRKs activity. The aim of this study is to modify the structure of these molecules to obtain new molecules with improved TRK inhibitory activity and pharmacokinetic properties favorable to the design of new drugs. Based on these series, we carried out a 3D-QSAR study. As a result, robust and reliable CoMFA and CoMSIA models are developed and applied to the design of 11 new molecules. These new molecules have a biological activity superior to the most active molecule in the starting series. The eleven designed molecules are screened using drug-likeness, ADMET proprieties, molecular docking, and MM-GBSA filters. The results of this screening identified the T1, T3, and T4 molecules as the best candidates for strong inhibition of TRKs enzymatic activity. In addition, molecular dynamics simulations are performed for TRK free and complexed with ligands T1, T3, and T4 to evaluate the stability of ligand-protein complexes over the simulation time. On the other hand, we proposed experimental synthesis routes for these newly designed molecules. Finally, the designed molecules T1, T2, and T3 have great potential to become reliable candidates for the conception of new drug inhibitors of TRKs.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2024-01-13
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2302944
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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: Insights into the inhibitory potential of novel hydrazinyl thiazole-linked indenoquinoxaline against alpha-amylase: a comprehensive QSAR, pharmacokinetic, and molecular modeling study.

Abchir, Oussama / Yamari, Imane / Shtaiwi, Amneh Mohammad / Nour, Hassan / Kouali, Mhammed El / Talbi, Mohammed / Errougui, Abdelkbir / Chtita, Samir

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–18

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 ...

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 IC
Language	English
Publishing date	2024-02-02
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2310778
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