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Article ; Online: Development of superior antibodies against the S-protein of SARS-Cov-2 using macrocyclic epitopes

Hassan Traboulsi / Mohammed A. Khedr / Rafea Elgorashe / Yasair Al-Faiyz / Amr Negm

Arabian Journal of Chemistry, Vol 15, Iss 3, Pp 103631- (2022)

2022

Abstract: One of the proven methods to prevent and inhibit viral infections is to use antibodies to block the initial Receptor Binding Domain (RBD) of SARS-CoV-2 S protein and avoid its binding with the host cells. Thus, developing these RBD-targeting antibodies ... ...

Abstract	One of the proven methods to prevent and inhibit viral infections is to use antibodies to block the initial Receptor Binding Domain (RBD) of SARS-CoV-2 S protein and avoid its binding with the host cells. Thus, developing these RBD-targeting antibodies would be a promising approach for treating the SARS-CoV-2 infectious disease and stop virus replication. Macrocyclic epitopes constitute closer mimics of the receptor's actual topology and, as such, are expected to be superior epitopes for antibody generation. This work demonstrated the vital effect of the three-dimensional shape of epitopes on the developed antibodies' activity against RBD protein of SARS-CoV-2. The molecular dynamics studies showed the greater stability of the cyclic epitopes in comparison with the linear counterpart, which was reflected in the activity of their produced antibodies. Indeed, the antibodies we developed using macrocyclic epitopes showed superiority with respect to binding to RBD proteins compared to antibodies formed from a linear peptide. The results of the present work constitute a roadmap for developing superior antibodies that could be used to inhibit the activity of the SARS-CoV-2 and prevent its reproduction.
Keywords	SARS-CoV-2 ; Spike protein ; Receptor binding domain ; Epitopes ; Macrocyclic peptides ; Molecular dynamics ; Chemistry ; QD1-999
Subject code	570
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Structure-Based Epitope Design

Hassan Traboulsi / Mohammed A. Khedr / Yasair S. S. Al-Faiyz / Rafea Elgorashe / Amr Negm

ACS Omega, Vol 6, Iss 47, Pp 31469-

Toward a Greater Antibody–SARS-CoV‑2 RBD Affinity

2021 Volume 31476

Keywords	Chemistry ; QD1-999
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	American Chemical Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Rational Discovery of (+) (S) Abscisic Acid as a Potential Antifungal Agent

Mohammed A. Khedr / Alberto Massarotti / Maged E. Mohamed

Scientific Reports, Vol 8, Iss 1, Pp 1-

a Repurposing Approach

2018 Volume 14

Abstract: Abstract Fungal infections are spreading widely worldwide, and the types of treatment are limited due to the lack of diverse therapeutic agents and their associated side effects and toxicity. The discovery of new antifungal classes is vital and critical. ...

Abstract	Abstract Fungal infections are spreading widely worldwide, and the types of treatment are limited due to the lack of diverse therapeutic agents and their associated side effects and toxicity. The discovery of new antifungal classes is vital and critical. We discovered the antifungal activity of abscisic acid through a rational drug design methodology that included the building of homology models for fungal chorismate mutases and a pharmacophore model derived from a transition state inhibitor. Ligand-based virtual screening resulted in some hits that were filtered using molecular docking and molecular dynamic simulations studies. Both in silico methods and in vitro antifungal assays were used as tools to select and validate the abscisic acid repurposing. Abscisic acid inhibition assays confirmed the inhibitory effect of abscisic acid on chorismate mutase through the inhibition of phenylpyruvate production. The repositioning of abscisic acid, the well-known and naturally occurring plant growth regulator, as a potential antifungal agent because of its suggested action as an inhibitor to several fungal chorismate mutases was the main result of this work.
Keywords	Medicine ; R ; Science ; Q
Subject code	540
Language	English
Publishing date	2018-06-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Discovery of New Coumarin-Based Lead with Potential Anticancer, CDK4 Inhibition and Selective Radiotheranostic Effect

Mona O. Sarhan / Somaia S. Abd El-Karim / Manal M. Anwar / Raghda H. Gouda / Wafaa A. Zaghary / Mohammed A. Khedr

Molecules, Vol 26, Iss 2273, p

Synthesis, 2D & 3D QSAR , Molecular Dynamics, In Vitro Cytotoxicity, Radioiodination and Biodistribution Studies

2021 Volume 2273

Abstract: Novel 6-bromo-coumarin-ethylidene-hydrazonyl-thiazolyl and 6-bromo-coumarin-thiazolyl-based derivatives were synthesized. A quantitative structure activity relationship ( QSAR) model with high predictive power r 2 = 0.92, and RMSE = 0.44 predicted five ... ...

Abstract	Novel 6-bromo-coumarin-ethylidene-hydrazonyl-thiazolyl and 6-bromo-coumarin-thiazolyl-based derivatives were synthesized. A quantitative structure activity relationship ( QSAR) model with high predictive power r 2 = 0.92, and RMSE = 0.44 predicted five compounds; 2b , 3b , 5a , 9a and 9i to have potential anticancer activities. Compound 2b achieved the best ΔG of –15.34 kcal/mol with an affinity of 40.05 pki. In a molecular dynamic study 2b showed an equilibrium at 0.8 Å after 3.5 ns, while flavopiridol did so at 0.5 Å after the same time (3.5 ns). 2b showed an IC 50 of 0.0136 µM, 0.015 µM, and 0.054 µM against MCF-7, A-549, and CHO-K1 cell lines, respectively. The CDK4 enzyme assay revealed the significant CDK4 inhibitory activity of compound 2b with IC 50 of 0.036 µM. The selectivity of the newly discovered lead compound 2b toward localization in tumor cells was confirmed by a radioiodination biological assay that was done via electrophilic substitution reaction utilizing the oxidative effect of chloramine-t. 131 I-2b showed good in vitro stability up to 4 h. In solid tumor bearing mice, the values of tumor uptake reached a height of 5.97 ± 0.82%ID/g at 60 min p.i. 131 I-2b can be considered as a selective radiotheranostic agent for solid tumors with promising anticancer activity.
Keywords	coumarin ; synthesis ; molecular dynamics ; radioiodination ; CDK4 ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: QSAR-based rational discovery of novel substituted-4′-iminospiro[indoline-3,3′-[1,2,5]thiadiazolidinyl]-2-one 1′,1′-dioxide with potent in vitro anticancer activity

Mohammed A. Khedr / Reem I. Al-Wabli / Maha S. Almutairi / Wafaa A. Zaghary

BMC Chemistry, Vol 13, Iss 1, Pp 1-

2019 Volume 17

Abstract: Abstract Recent studies have suggested that aldose reductase inhibition preferentially inhibits the growth of cancer cells. However, the investigations of this issue are not many. Novel nine substituted- 4′-iminospiro[indoline-3,3′-[1,2,5] ... ...

Abstract	Abstract Recent studies have suggested that aldose reductase inhibition preferentially inhibits the growth of cancer cells. However, the investigations of this issue are not many. Novel nine substituted- 4′-iminospiro[indoline-3,3′-[1,2,5] thiadiazolidinyl]-2-one 1′,1′-dioxide derivatives were designed by both isosteric replacement of the imidazolidine-2,5-dione moiety in spirohydantoin scaffold and conformational rigidification approaches. A QSAR with high predictive power (r2 = 0.99) was created from a series of potent aldose reductase inhibitors and was used to predict the activity of our new compounds. Compound 5 showed the best docking score (− 33.24 kcal/mol) with the least RMSD value (< 1.5) obtained by molecular dynamic simulations over 20 ns. All compounds showed promising anticancer activities especially compound 5 that achieved the highest inhibitory activities with IC50; 0.013, 0.031, 0.064, and 0.048 mmol/L against breast, colon, prostate, and lung cell lines respectively. The discovery of this lead compound confirmed the rational design. Further investigations may be required for optimization of this compound.
Keywords	QSAR ; Conformational rigidification ; Molecular docking ; Molecular dynamics ; In vitro anticancer activity ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Synthesis and Structure Activity Relationship of Some Indole Derivatives as Potential Anti-inflammatory Agents

Samar S. Fatahala / Mohammed A. Khedr / Mossad S. Mohamed

Acta Chimica Slovenica, Vol 64, Iss 4, Pp 865-

2017 Volume 876

Abstract: A series of fused pyrroles were synthesized and tested for their in vivo anti-inflammatory activity. Among 14 examined derivatives, 5 derivatives (1b–e,g and 5b), showed a promising anti-inflammatory activity equivalent to reference anti-inflammatory ... ...

Abstract	A series of fused pyrroles were synthesized and tested for their in vivo anti-inflammatory activity. Among 14 examined derivatives, 5 derivatives (1b–e,g and 5b), showed a promising anti-inflammatory activity equivalent to reference anti-inflammatory drugs (indomethacin and ibuprofen). A molecular docking study was conducted to interpret the biological activities of the tested compounds. The docking results were complementary with the phase of the biological survey and confirmed the biological effects.
Keywords	Fused pyrroles ; tetrahydroindoles ; Molecular Docking ; anti-inflammatory assay ; Chemistry ; QD1-999
Language	English
Publishing date	2017-12-01T00:00:00Z
Publisher	Slovenian Chemical Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Synthesis, Characterization and Molecular Docking of Novel Bioactive Thiazolyl-Thiazole Derivatives as Promising Cytotoxic Antitumor Drug

Sobhi M. Gomha / Taher A. Salaheldin / Huwaida M. E. Hassaneen / Hassan M. Abdel-Aziz / Mohammed A. Khedr

Molecules, Vol 21, Iss 1, p

2015 Volume 3

Abstract: Reactions of ethylidenethiocarbohydrazide with hydrazonoyl halides gave 1,3-thiazole or 1,3,4-thiadiazole derivatives according to the type of hydrazonoyl halides. Treatment of ethylidenethiosemicarbazide with hydrazonoyl halides and dimethylacetylene ... ...

Abstract	Reactions of ethylidenethiocarbohydrazide with hydrazonoyl halides gave 1,3-thiazole or 1,3,4-thiadiazole derivatives according to the type of hydrazonoyl halides. Treatment of ethylidenethiosemicarbazide with hydrazonoyl halides and dimethylacetylene dicarboxylate (DMAD) afforded the corresponding arylazothiazoles and 1,3-thiazolidin-4-one derivatives, respectively. The structures of the synthesized products were confirmed by IR, 1H-NMR, 13C-NMR and mass spectral techniques. The cytotoxic activity of the selected products against the Hepatic carcinoma cell line (Hepg-2) was determined by MTT assay indicating a concentration dependent cellular growth inhibitory effect, especially for compounds 14c and 14e. The dose response curves indicated the IC50 (the concentration of test compounds required to kill 50% of cell population) were 0.54 μM and 0.50 μM, respectively. Confocal laser scanning imaging of the treated cells stained by Rhodamin 123 and Acridine orange dyes confirmed that the selected compounds inhibit the mitochondrial lactate dehydrogenase enzymes. The binding mode of the active compounds was interpreted by a molecular docking study. The obtained results revealed promising cytotoxic activity.
Keywords	ethylidenethiocarbohydrazide ; ethylidenethiosemicarbazide ; hydrazonoyl halides ; 1,3-thiazole ; 1,3,4-thiadiazole ; cytotoxic activity ; molecular docking ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2015-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Assessment of intrahepatic regulatory T cells in children with autoimmune hepatitis

Behairy E. Behairy / Hanaa A. El-Araby / Hasan H. Abd El kader / Nermin A. Ehsan / Menan E. Salem / Haidy M. Zakaria / Mohammed A. Khedr

Annals of Hepatology, Vol 15, Iss 5, Pp 682-

2016 Volume 690

Abstract: Background. T-cell populations regulate the balance of immune responses. The CD (Cluster of differentiation) 4+CD25+ regulatory T cells (Tregs) are crucial for maintaining negative control of various immune responses. There are different T-cell ... ...

Abstract	Background. T-cell populations regulate the balance of immune responses. The CD (Cluster of differentiation) 4+CD25+ regulatory T cells (Tregs) are crucial for maintaining negative control of various immune responses. There are different T-cell subpopulations with regulatory functions, as natural killer T cells, CD8+ and CD28. The forkhead box P3 (FOXP3) regulates Treg development and is required for its suppressive function.Aim. To evaluate the hepatic expression of the intrahepatic Tregs, Ig (immunoglobulin) G and IgM plasma cells in autoimmune hepatitis (AIH) and other chronic liver diseases (CLDs).Material and methods. This study included 100 pediatric patients; 50 AIH and 50 CLDs other than AIH. All patients were subjected to routine investigations of CLDs plus immune-staining of liver tissue for FOXp3, IgG and IgM plasma cells, CD4 and CD8 T-cells.Results. The FOXP3+ T cells in patients with AIH (6.3 ± 5) were significantly higher than that in the non-AIH (2.1 ± 2.6). FOXP3+ T cells were abundant in liver tissue with marked inflammatory cellular infiltrate. CD4+ and CD8+ infiltrating the liver tissue and IgG positive cells were significantly higher in AIH group, while the expression of IgM positive cells showed no significant difference. The IgG/IgM was significantly higher in the AIH treatment responders (3 ± 3) than non-responders (1.6 ± 0.5), while there was no significant difference regarding the intrahepatic expression of FOXP3+, CD4+, CD8+ cells, T-cells, IgG and IgM plasma cells.Conclusion. Intrahepatic Tregs were increased in number in patients with AIH in the initial presentation, and their presence is associated with increased activity and inflammation in liver biopsy.
Keywords	Cluster of differentiation ; Chronic liver diseases ; Forkhead box P3 ; Immunoglobulin ; Specialties of internal medicine ; RC581-951
Subject code	610 ; 570
Language	English
Publishing date	2016-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Synthesis, Molecular Docking and Preliminary in-Vitro Cytotoxic Evaluation of Some Substituted Tetrahydro-naphthalene (2',3',4',6'-Tetra-O-Acetyl-β-D-Gluco/-Galactopyranosyl) Derivatives

Wafaa A. Zaghary / Maha S. Al-Mutairi / Ebtehal S. Al-Abdullah / Mogedda E. Haiba / Mohammed A. Khedr

Molecules, Vol 17, Iss 4, Pp 4717-

2012 Volume 4732

Abstract: A facile, convenient and high yielding synthesis of novel S-glycosides and N-glycosides incorporating 1,2,3,4-tetrahydronaphthalene and or 1,2-dihydropyridines moieties has been described. The aglycons 2, 4, and 7 were coupled with different activated ... ...

Abstract	A facile, convenient and high yielding synthesis of novel S-glycosides and N-glycosides incorporating 1,2,3,4-tetrahydronaphthalene and or 1,2-dihydropyridines moieties has been described. The aglycons 2, 4, and 7 were coupled with different activated halosugars in the presence of basic and acidic medium. The preliminary in-vitro cytotoxic evaluation revealed that compounds 3c, 3f, 5c and 7b show promising activity. A molecular docking study was performed against tyrosine kinase (TK) (PDB code: 1t46) by Autodock Vina. The docking output was analyzed and some compounds have shown hydrogen bond (H-B) formation with reasonable distances ranged from 2.06 A° to 3.06 A° with Thr 670 and Cys 673 residues found in the specified pocket. No hydrogen bond was observed with either Glu 640 nor Asp 810 residues, as was expected from pdbsum.
Keywords	tetrahydronaphthalene ; pyridine ; glycoside ; cytotoxic ; molecular docking ; Organic chemistry ; QD241-441 ; Chemistry ; QD1-999 ; Science ; Q ; DOAJ:Organic Chemistry ; DOAJ:Chemistry
Subject code	540
Language	English
Publishing date	2012-04-01T00:00:00Z
Publisher	Molecular Diversity Preservation International
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Synthesis, Molecular Docking and Preliminary in-Vitro Cytotoxic Evaluation of Some Substituted Tetrahydro-naphthalene (2',3',4',6'-Tetra-O-Acetyl-β-D-Gluco/-Galactopyranosyl) Derivatives

Maha S. Al-Mutairi / Ebtehal S. Al-Abdullah / Mogedda E. Haiba / Mohammed A. Khedr / Wafaa A. Zaghary

Molecules, Vol 17, Iss 4, Pp 4717-

2012 Volume 4732

Abstract: A facile, convenient and high yielding synthesis of novel S -glycosides and N -glycosides incorporating 1,2,3,4-tetrahydronaphthalene and or 1,2-dihydropyridines moieties has been described. The aglycons 2 , 4 , and 7 were coupled with different ... ...

Abstract	A facile, convenient and high yielding synthesis of novel S -glycosides and N -glycosides incorporating 1,2,3,4-tetrahydronaphthalene and or 1,2-dihydropyridines moieties has been described. The aglycons 2 , 4 , and 7 were coupled with different activated halosugars in the presence of basic and acidic medium. The preliminary in-vitro cytotoxic evaluation revealed that compounds 3c , 3f , 5c and 7b show promising activity. A molecular docking study was performed against tyrosine kinase (TK) (PDB code: 1t46) by Autodock Vina. The docking output was analyzed and some compounds have shown hydrogen bond (H-B) formation with reasonable distances ranged from 2.06 A° to 3.06 A° with Thr 670 and Cys 673 residues found in the specified pocket. No hydrogen bond was observed with either Glu 640 nor Asp 810 residues, as was expected from pdbsum.
Keywords	tetrahydronaphthalene ; pyridine ; glycoside ; cytotoxic ; molecular docking ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2012-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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