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Article: In Silico

Magri, Meryam / Bouricha, El Mehdi / Hakmi, Mohammed / Jaoudi, Rachid El / Belyamani, Lahcen / Ibrahimi, Azeddine

2023 Volume 17, Page(s) 11779322231212755

Abstract: Pseudomonas ... ...

Abstract	Pseudomonas aeruginosa
Language	English
Publishing date	2023-11-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2423808-9
ISSN	1177-9322
ISSN	1177-9322
DOI	10.1177/11779322231212755
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Article: IDbSV: An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution.

Essabbar, Abdelmounim / Kartti, Souad / Alouane, Tarek / Hakmi, Mohammed / Belyamani, Lahcen / Ibrahimi, Azeddine

Frontiers in medicine

2021 Volume 8, Page(s) 765249

Abstract: Ending COVID-19 pandemic requires a collaborative understanding of SARS-CoV-2 and COVID-19 mechanisms. Yet, the evolving nature of coronaviruses results in a continuous emergence of new variants of the virus. Central to this is the need for a continuous ... ...

Abstract	Ending COVID-19 pandemic requires a collaborative understanding of SARS-CoV-2 and COVID-19 mechanisms. Yet, the evolving nature of coronaviruses results in a continuous emergence of new variants of the virus. Central to this is the need for a continuous monitoring system able to detect potentially harmful variants of the virus in real-time. In this manuscript, we present the International Database of SARS-CoV-2 Variations (IDbSV), the result of ongoing efforts in curating, analyzing, and sharing comprehensive interpretation of SARS-CoV-2's genetic variations and variants. Through user-friendly interactive data visualizations, we aim to provide a novel surveillance tool to the scientific and public health communities. The database is regularly updated with new records through a 4-step workflow (1-Quality control of curated sequences, 2-Call of variations, 3-Functional annotation, and 4-Metadata association). To the best of our knowledge, IDbSV provides access to the largest repository of SARS-CoV-2 variations and the largest analysis of SARS-CoV-2 genomes with over 60 thousand annotated variations curated from the 1,808,613 genomes alongside their functional annotations, first known appearance, and associated genetic lineages, enabling a robust interpretation tool for SARS-CoV-2 variations to help understanding SARS-CoV-2 dynamics across the world.
Language	English
Publishing date	2021-12-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2021.765249
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Article ; Online: In-silico

Bouricha, El Mehdi / Hakmi, Mohammed / Akachar, Jihane / Zouaidia, Fouad / Ibrahimi, Azeddine

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 11, Page(s) 5203–5210

Abstract: Estrogen receptor α (ERα) plays a critical role in breast cancer (BC) development. The standard therapeutic strategies for ERα- positive (ERα+) BC consist of impairing ERα signalling pathway by either estrogen competitors blocking its interaction with ... ...

Abstract	Estrogen receptor α (ERα) plays a critical role in breast cancer (BC) development. The standard therapeutic strategies for ERα- positive (ERα+) BC consist of impairing ERα signalling pathway by either estrogen competitors blocking its interaction with the ligand binding domain (LBD) or agents inhibiting the production of estrogen. These strategies are limited by many factors that lead to constitutive activation of ERα and consequently, resistance to treatment. Targeting the DNA binding domain (DBD) of ERα instead of its LBD with small-molecule inhibitors could be an alternative to impair ERα's signalling pathway. For this purpose, we conducted a structure based virtual screening of DrugBank against the crystal structure of ERα-DBD (PDB ID: 1HCQ) using the Glide module in standard precision (SP) and extra precision (XP) mode of docking. Molecules with XP Gscore less than -8 kcal/mol were selected and visually inspected to keep only the reasonable docking poses. Subsequently, these molecules were clustered using structural interaction fingerprints analysis and the complexes of the top ranked molecules of each cluster based on XP Gscore were subjected to 200 ns molecular dynamics simulations followed by MM-GBSA binding free energy calculation for the last 100 ns of each complex. In this study, we identified three molecules from DrugBank namely DB03450, DB02593 and DB08001 showing significant stability and strong interaction with the key amino acids during MD simulation suggesting a potential inhibition of the target. These molecules could be used as promising lead compounds to impair the ERα signalisation in hormone therapy-resistant breast cancer.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Antineoplastic Agents/chemistry ; Binding Sites ; Breast Neoplasms/drug therapy ; DNA/metabolism ; Estrogen Receptor alpha/antagonists & inhibitors ; Estrogens ; Female ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding
Chemical Substances	Antineoplastic Agents ; Estrogen Receptor alpha ; Estrogens ; Ligands ; DNA (9007-49-2)
Language	English
Publishing date	2021-01-06
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	10.1080/07391102.2020.1869094
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Article ; Online: Computational modeling and druggability assessment of Aggregatibacter actinomycetemcomitans leukotoxin.

Hakmi, Mohammed / Bouricha, El Mehdi / El Harti, Jaouad / Amzazi, Said / Belyamani, Lahcen / Khanfri, Jamal Eddine / Ibrahimi, Azeddine

Computer methods and programs in biomedicine

2022 Volume 222, Page(s) 106952

Abstract: The leukotoxin (LtxA) of Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) is a protein exotoxin belonging to the repeat-in-toxin family (RTX). Numerous studies have demonstrated that LtxA may play a critical role in the pathogenicity of A. ...

Abstract	The leukotoxin (LtxA) of Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) is a protein exotoxin belonging to the repeat-in-toxin family (RTX). Numerous studies have demonstrated that LtxA may play a critical role in the pathogenicity of A. actinomycetemcomitans since hyper-leukotoxic strains have been associated with severe disease. Accordingly, considerable effort has been made to elucidate the mechanisms by which LtxA interacts with host cells and induce their death. However, these attempts have been hampered by the unavailability of a tertiary structure of the toxin, which limits the understanding of its molecular properties and mechanisms. In this paper, we used homology and template free modeling algorithms to build the complete tertiary model of LtxA at atomic level in its calcium-bound Holo-state. The resulting model was refined by energy minimization, validated by Molprobity and ProSA tools, and subsequently subjected to a cumulative 600ns of all-atom classical molecular dynamics simulation to evaluate its structural aspects. The druggability of the proposed model was assessed using Fpocket and FTMap tools, resulting in the identification of four putative cavities and fifteen binding hotspots that could be targeted by rational drug design tools to find new ligands to inhibit LtxA activity.
MeSH term(s)	Aggregatibacter actinomycetemcomitans/chemistry ; Aggregatibacter actinomycetemcomitans/metabolism ; Computer Simulation ; Exotoxins/chemistry ; Exotoxins/metabolism ; Exotoxins/pharmacology
Chemical Substances	Exotoxins ; leukotoxin
Language	English
Publishing date	2022-06-13
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	632564-6
ISSN	1872-7565 ; 0169-2607
ISSN (online)	1872-7565
ISSN	0169-2607
DOI	10.1016/j.cmpb.2022.106952
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Article: In silico analysis of ACE2 orthologues to predict animal host range with high susceptibility to SARS-CoV-2

Bouricha, El Mehdi / Hakmi, Mohammed / Akachar, Jihane / Belyamani, Lahcen / Ibrahimi, Azeddine

3 Biotech. 2020 Nov., v. 10, no. 11

2020

Abstract: SARS-CoV-2, which causes severe pneumonia epidemics, probably originated from Chinese horseshoe bats, but the intermediate and host range is still unknown. ACE2 is the entry receptor for SARS-CoV-2. The binding capacity of SARS-CoV-2 spike protein to ... ...

Abstract	SARS-CoV-2, which causes severe pneumonia epidemics, probably originated from Chinese horseshoe bats, but the intermediate and host range is still unknown. ACE2 is the entry receptor for SARS-CoV-2. The binding capacity of SARS-CoV-2 spike protein to ACE2 is the critical determinant of viral host range and cross-species infection. Here, we used an in silico approach to predict the potential animals range with high susceptibility to SARS-CoV-2 by modelling and studying the Spike–ACE2 interaction of 22 domestic and wild animals. Our results showed that all studied animals are potentially susceptible to SARS-CoV-2 infection with a slight difference in the binding affinity and stability of their ACE2–RBD complexes. Furthermore, we identified a specific substitution of tyrosine to histidine at position 41 in ACE2 that likely reduces the affinity to SARS-CoV-2 in horses and greater horseshoe bats. These results may help to provide important insights into SARS-CoV-2 host range which will make it possible to control the spread of the virus and identify animal models that could be used for screening antiviral drugs or vaccine candidates against SARS-CoV-2.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; computer simulation ; histidine ; host range ; pneumonia ; tyrosine ; vaccines ; viruses
Language	English
Dates of publication	2020-11
Size	p. 483.
Publishing place	Springer International Publishing
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-020-02471-3
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Identifying epitopes for cluster of differentiation and design of new peptides inhibitors against human SARS-CoV-2 spike RBD by an in-silico approach

Akachar, Jihane / Bouricha, El Mehdi / Hakmi, Mohammed / Belyamani, Lahcen / El Jaoudi, Rachid / Ibrahimi, Azeddine

Heliyon. 2020 Dec., v. 6, no. 12 p.e05739-

2020

Abstract: The coronavirus disease 19 (COVID-19) is a highly contagious and rapidly spreading infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some cases, the disease can be fatal which resulted in more than one million ... ...

Abstract	The coronavirus disease 19 (COVID-19) is a highly contagious and rapidly spreading infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some cases, the disease can be fatal which resulted in more than one million deaths worldwide according the WHO. Currently, there is no effective vaccine or treatment for COVID-19, however many small-molecule inhibitors have shown potent antiviral activity against SARS-CoV-2 and some of them are now under clinical trials. Despite their promising activities, the development of these small molecules for the clinical use can be limited by many factors like the off-target effect, the poor stability, and the low bioavailability. The clusters of differentiation CD147, CD209, CD299 have been identified as essential entry co-receptors for SARS-CoV-2 species specificity to humans, although the underlying mechanisms are yet to be fully elucidated. In this paper, protein-protein docking was utilized for identifying the critical epitopes in CD147, CD209 and CD299 which are involved in the binding with SARS-CoV-2 Spike receptor binding domain (RBD). The results of binding free energies showed a high affinity of SARS-CoV-2 RBD to CD299 receptor which was used as a reference to derive hypothetical peptide sequences with specific binding activities to SARS-CoV-2 RBD. Molecular docking and molecular dynamics simulations of the newly designed peptides showed favorable binding features and stability with SARS-CoV-2 RBD and therefore can be further considered as potential candidates in future anti-SARS CoV-2 drug discovery studies.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; antiviral properties ; bioavailability ; computer simulation ; epitopes ; humans ; molecular dynamics ; peptides ; vaccines ; Coronavirus 19 ; Molecular docking ; Peptide-based drugs ; Spike protein ; Cluster of differentiation ; Computer science ; Engineering ; Physics ; Chemistry ; Biological sciences
Language	English
Dates of publication	2020-12
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.2020.e05739
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Article: Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis.

Hakmi, Mohammed / Bouricha, El Mehdi / Kandoussi, Ilham / Harti, Jaouad El / Ibrahimi, Azeddine

Bioinformation

2020 Volume 16, Issue 4, Page(s) 301–306

Abstract: The new SARS-CoV-2 coronavirus is the causative agent of the COVID-19 pandemic outbreak that affected more than 190 countries worldwide with more than 292,000 confirmed cases and over 12,700 deaths. There is at the moment no vaccine or effective ... ...

Abstract	The new SARS-CoV-2 coronavirus is the causative agent of the COVID-19 pandemic outbreak that affected more than 190 countries worldwide with more than 292,000 confirmed cases and over 12,700 deaths. There is at the moment no vaccine or effective treatment for this disease which constitutes a serious global health problem. It is of interest to use a structure based virtual screening approach for the identification of potential inhibitors of the main protease of SARS-CoV-2 (M
Keywords	covid19
Language	English
Publishing date	2020-04-30
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2203786-X
ISSN	0973-2063
ISSN	0973-2063
DOI	10.6026/97320630016301
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Article: In silico

Bouricha, El Mehdi / Hakmi, Mohammed / Akachar, Jihane / Belyamani, Lahcen / Ibrahimi, Azeddine

3 Biotech

2020 Volume 10, Issue 11, Page(s) 483

Abstract	SARS-CoV-2, which causes severe pneumonia epidemics, probably originated from Chinese horseshoe bats, but the intermediate and host range is still unknown. ACE2 is the entry receptor for SARS-CoV-2. The binding capacity of SARS-CoV-2 spike protein to ACE2 is the critical determinant of viral host range and cross-species infection. Here, we used an
Keywords	covid19
Language	English
Publishing date	2020-10-21
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-020-02471-3
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Article: Identifying epitopes for cluster of differentiation and design of new peptides inhibitors against human SARS-CoV-2 spike RBD by an

Akachar, Jihane / Bouricha, El Mehdi / Hakmi, Mohammed / Belyamani, Lahcen / El Jaoudi, Rachid / Ibrahimi, Azeddine

Heliyon

2020 Volume 6, Issue 12, Page(s) e05739

Abstract	The coronavirus disease 19 (COVID-19) is a highly contagious and rapidly spreading infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some cases, the disease can be fatal which resulted in more than one million deaths worldwide according the WHO. Currently, there is no effective vaccine or treatment for COVID-19, however many small-molecule inhibitors have shown potent antiviral activity against SARS-CoV-2 and some of them are now under clinical trials. Despite their promising activities, the development of these small molecules for the clinical use can be limited by many factors like the off-target effect, the poor stability, and the low bioavailability. The clusters of differentiation CD147, CD209, CD299 have been identified as essential entry co-receptors for SARS-CoV-2 species specificity to humans, although the underlying mechanisms are yet to be fully elucidated. In this paper, protein-protein docking was utilized for identifying the critical epitopes in CD147, CD209 and CD299 which are involved in the binding with SARS-CoV-2 Spike receptor binding domain (RBD). The results of binding free energies showed a high affinity of SARS-CoV-2 RBD to CD299 receptor which was used as a reference to derive hypothetical peptide sequences with specific binding activities to SARS-CoV-2 RBD. Molecular docking and molecular dynamics simulations of the newly designed peptides showed favorable binding features and stability with SARS-CoV-2 RBD and therefore can be further considered as potential candidates in future anti-SARS CoV-2 drug discovery studies.
Language	English
Publishing date	2020-12-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2020.e05739
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Article: In Silico Analyses of All STAT3 Missense Variants Leading to Explore Divergent AD-HIES Clinical Phenotypes.

Mansouri, Mariam / El Haddoumi, Ghyzlane / Bendani, Houda / Boumajdi, Nasma / Hakmi, Mohammed / Abbou, Hanane / Bouricha, El Mehdi / Elgharbaoui, Boutaina / Kartti, Souad / El Jaoudi, Rachid / Belyamani, Lahcen / Kandoussi, Ilham / Ibrahimi, Azeddine / El Hafidi, Naima

Evolutionary bioinformatics online

2023 Volume 19, Page(s) 11769343231169374

Abstract: Autosomal dominant hyper-IgE syndrome (AD-HIES) is linked to dominant negative mutations of the STAT3 protein whose molecular basis for dysfunction is unclear and presenting with a variety of clinical manifestations with only supportive treatment. To ... ...

Abstract	Autosomal dominant hyper-IgE syndrome (AD-HIES) is linked to dominant negative mutations of the STAT3 protein whose molecular basis for dysfunction is unclear and presenting with a variety of clinical manifestations with only supportive treatment. To establish the relationship between the impact of STAT3 mutations in different domains and the severity of the clinical manifestations, 105 STAT3 mutations were analyzed for their impact on protein stability, flexibility, function, and binding affinity using in Silico approaches. Our results showed that 73% of the studied mutations have an impact on the physicochemical properties of the protein, altering the stability, flexibility and function to varying degrees. In particular, mutations affecting the DNA binding domain (DBD) and the Src Homology 2 (SH2) have a significant impact on the protein structure and disrupt its interaction either with DNA or other STAT3 to form a heterodomain complex, leading to severe clinical phenotypes. Collectively, this study suggests that there is a close relationship between the domain involving the mutation, the degree of variation in the properties of the protein and the degree of loss of function ranging from partial loss to complete loss, explaining the variability of clinical manifestations between mild and severe.
Language	English
Publishing date	2023-04-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2227610-5
ISSN	1176-9343
ISSN	1176-9343
DOI	10.1177/11769343231169374
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