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Article: Advances in Polysaccharide-Based Oral Colon-Targeted Delivery Systems: The Journey So Far and the Road Ahead.

Ibrahim, Ibrahim M

2023 Volume 15, Issue 1, Page(s) e33636

Abstract: Various colon-targeted oral delivery systems have been explored so far to treat colorectal diseases, including timed-release systems, prodrugs, pH-based polymer coatings, and microflora-triggered systems. Among them, the microbially triggered system has ... ...

Abstract	Various colon-targeted oral delivery systems have been explored so far to treat colorectal diseases, including timed-release systems, prodrugs, pH-based polymer coatings, and microflora-triggered systems. Among them, the microbially triggered system has gained attention. Among various oral colon-targeted delivery systems discussed, the polysaccharide-based colon-targeted delivery system has been found to be quite promising as polysaccharides remain unaffected by gastric as well as upper intestine milieu and are only digested by colonic bacteria upon reaching the colon. The major bottleneck associated with this delivery is that non-suitability of this system during the diseased state due to decrease in bacterial count at that time. This causes the failure of delivery system to release the drug even at colonic site as the polysaccharide matrix/coat cannot be digested properly due to lack of bacteria. The co-administration of probiotics is reported to compensate for the bacterial loss besides facilitating site-specific release. However, this research is also limited at the preclinical level. Hence, efforts are required to make this technology scalable and clinically applicable. This article entails in detail various oral colon-targeted delivery systems prepared so far, as well as the limitations and benefits of polysaccharide-based oral colon-targeted delivery systems.
Language	English
Publishing date	2023-01-11
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.33636
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Article ; Online: Host-cell recognition through Cs-GRP78 is enhanced in the new Omicron variant of SARS-CoV-2, in silico structural point of view.

Elfiky, Abdo A / Ibrahim, Ibrahim M

The Journal of infection

2022 Volume 84, Issue 5, Page(s) 722–746

MeSH term(s)	Angiotensin-Converting Enzyme 2 ; COVID-19 ; Endoplasmic Reticulum Chaperone BiP ; Humans ; Mutation ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Endoplasmic Reticulum Chaperone BiP ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-01-19
Publishing country	England
Document type	Letter
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2022.01.019
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Zs.A 1501: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Host-cell recognition through GRP78 is enhanced in the new UK variant of SARS-CoV-2, in silico.

Elfiky, Abdo A / Ibrahim, Ibrahim M

The Journal of infection

2021 Volume 82, Issue 5, Page(s) 186–230

MeSH term(s)	COVID-19 ; Computer Simulation ; Humans ; Protein Binding ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; United Kingdom
Chemical Substances	Spike Glycoprotein, Coronavirus
Language	English
Publishing date	2021-01-22
Publishing country	England
Document type	Letter
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2021.01.015
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Zs.A 1501: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: In silico discovery of potent and selective Janus kinase 3 (JAK3) inhibitors through 3D-QSAR, covalent docking, ADMET analysis, molecular dynamics simulations, and binding free energy of pyrazolopyrimidine derivatives.

Faris, Abdelmoujoud / Hadni, Hanine / Ibrahim, Ibrahim M / Elhallaoui, Menana

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–17

Abstract: Rheumatoid arthritis is a prevalent and debilitating chronic disease worldwide. Targeting Janus kinase 3 (JAK3) has emerged as a crucial molecular strategy to treat this condition. In this study, we employed a comprehensive theoretical approach that ... ...

Abstract	Rheumatoid arthritis is a prevalent and debilitating chronic disease worldwide. Targeting Janus kinase 3 (JAK3) has emerged as a crucial molecular strategy to treat this condition. In this study, we employed a comprehensive theoretical approach that included 3D-QSAR, covalent docking, ADMET, and molecular dynamics to propose and optimize new anti-JAK3 compounds. We investigated a series of 28 1H-pyrazolo[3.4-d]pyrimidin-4-amino inhibitors and developed a highly accurate 3D-QSAR model using comparative molecular similarity index analysis (COMSIA). The model predicted with Q
Language	English
Publishing date	2023-06-20
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2222839
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Article ; Online: High-throughput virtual screening of phenylpyrimidine derivatives as selective JAK3 antagonists using computational methods.

Faris, Abdelmoujoud / Ibrahim, Ibrahim M / Hadni, Hanine / Elhallaoui, Menana

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–26

Abstract: In this study, we used phenylpyrimidine derivatives with known biological activity against JAK3, a critical tyrosine kinase enzyme involved in signaling pathways, to find similar compounds as potential treatments for rheumatoid arthritis. These ... ...

Abstract	In this study, we used phenylpyrimidine derivatives with known biological activity against JAK3, a critical tyrosine kinase enzyme involved in signaling pathways, to find similar compounds as potential treatments for rheumatoid arthritis. These inhibitors inhibited JAK3 activity by forming a covalent bond with the Cys909 residue, which resulted in a strong inhibitory effect. Phenylpyrimidine is considered a promising therapeutic target. For pharmacophore modeling, 39 phenylpyrimidine derivatives with high pIC50 (Exp) values were chosen. The best pharmacophore model produced 28 molecules, and the five-point common pharmacophore hypothesis from P HASE (DHRRR_1) revealed the requirement for a hydrogen bond donor feature, a hydrophobic group feature, and three aromatic ring features for further design. The validation of the pharmacophore model phase was performed through 3D-QSAR using partial least squares (P LS). The 3D-QSAR study produced two successful models, an atom-based model (R2 = 0.95; Q2 = 0.67) and a field-based model (R2 = 0.93; Q2 = 0.76), which were used to predict the biological activity of new compounds. The pharmacophore model successfully distinguished between active and inactive medications, discovered potential JAK3 inhibitors, and demonstrated validity with a ROC of 0. 77. ADME-Tox was used to eliminate compounds that might have adverse effects. The best pharmacokinetics and affinity derivatives were selected for covalent docking. A molecular dynamics simulation of the selected molecules and the protein complex was performed to confirm the stability of the interaction with JAK3, whereas MM/GBSA simulations further confirmed their binding affinity. By using the principle of retrosynthesis, we were able to map out a pathway for synthesizing these potential drug candidates. This study has the potential to offer valuable and practical insights for optimizing novel derivatives of phenylpyrimidine.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2023-08-04
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2240413
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Article: SARS-CoV-2 Delta Variant is Recognized Through GRP78 Host-Cell Surface Receptor, In Silico Perspective.

Elfiky, Abdo A / Ibrahim, Ibrahim M / Elgohary, Alaa M

International journal of peptide research and therapeutics

2022 Volume 28, Issue 5, Page(s) 146

Abstract: Different SARS-CoV-2 new variants emerged and spread during the past few months, sparking infections and death counts. The new variant B.1.617 (delta variant) sparked in India in the past few months, causing the highest records. The B.1.617 variant of ... ...

Abstract	Different SARS-CoV-2 new variants emerged and spread during the past few months, sparking infections and death counts. The new variant B.1.617 (delta variant) sparked in India in the past few months, causing the highest records. The B.1.617 variant of SARS-CoV-2 has the double mutations E484Q and L452R on its spike Receptor Binding Domain (RBD). The first mutation is like the reported South African and the Brazilian variants (501.V2 and B.1.1.248). This mutation lies in the region C480-C488, which we predicted before to be recognized by the host-cell receptor; Glucose Regulated Protein 78 (GRP78). In the current study, we test the binding affinity of the host-cell receptor GRP78 to the delta variant spike RBD using molecular docking and molecular dynamics simulations of up to 100 ns. Additionally, the ACE2-RBD is tested by protein-protein docking. The results reveal equal average binding affinities of the GRP78 against wildtype and delta variant spikes. This supports our previous predictions of the contribution of GRP78 in SARS-CoV-2 spike recognition as an auxiliary route for entry.
Language	English
Publishing date	2022-08-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	2192632-3
ISSN	1573-3904 ; 1573-3149
ISSN (online)	1573-3904
ISSN	1573-3149
DOI	10.1007/s10989-022-10450-w
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Article ; Online: Zika virus envelope - heat shock protein A5 (GRP78) binding site prediction.

Elfiky, Abdo A / Ibrahim, Ibrahim M

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 14, Page(s) 5248–5260

Abstract: Recent studies reported the association of the Zika virus (ZIKV) with a stress response receptor on the host cell membrane that facilitates viral entry. This host receptor was the heat shock protein A5 (HSPA5), also termed glucose-regulating protein 78 ( ... ...

Abstract	Recent studies reported the association of the Zika virus (ZIKV) with a stress response receptor on the host cell membrane that facilitates viral entry. This host receptor was the heat shock protein A5 (HSPA5), also termed glucose-regulating protein 78 (GRP78). In this study, structural bioinformatics and molecular dynamics simulations were utilized to suggest the binding site of ZIKV envelope protein during the interaction with cell-surface GRP78. The Pep42 cyclic peptide was used as a profiler, as it was reported earlier, to target GRP78 on the cancer cell membrane selectively. Sequence and structural alignments show that part of the ZIKV envelope protein (C308-C339 region), in addition to its cyclic nature, has somehow sequence and structural similarities to the cyclic Pep42. Three amino acids in the ZIKV envelope were identical to those in the Pep42 peptide. Cyclic peptides dynamics are studied, and its binding to GRP78 is predicted. Protein-protein docking is further performed to explore the binding characteristics of the ZIKV envelope to GRP78. Results revealed that the binding was favorable between ZIKV envelope protein and GRP78. The docking pose revealed the involvement of the substrate-binding domain ß of GRP78 and the domain III of the ZIKV envelope protein in viral recognition for the host-cell.
MeSH term(s)	Binding Sites ; Endoplasmic Reticulum Chaperone BiP ; Heat-Shock Proteins/metabolism ; Humans ; Protein Binding ; Viral Envelope ; Viral Envelope Proteins/metabolism ; Zika Virus ; Zika Virus Infection
Chemical Substances	Endoplasmic Reticulum Chaperone BiP ; HSPA5 protein, human ; Heat-Shock Proteins ; Viral Envelope Proteins
Language	English
Publishing date	2020-06-24
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1784794
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Article ; Online: Local Delivery of Azithromycin Nanoformulation Attenuated Acute Lung Injury in Mice.

Alrashedi, Mohsen G / Ali, Ahmed Shaker / Ahmed, Osama Abdelhakim / Ibrahim, Ibrahim M

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 23

Abstract: Humanity has suffered from the coronavirus disease 2019 (COVID-19) pandemic over the past two years, which has left behind millions of deaths. Azithromycin (AZ), an antibiotic used for the treatment of several bacterial infections, has shown antiviral ... ...

Abstract	Humanity has suffered from the coronavirus disease 2019 (COVID-19) pandemic over the past two years, which has left behind millions of deaths. Azithromycin (AZ), an antibiotic used for the treatment of several bacterial infections, has shown antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as well as against the dengue, Zika, Ebola, and influenza viruses. Additionally, AZ has shown beneficial effects in non-infective diseases such as cystic fibrosis and bronchiectasis. However, the systemic use of AZ in several diseases showed low efficacy and potential cardiac toxicity. The application of nanotechnology to formulate a lung delivery system of AZ could prove to be one of the solutions to overcome these drawbacks. Therefore, we aimed to evaluate the attenuation of acute lung injury in mice via the local delivery of an AZ nanoformulation. The hot emulsification-ultrasonication method was used to prepare nanostructured lipid carrier of AZ (AZ-NLC) pulmonary delivery systems. The developed formulation was evaluated and characterized in vitro and in vivo. The efficacy of the prepared formulation was tested in the bleomycin (BLM) -mice model for acute lung injury. AZ-NLC was given by the intratracheal (IT) route for 6 days at a dose of about one-eighth oral dose of AZ suspension. Samples of lung tissues were taken at the end of the experiment for immunological and histological assessments. AZ-NLC showed an average particle size of 453 nm, polydispersity index of 0.228 ± 0.07, zeta potential of -30 ± 0.21 mV, and a sustained release pattern after the initial 50% drug release within the first 2 h. BLM successfully induced a marked increase in pro-inflammatory markers and also induced histological changes in pulmonary tissues. All these alterations were significantly reversed by the concomitant administration of AZ-NLC (IT). Pulmonary delivery of AZ-NLC offered delivery of the drug locally to lung tissues. Its attenuation of lung tissue inflammation and histological injury induced by bleomycin was likely through the downregulation of the p53 gene and the modulation of Bcl-2 expression. This novel strategy could eventually improve the effectiveness and diminish the adverse drug reactions of AZ. Lung delivery could be a promising treatment for acute lung injury regardless of its cause. However, further work is needed to explore the stability of the formulation, its pharmacokinetics, and its safety.
Language	English
Publishing date	2022-11-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27238293
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Article ; Online: Host-cell recognition of SARS-CoV-2 spike receptor binding domain from different variants.

Elfiky, Abdo A / Ibrahim, Ibrahim M / Ibrahim, Mohamed N / Elshemey, Wael M

The Journal of infection

2022 Volume 85, Issue 6, Page(s) 702–769

MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Spike Glycoprotein, Coronavirus ; Protein Binding ; Mutation
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-10-09
Publishing country	England
Document type	Letter
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2022.10.009
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Article ; Online: Interference of Chaga mushroom terpenoids with the attachment of SARS-CoV-2; in silico perspective.

Elshemey, Wael M / Elfiky, Abdo A / Ibrahim, Ibrahim M / Elgohary, Alaa M

Computers in biology and medicine

2022 Volume 145, Page(s) 105478

Abstract: Finding a potent inhibitor to the pandemic SARS-CoV-2 is indispensable nowadays. Currently, in-silico methods work as expeditious investigators to screen drugs for possible repurposing or design new ones. Targeting one of the possible SARS-CoV-2 ... ...

Abstract	Finding a potent inhibitor to the pandemic SARS-CoV-2 is indispensable nowadays. Currently, in-silico methods work as expeditious investigators to screen drugs for possible repurposing or design new ones. Targeting one of the possible SARS-CoV-2 attachment and entry receptors, Glucose-regulated protein 78 (GRP78), is an approach of major interest. Recently, GRP78 was reported as a recognized representative in recognition of the latest variants of SARS-CoV-2. In this work, molecular docking and molecular dynamics simulations were performed on the host cell receptor GRP78. With its many terpenoid compounds, Chaga mushroom was tested as a potential therapeutic against the SARS-CoV-2 receptor, GRP78. Results revealed low binding energies (high affinities) toward the GRP78 substrate-binding domain β (SBDβ) of Chaga mushroom terpenoids. Even the highly specific cyclic peptide Pep42, which selectively targeted GRP78 over cancer cells in vivo, showed lower binding affinity against GRP78 SBDβ compared to the binding affinities of terpenoids. These are auspicious results that need to be tested experimentally. Intriguingly, terpenoids work as a double sword as they can be used to interfere with VUI 202,012/01, 501.V2, and B.1.1.248 variants of SARS-CoV-2 spike recognition.
MeSH term(s)	COVID-19/drug therapy ; Humans ; Inonotus ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; SARS-CoV-2 ; Terpenes/pharmacology
Chemical Substances	Terpenes
Language	English
Publishing date	2022-04-07
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.2022.105478
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