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Article: Molecular docking analysis of N-substituted Oseltamivir derivatives with the SARS-CoV-2 main protease.

Belhassan, Assia / Chtita, Samir / Zaki, Hanane / Lakhlifi, Tahar / Bouachrine, Mohammed

2020 Volume 16, Issue 5, Page(s) 404–410

Abstract: The identification of chemotherapeutic drugs against Novel Coronavirus (2019-nCoV) is a significant requirement due to the rapid rise in deaths due to Corona Viral Infection all around the world. Therefore, it is of interest to document the molecular ... ...

Abstract	The identification of chemotherapeutic drugs against Novel Coronavirus (2019-nCoV) is a significant requirement due to the rapid rise in deaths due to Corona Viral Infection all around the world. Therefore, it is of interest to document the molecular docking analysis data of 32 N-substituted Oseltamivir derivatives inhibitors of influenza virus H5N1 with the Novel Coronavirus main protease (2019-nCoV). We describe the optimal binding features of Oseltamivir derivatives with the SARS-Cov-2 main protease (Code PDB: 6LU7) for further consideration.
Keywords	covid19
Language	English
Publishing date	2020-05-31
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2203786-X
ISSN	0973-2063
ISSN	0973-2063
DOI	10.6026/97320630016404
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Article ; Online: New dehydroabietic acid (DHA) derivatives with anticancer activity against HepG2 cancer cell lines as a potential drug targeting EGFR kinase domain. CoMFA study and virtual ligand-based screening.

Zaki, Hanane / Belhassan, Assia / Benlyas, Mohamed / Lakhlifi, Tahar / Bouachrine, Mohammed

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 8, Page(s) 2993–3003

Abstract: Liver cancer has become the third type of cancer that causes death; this is why the design of new chemotherapeutic drugs against this disease is a major need. With this idea, a series of Dehydroabietic Acid-Based Acylhydrazones have been used to generate ...

Abstract	Liver cancer has become the third type of cancer that causes death; this is why the design of new chemotherapeutic drugs against this disease is a major need. With this idea, a series of Dehydroabietic Acid-Based Acylhydrazones have been used to generate a CoMFA model to design new anticancer agents. In this study, we employed a Comparative Molecular Field Analysis studies, we performed those methods on Dehydroabietic Acid-Based Acylhydrazones against HepG2 human cancer cell line. The statistical results are encouraging with Q2 equal to 0.527 and R2 equal to 0.962. The predictive ability of this model was determined using a test set of Dehydroabietic Acid-Based Acylhydrazones that gave an acceptable predictive correlation (R2test) value of 0.614. The developed model guides to design five new molecules with enhanced activity as potential drugs. On the other hand to determine a potential target to these ligands we have established a virtual screening using reverse docking with the most active molecule and 42 antiproliferative targets. Based on the affinity of complex ligand-Target, the intracellular domain of EGFR shows high stability. This suggests that our designed molecules can inhibit the target EGFR which is an important target on targeted therapy of many types of cancer.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Abietanes ; Drug Delivery Systems ; Early Detection of Cancer ; ErbB Receptors ; Hep G2 Cells ; Humans ; Ligands ; Molecular Docking Simulation ; Neoplasms ; Quantitative Structure-Activity Relationship
Chemical Substances	Abietanes ; Ligands ; dehydroabietic acid (0S5XP6S3AU) ; EGFR protein, human (EC 2.7.10.1) ; ErbB Receptors (EC 2.7.10.1)
Language	English
Publishing date	2020-05-04
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1759452
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Article ; Online: 2D-QSPR Study of Olfactive Thresholds for Pyrazine Derivatives Using DFT and Statistical Methods

Assia Belhassan / Samir Chtita / Tahar Lakhlifi / Mohammed Bouachrine

Emerging Science Journal, Vol 3, Iss 3, Pp 179-

2019 Volume 186

Abstract: In this study, we have established two-dimensional quantitative structure propriety relationships (2D-QSPR) model, for a group of 78 molecules based on pyrazine, these molecules were subjected to a 2D-QSPR analyze for their odors thresholds propriety ... ...

Abstract	In this study, we have established two-dimensional quantitative structure propriety relationships (2D-QSPR) model, for a group of 78 molecules based on pyrazine, these molecules were subjected to a 2D-QSPR analyze for their odors thresholds propriety using stepwise Multiple Linear Regression (MLR). The 35 parameters are calculated for the 78 studied compounds using the Gaussian 09W, ChemOffice and ChemSketch softwares. Quantum chemical calculations are used to calculate electronic and quantum chemical descriptors, using the density functional theory (B3LYP/6-31G (d) DFT) methods. The model was used to predict the odors thresholds propriety of the test and training set compounds, and the statistical results exhibited high internal and external consistency as demonstrated by the validation methods.
Keywords	Olfactive thresholds ; Pyrazine ; Quantitative Structure Propriety Relationship ; Density Functional Theory ; Multiple Linear Regression ; Technology (General) ; T1-995 ; Social sciences (General) ; H1-99
Subject code	541
Language	English
Publishing date	2019-06-01T00:00:00Z
Publisher	Ital Publication
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: In silico

Belhassan, Assia / Chtita, Samir / Zaki, Hanane / Alaqarbeh, Marwa / Alsakhen, Nada / Almohtaseb, Firas / Lakhlifi, Tahar / Bouachrine, Mohammed

Journal of molecular structure

2022 Volume 1258, Page(s) 132652

Abstract: COVID-19 is a new infectious disease caused by SARS-COV-2 virus of the coronavirus Family. The identification of drugs against this serious infection is a significant requirement due to the rapid rise in the positive cases and deaths around the world. ... ...

Abstract	COVID-19 is a new infectious disease caused by SARS-COV-2 virus of the coronavirus Family. The identification of drugs against this serious infection is a significant requirement due to the rapid rise in the positive cases and deaths around the world. With this concept, a molecular docking analysis for vitamins and their derivatives (28 molecules) with the active site of SARS-CoV-2 main protease was carried out. The results of molecular docking indicate that the structures with best binding energy in the binding site of the studied enzyme (lowest energy level) are observed for the compounds; Folacin, Riboflavin, and Phylloquinone oxide (Vitamin K1 oxide). A Molecular Dynamic simulation was carried out to study the binding stability for the selected vitamins with the active site of SARS-CoV-2 main protease enzyme. Molecular Dynamic shows that Phylloquinone oxide and Folacin are quite unstable in binding to SARS-CoV-2 main protease, while the Riboflavin is comparatively rigid. The higher fluctuations in Phylloquinone oxide and Folacin indicate that they may not fit very well into the binding site. As expected, the Phylloquinone oxide exhibits small number of H-bonds with protein and Folacin does not form a good interaction with protein. Riboflavin exhibits the highest number of Hydrogen bonds and forms consistent interactions with protein. Additionally, this molecule respect the conditions mentioned in Lipinski's rule and have acceptable ADMET proprieties which indicates that Riboflavin (Vitamin B2) could be interesting for the antiviral treatment of COVID-19.
Language	English
Publishing date	2022-02-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	194476-9
ISSN	0022-2860 ; 0377-046X
ISSN	0022-2860 ; 0377-046X
DOI	10.1016/j.molstruc.2022.132652
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Article ; Online: 3D-QSAR Study of the Chalcone Derivatives as Anticancer Agents

Larbi ElMchichi / Assia Belhassan / Tahar Lakhlifi / Mohammed Bouachrine

Journal of Chemistry, Vol

2020 Volume 2020

Abstract: For their biological properties and particularly for their anticancer activities, chalcones are widely studied. In this work, we have submitted diverse sets of chalcone derivatives to the 3D-QSAR (3-dimensional quantitative structural-activity ... ...

Abstract	For their biological properties and particularly for their anticancer activities, chalcones are widely studied. In this work, we have submitted diverse sets of chalcone derivatives to the 3D-QSAR (3-dimensional quantitative structural-activity relationship) to study their anticancer activities against HTC116 (human colon cancer), relying on the 3-dimensional descriptors: steric and electrostatic descriptors for the CoMFA (comparative molecular field analysis) method and steric, electrostatic, hydrophobic, H-bond donor, and H-bond acceptor descriptors for the CoMSIA method. CoMFA as well as the CoMSIA model have encouraging values of the cross-validation coefficient (Q2) of 0.608 and 0.806 and conventional correlation coefficient (R2) of 0.960 and 0.934, respectively. Furthermore, values of R2test have been obtained as 0.75 and 0.90, respectively. Besides, y-randomization test was also performed to validate our 3D-QSAR models. Based on these satisfactory results, ten new compounds have been designed and predicted by in silico ADMET method. This study could expand the understanding of chalcone derivatives as anticancer agents and would be of great help in lead optimization for early drug discovery of highly potent anticancer activity.
Keywords	Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Study of novel triazolo-benzodiazepine analogues as antidepressants targeting by molecular docking and ADMET properties prediction.

Belhassan, Assia / Zaki, Hanane / Benlyas, Mohamed / Lakhlifi, Tahar / Bouachrine, Mohammed

Heliyon

2019 Volume 5, Issue 9, Page(s) e02446

Abstract: In this study, we have selected a series of a new family of molecules bearing Triazolo-benzodiazepines, an eleven membered heterocyclic ring has been studied for antidepression activity. Docking studies suggested that all the eleven ligands interacted ... ...

Abstract	In this study, we have selected a series of a new family of molecules bearing Triazolo-benzodiazepines, an eleven membered heterocyclic ring has been studied for antidepression activity. Docking studies suggested that all the eleven ligands interacted well within active site of Drosophila melanogaster dopamine transporter (dDAT) (PDB ID: 4M48). Most ligands formed H-bond with amino acid Phe43, Asp46, Asp475, Tyr123, Ser421 and/or Gln316 and also exhibited Pi and Pi-Pi interactions with amino acid residues Tyr124, Phe319, Phe43, Phe325, Ala479 and Val120. In silico ADME evaluations of compounds showed more than 96% intestinal absorption for all compounds. During in vitro Toxicity properties prediction, the Triazolo-benzodiazepines derivatives: M
Language	English
Publishing date	2019-09-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2019.e02446
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Article ; Online: Identification of natural diterpenes isolated from Azorella species targeting dispersin B using in silico approaches.

Rasul, Hezha O / Sabir, Dana Khdr / Aziz, Bakhtyar K / Guillermo Salgado, M / Mendoza-Huizar, L H / Belhassan, Assia / Candia, Lorena Gerli / Villada, Wilson Cardona / Thomas, Noel Vinay / Ghafour, Dlzar D

Journal of molecular modeling

2023 Volume 29, Issue 6, Page(s) 182

Abstract: Context: A bacterial biofilm is a cluster of bacterial cells embedded in a self-produced matrix of extracellular polymeric substances such as DNA, proteins, and polysaccharides. Several diseases have been reported to cause by bacterial biofilms, and ... ...

Abstract	Context: A bacterial biofilm is a cluster of bacterial cells embedded in a self-produced matrix of extracellular polymeric substances such as DNA, proteins, and polysaccharides. Several diseases have been reported to cause by bacterial biofilms, and difficulties in treating these infections are of concern. This work aimed to identify the inhibitor with the highest binding affinity for the receptor protein by screening various inhibitors obtained from Azorella species for a potential target to inhibit dispersin B. This work shows that azorellolide has the highest binding affinity (- 8.2 kcal/mol) among the compounds tested, followed by dyhydroazorellolide, mulinone A, and 7-acetoxy-mulin-9,12-diene which all had a binding affinity of - 8.0 kcal/mol. To the best of our knowledge, this is the first study to evaluate and contrast several diterpene compounds as antibacterial biofilm chemicals. Methods: Here, molecular modelling techniques tested 49 diterpene compounds of Azorella and six FDA-approved antibiotics medicines for antibiofilm activity. Since protein-like interactions are crucial in drug discovery, AutoDock Vina was initially employed to carry out structure-based virtual screening. The drug-likeness and ADMET properties of the chosen compounds were examined to assess the antibiofilm activity further. Lipinski's rule of five was then applied to determine the antibiofilm activity. Then, molecular electrostatic potential was used to determine the relative polarity of a molecule using the Gaussian 09 package and GaussView 5.08. Following three replica molecular dynamic simulations (using the Schrodinger program, Desmond 2019-4 package) that each lasted 100 ns on the promising candidates, binding free energy was estimated using MM-GBSA. Structural visualisation was used to test the binding affinity of each compound to the crystal structure of dispersin B protein (PDB: 1YHT), a well-known antibiofilm compound.
MeSH term(s)	Molecular Docking Simulation ; Apiaceae/chemistry ; Molecular Dynamics Simulation ; Anti-Bacterial Agents/pharmacology ; Diterpenes/pharmacology ; Diterpenes/chemistry
Chemical Substances	Anti-Bacterial Agents ; Diterpenes
Language	English
Publishing date	2023-05-20
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/s00894-023-05592-7
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Article: Assessment of effective imidazole derivatives against SARS-CoV-2 main protease through computational approach

Belhassan, Assia / En-nahli, Fatima / Zaki, Hanane / Lakhlifi, Tahar / Bouachrine, Mohammed

Life sciences. 2020 Dec. 01, v. 262

2020

Abstract: Because of the fast increase in deaths due to Corona Viral Infection in majority region in the world, the detection of drugs potent of this infection is a major need. With this idea, docking study was executed on eighteen imidazole derivatives based on 7- ...

Abstract	Because of the fast increase in deaths due to Corona Viral Infection in majority region in the world, the detection of drugs potent of this infection is a major need. With this idea, docking study was executed on eighteen imidazole derivatives based on 7-chloro-4-aminoquinoline against novel Coronavirus (SARS-CoV-2).In this study, we carried out a docking study of these molecules in the active site of SARS-CoV-2 main protease. The result indicate that Molecules N° 3, 7 and 14 have more binding energy with SARS-CoV-2 main protease recently crystallized (pdb code 6LU7) in comparison with the other imidazole derivatives and the two drug; Chloroquine and hydroxychloroquine. Because of the best energy of interaction, these three molecules could have the most potential antiviral treatment of COVID-19 than the other studied compounds. The structures with best affinity in the binding site of the protease have more than 3 cycles and electronegative atoms in the structure. This may increase the binding affinity of these molecules because of formation of π-bonds, halogen interactions and/or Hydrogen bond interactions between compounds and the enzyme. So, compounds with more cycles and electronegative atoms could have a potent inhibition of SARS-CoV-2 main protease.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; active sites ; chloroquine ; energy ; halogens ; hydrogen bonding ; imidazole ; proteinases
Language	English
Dates of publication	2020-1201
Publishing place	Elsevier Inc.
Document type	Article
Note	NAL-light
ZDB-ID	3378-9
ISSN	1879-0631 ; 0024-3205
ISSN (online)	1879-0631
ISSN	0024-3205
DOI	10.1016/j.lfs.2020.118469
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Article ; Online: Assessment of effective imidazole derivatives against SARS-CoV-2 main protease through computational approach.

Belhassan, Assia / En-Nahli, Fatima / Zaki, Hanane / Lakhlifi, Tahar / Bouachrine, Mohammed

Life sciences

2020 Volume 262, Page(s) 118469

Abstract	Because of the fast increase in deaths due to Corona Viral Infection in majority region in the world, the detection of drugs potent of this infection is a major need. With this idea, docking study was executed on eighteen imidazole derivatives based on 7-chloro-4-aminoquinoline against novel Coronavirus (SARS-CoV-2). In this study, we carried out a docking study of these molecules in the active site of SARS-CoV-2 main protease. The result indicate that Molecules N° 3, 7 and 14 have more binding energy with SARS-CoV-2 main protease recently crystallized (pdb code 6LU7) in comparison with the other imidazole derivatives and the two drug; Chloroquine and hydroxychloroquine. Because of the best energy of interaction, these three molecules could have the most potential antiviral treatment of COVID-19 than the other studied compounds. The structures with best affinity in the binding site of the protease have more than 3 cycles and electronegative atoms in the structure. This may increase the binding affinity of these molecules because of formation of π-bonds, halogen interactions and/or Hydrogen bond interactions between compounds and the enzyme. So, compounds with more cycles and electronegative atoms could have a potent inhibition of SARS-CoV-2 main protease.
MeSH term(s)	Aminoquinolines/pharmacology ; Binding Sites/drug effects ; COVID-19/drug therapy ; Chloroquine/pharmacology ; Coronavirus 3C Proteases/antagonists & inhibitors ; Hydroxychloroquine/pharmacology ; Imidazoles/chemistry ; Imidazoles/pharmacology ; Molecular Docking Simulation ; Molecular Structure ; Pandemics ; Protease Inhibitors/pharmacology ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology
Chemical Substances	Aminoquinolines ; Imidazoles ; Protease Inhibitors ; 7-chloro-4-aminoquinoline (1198-40-9) ; Hydroxychloroquine (4QWG6N8QKH) ; Chloroquine (886U3H6UFF) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Keywords	covid19
Language	English
Publishing date	2020-09-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	3378-9
ISSN	1879-0631 ; 0024-3205
ISSN (online)	1879-0631
ISSN	0024-3205
DOI	10.1016/j.lfs.2020.118469
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Article ; Online: Discovery of Potent SARS-CoV-2 Inhibitors from Approved Antiviral Drugs via Docking and Virtual Screening.

Chtita, Samir / Belhassan, Assia / Aouidate, Adnane / Belaidi, Salah / Bouachrine, Mohammed / Lakhlifi, Tahar

Combinatorial chemistry & high throughput screening

2020 Volume 24, Issue 3, Page(s) 441–454

Abstract: Background: Coronavirus Disease 2019 (COVID-19) pandemic continues to threaten patients, societies and healthcare systems around the world. There is an urgent need to search for possible medications.: Objective: This article intends to use virtual ... ...

Abstract	Background: Coronavirus Disease 2019 (COVID-19) pandemic continues to threaten patients, societies and healthcare systems around the world. There is an urgent need to search for possible medications. Objective: This article intends to use virtual screening and molecular docking methods to find potential inhibitors from existing drugs that can respond to COVID-19. Methods: To take part in the current research investigation and to define a potential target drug that may protect the world from the pandemic of corona disease, a virtual screening study of 129 approved drugs was carried out which showed that their metabolic characteristics, dosages used, potential efficacy and side effects are clear as they have been approved for treating existing infections. Especially 12 drugs against chronic hepatitis B virus, 37 against chronic hepatitis C virus, 37 against human immunodeficiency virus, 14 anti-herpesvirus, 11 anti-influenza, and 18 other drugs currently on the market were considered for this study. These drugs were then evaluated using virtual screening and molecular docking studies on the active site of the (SARS-CoV-2) main protease (6lu7). Once the efficacy of the drug is determined, it can be approved for its in vitro and in vivo activity against the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which can be beneficial for the rapid clinical treatment of patients. These drugs were considered potentially effective against SARS-CoV-2 and those with high molecular docking scores were proposed as novel candidates for repurposing. The N3 inhibitor cocrystallized with protease (6lu7) and the anti-HIV protease inhibitor Lopinavir were used as standards for comparison. Results: The results suggest the effectiveness of Beclabuvir, Nilotinib, Tirilazad, Trametinib and Glecaprevir as potent drugs against SARS-CoV-2 since they tightly bind to its main protease. Conclusion: These promising drugs can inhibit the replication of the virus; hence, the repurposing of these compounds is suggested for the treatment of COVID-19. No toxicity measurements are required for these drugs since they were previously tested prior to their approval by the FDA. However, the assessment of these potential inhibitors as clinical drugs requires further in vivo tests of these drugs.
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/metabolism ; Antiviral Agents/pharmacology ; Binding Sites ; Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/chemistry ; Coronavirus 3C Proteases/metabolism ; Drug Evaluation, Preclinical/methods ; Drug Repositioning ; Hepacivirus/drug effects ; Influenza A virus/drug effects ; Lopinavir/chemistry ; Lopinavir/pharmacology ; Molecular Docking Simulation ; Pyridones/chemistry ; Pyridones/pharmacology ; Pyrimidinones/chemistry ; Pyrimidinones/pharmacology ; SARS-CoV-2/drug effects
Chemical Substances	Antiviral Agents ; Pyridones ; Pyrimidinones ; Lopinavir (2494G1JF75) ; trametinib (33E86K87QN) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Keywords	covid19
Language	English
Publishing date	2020-08-03
Publishing country	United Arab Emirates
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2064785-2
ISSN	1875-5402 ; 1386-2073
ISSN (online)	1875-5402
ISSN	1386-2073
DOI	10.2174/1386207323999200730205447
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