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Article ; Online: Design of novel isoxazole derivatives as tubulin inhibitors using computer-aided techniques: QSAR modeling,

Moukhliss, Youness / Koubi, Yassine / Zafar, Imran / Alaqarbeh, Marwa / Maghat, Hamid / Sbai, Abdelouahid / Lakhlifi, Tahar / Bouachrine, Mohammed

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–12

Abstract: In the current work, computational methods were used to investigate new isoxazole derivatives that could be used as tubulin inhibitors. The study aims to develop a reliable quantitative structure-activity relationship (QSAR) model, following the criteria ...

Abstract	In the current work, computational methods were used to investigate new isoxazole derivatives that could be used as tubulin inhibitors. The study aims to develop a reliable quantitative structure-activity relationship (QSAR) model, following the criteria set by Golbraikh, Tropsha, and Roy. As a result, seven candidate compounds were developed, all having higher activity than the well-established anticancer agent Cisplatin (Cisp). According to the ADMETox
Language	English
Publishing date	2024-02-14
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2306493
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Article ; Online: Exploring azomethine ylides reactivity with acrolein through cycloaddition reaction and computational antiviral activity assessment against hepatitis C virus.

Abdessadak, Oumayma / Kandwal, Pankaj / Alaqarbeh, Marwa / Tabti, Kamal / Sbai, Abdelouahid / Ajana, Mohammed Aziz / Lakhlifi, Tahar / Bouachrine, Mohammed

Journal of molecular modeling

2024 Volume 30, Issue 1, Page(s) 23

Abstract: Context: The regioselectivity and diastereoselectivity of the 1,3-dipolar cycloaddition reaction between azomethine ylides and acrolein were investigated. The DFT studies revealed that the favored pathway leads to the formation of cis-cycloadduct ... ...

Abstract	Context: The regioselectivity and diastereoselectivity of the 1,3-dipolar cycloaddition reaction between azomethine ylides and acrolein were investigated. The DFT studies revealed that the favored pathway leads to the formation of cis-cycloadduct pyrrolidine and these computational findings align with experimental observations. The cis-cycloadduct pyrrolidine product serves as an advanced intermediate in the synthesis of a hepatitis C virus inhibitor. For this, the antiviral activity of cis-cycloadduct pyrrolidine against cyclophilin A, the co-factor responsible for hepatitis C virus, was also evaluated through molecular docking simulations which revealed intriguing interactions and a high C-score, which were further confirmed by molecular dynamics simulations, demonstrating stability over a 100-ns simulation period. Furthermore, the cis-cycloadduct pyrrolidine exhibits favorable drug-like properties and a better ADMET profile compared to hepatitis C virus inhibitor. Methods: Chemical reactivity studies were performed using DFT method by the functional B3LYP at 6-31G (d, p) computational level by GAUSSIAN 16 program. Frontal molecular orbitals theory used to investigate HOMO/LUMO interactions between azomethine ylides and acrolein. Findings of this approach were confirmed by global reactivity indices and electron displacement was investigated based on Fukui functions. Furthermore, the activation energies were determined after frequency calculations using TS Berny algorithm and transition states were confirmed by the presence of a single imaginary frequency. Moreover, antiviral activity of cis-cycloadduct was explored through molecular docking using Surflex-Dock suite SYBYL X 2.0, and molecular dynamics simulation using GROMACS program. Finally, drug-like properties were investigated with SwissADME and ADMETlab 2.0.
MeSH term(s)	Molecular Docking Simulation ; Hepacivirus ; Acrolein/pharmacology ; Cycloaddition Reaction ; Pyrrolidines/chemistry ; Antiviral Agents/pharmacology
Chemical Substances	azomethine ; Acrolein (7864XYD3JJ) ; Pyrrolidines ; Antiviral Agents
Language	English
Publishing date	2024-01-05
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-023-05818-8
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Article ; Online: Profiling the structural determinants of pyrrolidine derivative as gelatinases (MMP-2 and MMP-9) inhibitors using in silico approaches.

Tabti, Kamal / Ahmad, Iqrar / Zafar, Imran / Sbai, Abdelouahid / Maghat, Hamid / Bouachrine, Mohammed / Lakhlifi, Tahar

Computational biology and chemistry

2023 Volume 104, Page(s) 107855

Abstract: Quantitative structure activity relationship (QSAR) studies on pyrrolidine derivatives have been established using CoMFA, CoMSIA, and Hologram QSAR analysis to estimate the values ( ... ...

Abstract	Quantitative structure activity relationship (QSAR) studies on pyrrolidine derivatives have been established using CoMFA, CoMSIA, and Hologram QSAR analysis to estimate the values (pIC
MeSH term(s)	Molecular Docking Simulation ; Gelatinases ; Matrix Metalloproteinase 2 ; Matrix Metalloproteinase 9 ; Binding Sites ; Quantitative Structure-Activity Relationship
Chemical Substances	Gelatinases (EC 3.4.24.-) ; Matrix Metalloproteinase 2 (EC 3.4.24.24) ; Matrix Metalloproteinase 9 (EC 3.4.24.35)
Language	English
Publishing date	2023-03-26
Publishing country	England
Document type	Journal Article
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2023.107855
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Article ; Online: Molecular modeling study of pyrrolidine derivatives as novel myeloid cell leukemia-1 inhibitors through combined 3D-QSAR, molecular docking, ADME/Tox and MD simulation techniques.

Tabti, Kamal / Baammi, Soukayna / Sbai, Abdelouahid / Maghat, Hamid / Lakhlifi, Tahar / Bouachrine, Mohammed

Journal of biomolecular structure & dynamics

2023 Volume 41, Issue 23, Page(s) 13798–13814

Abstract: A series of pyrrolidine derivatives have been used to study the main structural requirements for designing novel Mcl-1 inhibitors. For this purpose, three models CoMSIA, CoMFA and HQSAR were generated using QSAR molecular modeling techniques. The ... ...

Abstract	A series of pyrrolidine derivatives have been used to study the main structural requirements for designing novel Mcl-1 inhibitors. For this purpose, three models CoMSIA, CoMFA and HQSAR were generated using QSAR molecular modeling techniques. The statistical results of the CoMFA (
MeSH term(s)	Humans ; Molecular Docking Simulation ; Quantitative Structure-Activity Relationship ; Myeloid Cell Leukemia Sequence 1 Protein ; Myeloid Cells ; Leukemia ; Molecular Dynamics Simulation
Chemical Substances	Myeloid Cell Leukemia Sequence 1 Protein
Language	English
Publishing date	2023-02-25
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2183032
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Article ; Online: High-throughput virtual screening approach of natural compounds as target inhibitors of plasmepsin-II.

En-Nahli, Fatima / Baammi, Soukayna / Hajji, Halima / Alaqarbeh, Marwa / Lakhlifi, Tahar / Bouachrine, Mohammed

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 19, Page(s) 10070–10080

Abstract: Plasmepsin II is a key enzyme in the life cycle of ... ...

Abstract	Plasmepsin II is a key enzyme in the life cycle of the
MeSH term(s)	Antimalarials/chemistry ; Molecular Dynamics Simulation ; Quinolines ; Molecular Docking Simulation
Chemical Substances	plasmepsin II (EC 3.4.23.39) ; plasmepsin (EC 3.4.23.38) ; Antimalarials ; Quinolines
Language	English
Publishing date	2022-12-05
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2152871
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Article ; Online: Computational approach investigation bioactive molecules from Saussurea Costus plant as SARS-CoV-2 main protease inhibitors using reverse docking, molecular dynamics simulation, and pharmacokinetic ADMET parameters.

Hajji, Halima / Alaqarbeh, Marwa / Lakhlifi, Tahar / Ajana, Mohammed Aziz / Alsakhen, Nada / Bouachrine, Mohammed

Computers in biology and medicine

2022 Volume 150, Page(s) 106209

Abstract: SARS-COV-2 virus causes (COVID-19) disease; it has become a global pandemic since 2019 and has negatively affected all aspects of human life. Scientists have made great efforts to find a reliable cure, vaccine, or treatment for this emerging disease. ... ...

Abstract	SARS-COV-2 virus causes (COVID-19) disease; it has become a global pandemic since 2019 and has negatively affected all aspects of human life. Scientists have made great efforts to find a reliable cure, vaccine, or treatment for this emerging disease. Efforts have been directed towards using medicinal plants as alternative medicines, as the active chemical compounds in them have been discovered as potential antiviral or anti-inflammatory agents. In this research, the potential of Saussurea costus (S. Costus) or QUST Al Hindi chemical consistent as potential antiviral agents was investigated by using computational methods such as Reverse Docking, ADMET, and Molecular Dynamics with different proteases COVID-19 such as PDB: 2GZ9; 6LU7; 7AOL, 6Y2E, 6Y84. The results of Reverse Docking the complex between 6LU7 proteases and Cynaropicrin compound being the best complex, as the same result, is achieved by molecular dynamics. Also, the toxicity testing result from ADMET method proved that the complex is the least toxic and the safest possible drug. In addition, 6LU7-Cynaropicrin complex obeyed Lipinski rule; it formed ≤5 H-bond donors and ≤10 H bond acceptors, MW < 500 Daltons, and octanol/water partition coefficient <5.
MeSH term(s)	Humans ; Molecular Dynamics Simulation ; Saussurea ; COVID-19 ; SARS-CoV-2 ; Peptide Hydrolases ; Molecular Docking Simulation ; Protease Inhibitors
Chemical Substances	cynaropicrin (M9233789I9) ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Peptide Hydrolases (EC 3.4.-) ; Protease Inhibitors
Language	English
Publishing date	2022-10-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.106209
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Article ; Online: In silico research on new sulfonamide derivatives as BRD4 inhibitors targeting acute myeloid leukemia using various computational techniques including 3D-QSAR, HQSAR, molecular docking, ADME/Tox, and molecular dynamics.

Belghalia, Etibaria / Ouabane, Mohamed / El Bahi, Salma / Rehman, Hafiz Muzzammel / Sbai, Abdelouahid / Lakhlifi, Tahar / Bouachrine, Mohammed

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–19

Abstract: Acute myeloid leukemia, a serious condition affecting stem cells, drives uncontrollable myeloblast proliferation, leading to accumulation. Extensive research seeks rapid, effective chemotherapeutics. A potential option is a BRD4 inhibitor, known for ... ...

Abstract	Acute myeloid leukemia, a serious condition affecting stem cells, drives uncontrollable myeloblast proliferation, leading to accumulation. Extensive research seeks rapid, effective chemotherapeutics. A potential option is a BRD4 inhibitor, known for suppressing cell proliferation. Sulfonamide derivatives probed essential structural elements for potent BRD4 inhibitors. To achieve this goal, we employed 3D-QSAR molecular modeling techniques, including CoMFA, CoMSIA, and HQSAR models, along with molecular docking and molecular dynamics simulations. The validation of the 2D/3D QSAR models, both internally and externally, underscores their robustness and reliability. The contour plots derived from CoMFA, CoMSIA, and HQSAR analyses played a pivotal role in shaping the design of effective BRD4 inhibitors. Importantly, our findings highlight the advantageous impact of incorporating bulkier substituents on the pyridinone ring and hydrophobic/electrostatic substituents on the methoxy-substituted phenyl ring, enhancing interactions with the BRD4 target. The interaction mode of the new compounds with the BRD4 receptor (PDB ID: 4BJX) was investigated using molecular docking simulations, revealing favorable binding energies, supported by the formation of hydrogen and hydrophobic bonds with key protein residues. Moreover, these novel inhibitors exhibited good oral bioavailability and demonstrated non-toxic properties based on ADMET analysis. Furthermore, the newly designed compounds along with the most active one from series 58, underwent a molecular dynamics simulation to analyze their behavior. The simulation provided additional evidence to support the molecular docking results, confirming the sustained stability of the analyzed molecules over the trajectory. This outcome could serve as a valuable reference for designing and developing novel and effective BRD4 inhibitors.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2023-09-01
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2250460
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Article ; Online: Molecular toxicity of nitrobenzene derivatives to tetrahymena pyriformis based on SMILES descriptors using Monte Carlo, docking, and MD simulations.

Ouabane, Mohamed / Zaki, Khadija / Tabti, Kamal / Alaqarbeh, Marwa / Sbai, Abdelouahid / Sekkate, Chakib / Bouachrine, Mohammed / Lakhlifi, Tahar

Computers in biology and medicine

2023 Volume 169, Page(s) 107880

Abstract: It is challenging to model the toxicity of nitroaromatic compounds due to limited experimental data. Nitrobenzene derivatives are commonly used in industry and can lead to environmental contamination. Extensive research, including several QSPR studies, ... ...

Abstract	It is challenging to model the toxicity of nitroaromatic compounds due to limited experimental data. Nitrobenzene derivatives are commonly used in industry and can lead to environmental contamination. Extensive research, including several QSPR studies, has been conducted to understand their toxicity. Predictive QSPR models can help improve chemical safety, but their limitations must be considered, and the molecular factors affecting toxicity should be carefully investigated. The latest QSPR methods, molecular modeling techniques, machine learning algorithms, and computational chemistry tools are essential for developing accurate and robust models. In this work, we used these methods to study a series of fifty compounds derived from nitrobenzene. The Monte Carlo approach was used for QSPR modeling by applying the SMILES molecular structure representation and optimal molecular descriptors. The correlation ideality index (CII) and correlation contradiction index (CCI) were further introduced as validation parameters to estimate the developed models' predictive ability. The statistical quality of the CII models was better than those without CII. The best QSPR model with the following statistical parameters (Split-3): (R
MeSH term(s)	Tetrahymena pyriformis ; Models, Molecular ; Nitrobenzenes ; Monte Carlo Method ; Quantitative Structure-Activity Relationship
Chemical Substances	nitrobenzene (E57JCN6SSY) ; Nitrobenzenes
Language	English
Publishing date	2023-12-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2023.107880
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Article ; Online: Design new organic material based on triphenylamine (TPA) with D-π-A-π-D structure used as an electron donor for organic solar cells: A DFT approach.

Azaid, Ahmed / Abram, Tayeb / Alaqarbeh, Marwa / Raftani, Marzouk / Kacimi, Rchid / Sbai, Abdelouahid / Lakhlifi, Tahar / Bouachrine, Mohammed

Journal of molecular graphics & modelling

2023 Volume 122, Page(s) 108470

Abstract: Because of the increasing scarcity of fossil fuels and the growing need for energy, it has become necessary to research new renewable energy resources. In this study, five new high-performance materials (TP- ... ...

Abstract	Because of the increasing scarcity of fossil fuels and the growing need for energy, it has become necessary to research new renewable energy resources. In this study, five new high-performance materials (TP-FA
MeSH term(s)	Electrons ; Amines ; Density Functional Theory ; Electronics ; Renewable Energy
Chemical Substances	Amines
Language	English
Publishing date	2023-04-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2023.108470
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Article ; Online: 3D-QSAR, molecular docking, simulation dynamic and ADMET studies on new quinolines derivatives against colorectal carcinoma activity.

El-Mernissi, Reda / Khaldan, Ayoub / Bouamrane, Soukaina / Rehman, Hafiz Muzzammel / Alaqarbeh, Marwa / Ajana, Mohammed Aziz / Lakhlifi, Tahar / Bouachrine, Mohammed

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 7, Page(s) 3682–3699

Abstract: Cancer is the uncontrolled spread of abnormal cells that results in abnormal tissue growth in the affected organ. One of the most important organs is exposed to the growth of colon cancer cells, which start in the large intestine (colon) or the rectum. ... ...

Abstract	Cancer is the uncontrolled spread of abnormal cells that results in abnormal tissue growth in the affected organ. One of the most important organs is exposed to the growth of colon cancer cells, which start in the large intestine (colon) or the rectum. Several therapeutic protocols were used to treat different kinds of cancer. Recently, several studies have targeted tubulin and microtubules due to their remarkable prefoliation. Also, recent research shows that quinoline compounds have significant efficacy against human colorectal cancer. So, the present work investigated the potential of thirty quinoline compounds as tubulin inhibitors using computational methods. A 3D-QSAR approach using two contours (CoMFA and CoMSIA), molecular docking simulation to determine the binding type of the complexes (ligand-receptor), molecular dynamics simulation and identifying pharmacokinetic characteristics were used to design molecules. For all compounds designed (T1-5), molecular docking was used to compare the stability by type of binding. The ADMET has been utilized for molecules with good stability in molecular docking (T1-3); these compounds have good medicinal characteristics. Furthermore, a molecular dynamics simulation (MD) at 100 ns was performed to confirm the stability of the T1-3 compounds; the molecules (T1-3) remained the most stable throughout the simulation. The compounds T1, T2 and T3 are the best-designed drugs for colorectal carcinoma treatments.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Molecular Docking Simulation ; Quantitative Structure-Activity Relationship ; Molecular Dynamics Simulation ; Quinolines/pharmacology ; Quinolines/chemistry ; Colorectal Neoplasms/drug therapy
Chemical Substances	Quinolines
Language	English
Publishing date	2023-05-25
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2214233
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