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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 ; Online: Spectrochemical study of a new albendazole derivative

El harti Jaouad / Taoufik Jamal / Ansar M’hammed

International Journal of Drug Development & Research, Vol 5, Iss 3, Pp 146-

2013 Volume 149

Abstract: The hydatidosis is a cosmopolitan parasitic disease that stays a real public health problem in the countries of strong endemic. The treatment essentially calls on the surgery that includes morbidity and mortality significant, from where the interest to ... ...

Abstract	The hydatidosis is a cosmopolitan parasitic disease that stays a real public health problem in the countries of strong endemic. The treatment essentially calls on the surgery that includes morbidity and mortality significant, from where the interest to develop the medical treatment whose main representative is the albendazole. The efficiency of this molecule is proven but limited by its bad biodisponibility due to its weak absorption by the organism. In order to improve the biodisponibility of this molecule we synthesized an ester prodrug of albendazole to solubility completely modified in relation to the princeps. This synthesis has been achieved with an output of 75%. The structure of the synthesis product has been verified and established by spectrometry of infrared molecular absorption, and by spectrometry of nuclear magnetic resonance of the proton.
Keywords	Albendazole ; Synthesis ; Prodrug ; Spectroscopy. ; Pharmacy and materia medica ; RS1-441 ; Medicine ; R
Subject code	540
Language	English
Publishing date	2013-09-01T00:00:00Z
Publisher	Chauhan Publishers
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Analyse du risque infectieux autour du patient dans l’unité d’hémodialyse de l’hôpital Ibn Sina de Rabat par application de la méthode d’analyse des modes de défaillance, de leurs effets et de leur criticité.

El Marnissi, Safaa / Khomsi, Zoubida / Kassy Raymond Sylvestre, Allou / El Harti, Jaouad / Taoufik, Jamal / Chaibi, Aicha / Benamar, Loubna / Bayahia, Rabia

Nephrologie & therapeutique

2020 Volume 16, Issue 2, Page(s) 105–117

Abstract: Introduction: Hemodialysis is a technique of extra-renal purification associated with high level of risk. The objective is to assess infectious risk during a hemodialysis session on hygiene around the patient in hospital.: Methods: An a priori risk ... ...

Title translation	Analysis of the infectious risk around the patient in the hemodialysis unit of Ibn Sina Rabat hospital using the failure modes, effects and criticality analysis method.
Abstract	Introduction: Hemodialysis is a technique of extra-renal purification associated with high level of risk. The objective is to assess infectious risk during a hemodialysis session on hygiene around the patient in hospital. Methods: An a priori risk assessment by Failure Modes, Effects and Criticality Analysis method (FMECA) was carried out from May to August 2018, in order to overview infectious risk during the process of hemodialysis in the Ibn Sina Hospital (Rabat, Morocco). Results: Twenty eight failure modes were identified during the hemodialysis process around the patient: fourteen criticality level 1, ten level 2, and four level 3. A prevention plan has been drafted. Three of the four level 3 failure modes were reduced to level 1 and one to level 2. Discussion: FMECA have enabled us to identify the potential risks, to reconsider certain procedures and to suggest measure matrix for the coverage of the most critical risks. Conclusion: This analysis makes it possible, through periodic evaluations, to enter a real quality approach, which reinforces the satisfaction of the patients as well as all the actors of the hemodialysis center.
MeSH term(s)	Cross Infection/epidemiology ; Cross Infection/etiology ; Cross Infection/prevention & control ; Cross-Sectional Studies ; Hemodialysis Units, Hospital ; Hospitals ; Humans ; Kidney Failure, Chronic/therapy ; Morocco ; Renal Dialysis ; Risk Assessment
Language	French
Publishing date	2020-03-16
Publishing country	France
Document type	Journal Article
ZDB-ID	2229575-6
ISSN	1872-9177 ; 1769-7255
ISSN (online)	1872-9177
ISSN	1769-7255
DOI	10.1016/j.nephro.2019.09.005
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Article ; Online: In silico exploration of small-molecule α-helix mimetics as inhibitors of SARS-COV-2 attachment to ACE2.

Hakmi, Mohammed / Bouricha, E L Mehdi / Akachar, Jihane / Lmimouni, Badreddine / El Harti, Jaouad / Belyamani, Lahcen / Ibrahimi, Azeddine

Journal of biomolecular structure & dynamics

2020 Volume 40, Issue 4, Page(s) 1546–1557

Abstract: The novel coronavirus, SARS-CoV-2, has infected more than 10 million people and caused more than 502,539 deaths worldwide as of June 2020. The explosive spread of the virus and the rapid increase in the number of cases require the immediate development ... ...

Abstract	The novel coronavirus, SARS-CoV-2, has infected more than 10 million people and caused more than 502,539 deaths worldwide as of June 2020. The explosive spread of the virus and the rapid increase in the number of cases require the immediate development of effective therapies and vaccines as well as accurate diagnosis tools. The pathogenesis of the disease is triggered by the entry of SARS-CoV-2 via its spike protein into ACE2-bearing host cells, particularly pneumocytes, resulting in overactivation of the immune system, which attacks the infected cells and damages the lung tissue. The interaction of the SARS-CoV-2 receptor binding domain (RBD) with host cells is primarily mediated by the N-terminal helix of ACE2; thus, inhibition of the spike-ACE2 interaction may be a promising therapeutic strategy for blocking the virus entry into host cells. In this paper, we used an in-silico approach to explore small-molecule α-helix mimetics as inhibitors that may disrupt the attachment of SARS-CoV-2 to ACE2. First, the RBD-ACE2 interface in the 6M0J structure was studied by the MM-GBSA decomposition module of the HawkDock server, which led to the identification of two critical target regions in the RBD. Next, two virtual screening experiments of 7236 α-helix mimetics from ASINEX were conducted on the above regions using the iDock tool, which resulted in 10 candidates with favorable binding affinities. Finally, the stability of RBD complexes with the top-two ranked compounds was further validated by 100
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; COVID-19 ; Humans ; Molecular Dynamics Simulation ; Protein Binding ; Protein Conformation, alpha-Helical ; SARS-CoV-2/drug effects ; Spike Glycoprotein, Coronavirus/antagonists & inhibitors
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-10-07
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	10.1080/07391102.2020.1830175
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Article: Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules

Allam, Loubna Ghrifi Fatima Mohammed Hakmi El Hafidi Naima El Jaoudi Rachid El Harti Jaouad Lmimouni Badreddine Belyamani Lahcen Ibrahimi Azeddine

Bioinformatics & Biology Insights

Abstract: The global burden of infections and the rapid spread of viral diseases show the need for new approaches in the prevention and development of effective therapies To this end, we aimed to explore novel inhibitor compounds that can stop replication or ... ...

Abstract	The global burden of infections and the rapid spread of viral diseases show the need for new approaches in the prevention and development of effective therapies To this end, we aimed to explore novel inhibitor compounds that can stop replication or decrease the viral load of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which there is currently no approved treatment Besides using the angiotensin-converting enzyme (ACE2) receptor as a main gate, the CoV-2 can bind to the glucose-regulating protein 78 (GRP78) receptor to get into the cells to start an infection Here, we report potential inhibitors comprising small molecules and peptides that could interfere with the interaction of SARS-CoV-2 and its target cells by blocking the recognition of the GRP78 cellular receptor by the viral Spike protein These inhibitors were discovered through an approach of in silico screening of available databases of bioactive peptides and polyphenolic compounds and the analysis of their docking modes This process led to the selection of 9 compounds with optimal binding affinities to the target sites The peptides (satpdb18674, satpdb18446, satpdb12488, satpdb14438, and satpdb28899) act on regions III and IV of the viral Spike protein and on its binding sites in GRP78 However, 4 polyphenols such as epigallocatechin gallate (EGCG), homoeriodictyol, isorhamnetin, and curcumin interact, in addition to the Spike protein and its binding sites in GRP78, with the ATPase domain of GRP78 Our work demonstrates that there are at least 2 approaches to block the spread of SARS-CoV-2 by preventing its fusion with the host cells via GRP78 [ABSTRACT FROM AUTHOR] Copyright of Bioinformatics & Biology Insights is the property of Sage Publications Inc and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission However, users may print, download, or email articles for individual use This abstract may be abridged No warranty is given about the accuracy of the copy Users should refer to the original published version of the material for the full abstract (Copyright applies to all Abstracts )
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #892352
Database	COVID19

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Article: Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules.

Allam, Loubna / Ghrifi, Fatima / Mohammed, Hakmi / El Hafidi, Naima / El Jaoudi, Rachid / El Harti, Jaouad / Lmimouni, Badreddine / Belyamani, Lahcen / Ibrahimi, Azeddine

Bioinformatics and biology insights

2020 Volume 14, Page(s) 1177932220965505

Abstract: The global burden of infections and the rapid spread of viral diseases show the need for new approaches in the prevention and development of effective therapies. To this end, we aimed to explore novel inhibitor compounds that can stop replication or ... ...

Abstract	The global burden of infections and the rapid spread of viral diseases show the need for new approaches in the prevention and development of effective therapies. To this end, we aimed to explore novel inhibitor compounds that can stop replication or decrease the viral load of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which there is currently no approved treatment. Besides using the angiotensin-converting enzyme (ACE2) receptor as a main gate, the CoV-2 can bind to the glucose-regulating protein 78 (GRP78) receptor to get into the cells to start an infection. Here, we report potential inhibitors comprising small molecules and peptides that could interfere with the interaction of SARS-CoV-2 and its target cells by blocking the recognition of the GRP78 cellular receptor by the viral Spike protein. These inhibitors were discovered through an approach of in silico screening of available databases of bioactive peptides and polyphenolic compounds and the analysis of their docking modes. This process led to the selection of 9 compounds with optimal binding affinities to the target sites. The peptides (satpdb18674, satpdb18446, satpdb12488, satpdb14438, and satpdb28899) act on regions III and IV of the viral Spike protein and on its binding sites in GRP78. However, 4 polyphenols such as epigallocatechin gallate (EGCG), homoeriodictyol, isorhamnetin, and curcumin interact, in addition to the Spike protein and its binding sites in GRP78, with the ATPase domain of GRP78. Our work demonstrates that there are at least 2 approaches to block the spread of SARS-CoV-2 by preventing its fusion with the host cells via GRP78.
Keywords	covid19
Language	English
Publishing date	2020-10-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2423808-9
ISSN	1177-9322
ISSN	1177-9322
DOI	10.1177/1177932220965505
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Article: In silico exploration of small-molecule α-helix mimetics as inhibitors of SARS-COV-2 attachment to ACE2

Hakmi, Mohammed / Bouricha, E L Mehdi / Akachar, Jihane / Lmimouni, Badreddine / El Harti, Jaouad / Belyamani, Lahcen / Ibrahimi, Azeddine

J Biomol Struct Dyn

Abstract	The novel coronavirus, SARS-CoV-2, has infected more than 10 million people and caused more than 502,539 deaths worldwide as of June 2020. The explosive spread of the virus and the rapid increase in the number of cases require the immediate development of effective therapies and vaccines as well as accurate diagnosis tools. The pathogenesis of the disease is triggered by the entry of SARS-CoV-2 via its spike protein into ACE2-bearing host cells, particularly pneumocytes, resulting in overactivation of the immune system, which attacks the infected cells and damages the lung tissue. The interaction of the SARS-CoV-2 receptor binding domain (RBD) with host cells is primarily mediated by the N-terminal helix of ACE2; thus, inhibition of the spike-ACE2 interaction may be a promising therapeutic strategy for blocking the virus entry into host cells. In this paper, we used an in-silico approach to explore small-molecule α-helix mimetics as inhibitors that may disrupt the attachment of SARS-CoV-2 to ACE2. First, the RBD-ACE2 interface in the 6M0J structure was studied by the MM-GBSA decomposition module of the HawkDock server, which led to the identification of two critical target regions in the RBD. Next, two virtual screening experiments of 7236 α-helix mimetics from ASINEX were conducted on the above regions using the iDock tool, which resulted in 10 candidates with favorable binding affinities. Finally, the stability of RBD complexes with the top-two ranked compounds was further validated by 100 ns of molecular dynamics simulations. Communicated by Ramaswamy H. Sarma.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #842248
Database	COVID19

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Book ; Online: In Silico Exploration of Small-Molecule α-Helix Mimetics as Inhibitors of SARS-COV-2 Attachment to ACE2

Hakmi, Mohammed / Bouricha, El Mehdi / Akachar, Jihane / Lmimouni, Badreddine / EL Harti, Jaouad / Belyamani, Lahcen / Ibrahimi, Azeddine

2020

Abstract	The novel coronavirus, SARS-CoV-2, has infected more than 10 million people and caused more than 502,539 deaths worldwide as of June 2020. The explosive spread of the virus and the rapid increase in the number of cases require the immediate development of effective therapies and vaccines as well as accurate diagnosis tools. The pathogenesis of the disease is triggered by the entry of SARS-CoV-2 via its spike protein into ACE2-bearing host cells, particularly pneumocytes, resulting in overactivation of the immune system, which attacks the infected cells and damages the lung tissue. The interaction of the SARS-CoV-2 receptor binding domain (RBD) with host cells is primarily mediated by the N-terminal helix of the ACE2; thus, inhibition of the spike-ACE2 interaction may be a promising therapeutic strategy for blocking the entry of the virus into host cells. In this paper, we used an in-silico approach to explore small-molecule α-helix mimetics as inhibitors that may disrupt the attachment of SARS-CoV-2 to ACE2. First, the RBD-ACE2 interface in the 6M0J structure was studied by the MM-GBSA decomposition module of the HawkDock server, which led to the identification of two critical target regions in the RBD. Next, two virtual screening experiments of 7236 α-helix mimetics from ASINEX were conducted on the above regions using the iDock tool, which resulted in 10 candidates with favorable binding affinities. Finally, the stability of RBD complexes with the top-two ranked compounds was further validated by 40 ns MD simulations using Desmond package of Schrodinger.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12592286.v1
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: In Silico Exploration of Small-Molecule α-Helix Mimetics as Inhibitors of SARS-COV-2 Attachment to ACE2

Hakmi, Mohammed / Bouricha, El Mehdi / Akachar, Jihane / Lmimouni, Badreddine / EL Harti, Jaouad / Belyamani, Lahcen / Ibrahimi, Azeddine

2020

Abstract	The novel coronavirus, SARS-CoV-2, has infected more than 10 million people and caused more than 502,539 deaths worldwide as of June 2020. The explosive spread of the virus and the rapid increase in the number of cases require the immediate development of effective therapies and vaccines as well as accurate diagnosis tools. The pathogenesis of the disease is triggered by the entry of SARS-CoV-2 via its spike protein into ACE2-bearing host cells, particularly pneumocytes, resulting in overactivation of the immune system, which attacks the infected cells and damages the lung tissue. The interaction of the SARS-CoV-2 receptor binding domain (RBD) with host cells is primarily mediated by the N-terminal helix of the ACE2; thus, inhibition of the spike-ACE2 interaction may be a promising therapeutic strategy for blocking the entry of the virus into host cells. In this paper, we used an in-silico approach to explore small-molecule α-helix mimetics as inhibitors that may disrupt the attachment of SARS-CoV-2 to ACE2. First, the RBD-ACE2 interface in the 6M0J structure was studied by the MM-GBSA decomposition module of the HawkDock server, which led to the identification of two critical target regions in the RBD. Next, two virtual screening experiments of 7236 α-helix mimetics from ASINEX were conducted on the above regions using the iDock tool, which resulted in 10 candidates with favorable binding affinities. Finally, the stability of RBD complexes with the top-two ranked compounds was further validated by 40 ns MD simulations using Desmond package of Schrodinger.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12592286
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules

Allam, Loubna / Ghrifi, Fatima / Mohammed, Hakmi / El Hafidi, Naima / El Jaoudi, Rachid / El Harti, Jaouad / Lmimouni, Badreddine / Belyamani, Lahcen / Ibrahimi, Azeddine

Bioinformatics and Biology Insights

2020 Volume 14, Page(s) 117793222096550

Abstract	The global burden of infections and the rapid spread of viral diseases show the need for new approaches in the prevention and development of effective therapies. To this end, we aimed to explore novel inhibitor compounds that can stop replication or decrease the viral load of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which there is currently no approved treatment. Besides using the angiotensin-converting enzyme (ACE2) receptor as a main gate, the CoV-2 can bind to the glucose-regulating protein 78 (GRP78) receptor to get into the cells to start an infection. Here, we report potential inhibitors comprising small molecules and peptides that could interfere with the interaction of SARS-CoV-2 and its target cells by blocking the recognition of the GRP78 cellular receptor by the viral Spike protein. These inhibitors were discovered through an approach of in silico screening of available databases of bioactive peptides and polyphenolic compounds and the analysis of their docking modes. This process led to the selection of 9 compounds with optimal binding affinities to the target sites. The peptides (satpdb18674, satpdb18446, satpdb12488, satpdb14438, and satpdb28899) act on regions III and IV of the viral Spike protein and on its binding sites in GRP78. However, 4 polyphenols such as epigallocatechin gallate (EGCG), homoeriodictyol, isorhamnetin, and curcumin interact, in addition to the Spike protein and its binding sites in GRP78, with the ATPase domain of GRP78. Our work demonstrates that there are at least 2 approaches to block the spread of SARS-CoV-2 by preventing its fusion with the host cells via GRP78.
Keywords	Biochemistry ; Applied Mathematics ; Molecular Biology ; Computational Mathematics ; Computer Science Applications ; covid19
Language	English
Publisher	SAGE Publications
Publishing country	us
Document type	Article ; Online
ZDB-ID	2423808-9
ISSN	1177-9322
ISSN	1177-9322
DOI	10.1177/1177932220965505
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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