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Article ; Online: Homology modeling, virtual screening, molecular docking, molecular dynamic (MD) simulation, and ADMET approaches for identification of natural anti-Parkinson agents targeting MAO-B protein.

El Aissouq, Abdellah / Bouachrine, Mohammed / Ouammou, Abdelkrim / Khalil, Fouad

2022 Volume 786, Page(s) 136803

Abstract: Monoamine oxidase-B (MAO-B) is a flavin-dependent enzyme involved in various neurodegenerative disorders. Here, a dataset of 142 chalcone derivatives, collected from various natural plants, was screened by combining structure-based virtual screening and ... ...

Abstract	Monoamine oxidase-B (MAO-B) is a flavin-dependent enzyme involved in various neurodegenerative disorders. Here, a dataset of 142 chalcone derivatives, collected from various natural plants, was screened by combining structure-based virtual screening and ADMET approaches. The goal is to discover novel natural chalcones as potential MAO-B inhibitors. With the help of the Gaussian 09.5 software, the 3D chemical structures of compounds were optimized using the DFT method. The 3D structure of the hMAO-B enzyme was built using the Modeller software. The optimized structures were subjected to virtual screening by Autodock Vina, implicated in PyRx software. Among the 142 natural substances, 43 were selected based on their binding affinity. Then, the pharmacokinetic proprieties and toxicity of these compounds were evaluated using ADMET analysis. Ten compounds were predicted to have ADMET characteristics with no side effects. The binding modes and interactions of the top selected compounds were then evaluated using AutoDock 4.2. Compounds P60 and P81 were found to be potential inhibitors of MAO-B compared to rasagiline, safinamid, and selegiline, the reference drugs. The stability of the selected compounds was confirmed by MD simulation. Based on this finding, compounds P60 and P81 could be considered potential hMAO-B inhibitors.
MeSH term(s)	Chalcones/chemistry ; Chalcones/pharmacology ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Monoamine Oxidase/metabolism ; Monoamine Oxidase Inhibitors/chemistry ; Monoamine Oxidase Inhibitors/metabolism ; Monoamine Oxidase Inhibitors/pharmacology ; Structure-Activity Relationship
Chemical Substances	Chalcones ; Monoamine Oxidase Inhibitors ; Monoamine Oxidase (EC 1.4.3.4)
Language	English
Publishing date	2022-07-14
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	194929-9
ISSN	1872-7972 ; 0304-3940
ISSN (online)	1872-7972
ISSN	0304-3940
DOI	10.1016/j.neulet.2022.136803
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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: Organic dyes based on selenophene for efficient dye-sensitized solar cell.

Bouaamlat, Hussam / Abram, Tayeb / Bouachrine, Mohammed / Abarkan, Mustapha

Journal of molecular modeling

2021 Volume 27, Issue 11, Page(s) 333

Abstract: The investigation of dye-sensitized solar cells (DSSCs) based on different donor groups linked with cyanoacrylic acid electron acceptor by Selenophene as π-bridged (D-π-A) was performed based on density functional theory (DFT) time-dependent DFT (TDDFT). ...

Abstract	The investigation of dye-sensitized solar cells (DSSCs) based on different donor groups linked with cyanoacrylic acid electron acceptor by Selenophene as π-bridged (D-π-A) was performed based on density functional theory (DFT) time-dependent DFT (TDDFT). Different functional were tested W97XD, PBEPBE, CAM-B3LYP, and B3PW91, and compared with experimental results of the reference D1. The theoretical results with CAM-B3LYP functional at 6-311G (d,p) basis sets were capable of predicting the absorption maximum that has been reported experimentally. Calculations were made to establish the conformational orientation of the cyanoacrylic acid group and evaluate the effect of changing donor units' on the electronic properties of the ground state. Structural and electronic properties, along with the photovoltaic properties, were investigated. The LUMO and HOMO energy levels of these dyes can positively affect the process of electron injection and dye regeneration. Light-harvesting efficiency (LHE), injection driving force (ΔG
Language	English
Publishing date	2021-10-29
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/s00894-021-04953-4
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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: Theoretical investigation of the effect of changing the auxiliary acceptor on the performance of organic D-A'-A dyes used as sensitizers in DSSCs.

Bouzineb, Yassir / Fitri, Asmae / Benjelloun, Adil Touimi / Benzakour, Mohammed / Mcharfi, Mohammed / Bouachrine, Mohammed

Journal of molecular modeling

2023 Volume 29, Issue 12, Page(s) 365

Abstract: Context: Dye-sensitized solar cells (DSSCs) have displayed huge potential in inexpensive, efficient, and clean solar energy technology. In this work, seven new dyes with the structure D-A'-A were designed in which the thiophene in the reference dye was ... ...

Abstract	Context: Dye-sensitized solar cells (DSSCs) have displayed huge potential in inexpensive, efficient, and clean solar energy technology. In this work, seven new dyes with the structure D-A'-A were designed in which the thiophene in the reference dye was replaced by auxiliary acceptors (A'). These dyes consist mainly of a pyranylidene-based electron donor D and the cyanoacrylic acid moiety as acceptor A. A computational investigation was carried out on the effect of various auxiliary acceptors A' on the efficiency of D-A'-A dyes in isolation and after binding to the semiconductor TiO Methods: Using Density Functional Theory (DFT) approaches with the B3LYP functional and the 6-31G(d,p) basis set, all ground state geometries of the isolated dyes were fully optimized. Time-Dependent Density Functional Theory (TD-DFT) method using the CAM-B3LYP/6-31G(d,p)/IEF-PCM level was applied to simulate the UV-visible absorption properties. All isolated dye calculations were performed using the Gaussian 09 software package. DFT calculations have been carried out with the DMol3 package included in Materials Studio for simulating the adsorption of the investigated dyestuff on the TiO2 surface of anatase (101), using the generalized gradient corrected approximation (GGA) approach of the Perdew-Burke-Ernzerhof (PBE) functional with the basic set of digital double polarisation (DNP). To study the optical performance of dye@TiO
Language	English
Publishing date	2023-11-10
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/s00894-023-05766-3
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Article ; Online: Analysis molecular design of novel D-A-Di-A-D conjugated compounds for high-efficiency organic solar cells.

El Mhamedi, Imane / El Malki, Zakaria / El Karkri, Anass / Bouachrine, Mohammed

Journal of molecular modeling

2023 Volume 29, Issue 10, Page(s) 324

Abstract: Context: The work described in this section uses DFT/TD-DFT/B3LYP/6-31G (d,p) (density functional theory and time-dependent density functional theory) to study and simulate the structural, optoelectronic, and optical properties of a series of conjugated ...

Abstract	Context: The work described in this section uses DFT/TD-DFT/B3LYP/6-31G (d,p) (density functional theory and time-dependent density functional theory) to study and simulate the structural, optoelectronic, and optical properties of a series of conjugated compounds based on a modular D-A-Di-A-D architecture. These compounds integrate the D donor unit (carbazole), the A acceptor unit (benzothiadiazole) and various Di donor units. Using AMPS-1D (analysis of micronic structure and photonics), work has been carried out to evaluate the photovoltaic performance of these conjugated compounds in the context of organic solar cells. The compounds show variable performance in terms of energy conversion efficiency, ranging from 7.11 to 11.70%. The addition of a PEDOT layer between the active layer and the anode results in a significant improvement in photovoltaic performance, with energy conversion efficiencies of up to 15.31%, the highest value achieved. The use of ZnO as an intermediate layer remarkably improves photovoltaic performance for all compounds, with notable energy conversion efficiencies reaching 17.13%, 17.20%, and 18%. All in all, the compounds studied present promising prospects as viable candidates for organic block heterojunction (BHJ) solar cell applications. Methods: DFT/TD-DFT/B3LYP/6-31G (d,p), these acronyms stand for the computational methods used to study the properties of compounds. DFT, for "Density Functional Theory", is a quantum computation method used to describe the electronic and structural properties of molecular systems. TD-DFT, for "Time-Dependent Density Functional Theory", is an extension of DFT that allows the treatment of optical and excitation properties. B3LYP is a density functional frequently used in DFT to calculate molecular properties. In addition, 6-31G (d,p) refers to a basic wave function used to approximate the distribution of electrons in molecules. AMPS-1D, or "Analysis of Micro and Photonic Structure", is a modeling tool for studying the photovoltaic properties of multilayer structures, particularly in the context of organic solar cells.
Language	English
Publishing date	2023-09-25
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/s00894-023-05729-8
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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: 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: 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: Structure-based virtual screening of novel natural products as chalcone derivatives against SARS-CoV-2 M

El Aissouq, Abdellah / Bouachrine, Mohammed / Bouayyadi, Lahcen / Ouammou, Abdelkrim / Khalil, Fouad

Journal of biomolecular structure & dynamics

2023 Volume 41, Issue 22, Page(s) 13235–13249

Abstract: Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, has spread quickly around the world, causing a global pandemic. It has infected more than 500 million people as of April 28, 2022. Much research has been reported to stop the virus from ... ...

Abstract	Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, has spread quickly around the world, causing a global pandemic. It has infected more than 500 million people as of April 28, 2022. Much research has been reported to stop the virus from spreading, but there are currently no approved medicines to treat COVID-19. In this work, a dataset of 142 natural products collected from various medicinal plants was used to perform structure-based virtual screening (SBVS) through the combined application of molecular docking and molecular dynamics (MD) simulation methods. First, the dataset of compounds was optimized using the density functional theory (DFT) approach. The optimized compounds were then submitted to the first screening, which was done by the pKCM web server to look for drug-likeness and the PyRx to look for binding affinity. Among the 142 natural substances, 10 compounds were selected for docking validation. Compounds that interact with CYS145 and LEU141, the essential catalytic residues, as well as compounds with binding affinities less than -8.0 kcal/mol, are considered promising anti-SARS-CoV-2 drug candidates. The top-ranked compounds were then evaluated by MD simulations and MM-GBSA method. These results could help researchers come up with new natural compounds that could be used to treat SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Chalcones ; Molecular Docking Simulation ; Biological Products/pharmacology ; Chalcone ; Molecular Dynamics Simulation ; Protease Inhibitors
Chemical Substances	Chalcones ; Biological Products ; Chalcone (5S5A2Q39HX) ; Protease Inhibitors
Language	English
Publishing date	2023-02-08
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2172456
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