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Article ; Online: Corrigendum to 'Exopolysaccharides from milk fermented by lactic acid bacteria enhance dietary carotenoid bioavailability in humans in a randomized crossover trial and in rats' [American Journal of Clinical Nutrition, 2020;111:903-914].

Morifuji, Masashi / Ichikawa, Satomi / Kitade, Masami / Fukasawa, Tomoyuki / Asami, Yukio / Manabe, Yuki / Sugawara, Tatsuya

The American journal of clinical nutrition

2023 Volume 118, Issue 2, Page(s) 485

Language	English
Publishing date	2023-06-15
Publishing country	United States
Document type	Published Erratum
ZDB-ID	280048-2
ISSN	1938-3207 ; 0002-9165
ISSN (online)	1938-3207
ISSN	0002-9165
DOI	10.1016/j.ajcnut.2023.06.003
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Article: Antiviral drug discovery by targeting the SARS-CoV-2 polyprotein processing by inhibition of the main protease.

Kandeel, Mahmoud / Kim, Jinsoo / Fayez, Mahmoud / Kitade, Yukio / Kwon, Hyung-Joo

PeerJ

2022 Volume 10, Page(s) e12929

Abstract: The spread of SARS-CoV-2, the causative agent for COVID-19, has led to a global and deadly pandemic. To date, few drugs have been approved for treating SARS-CoV-2 infections. In this study, a structure-based approach was adopted using the SARS-CoV-2 main ...

Abstract	The spread of SARS-CoV-2, the causative agent for COVID-19, has led to a global and deadly pandemic. To date, few drugs have been approved for treating SARS-CoV-2 infections. In this study, a structure-based approach was adopted using the SARS-CoV-2 main protease (M
Language	English
Publishing date	2022-02-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.12929
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Article ; Online: Molecular dynamics and binding selectivity of nucleotides and polynucleotide substrates with EIF2C2/Ago2 PAZ domain.

Kandeel, Mahmoud / Kitade, Yukio

International journal of biological macromolecules

2018 Volume 107, Issue Pt B, Page(s) 2566–2573

Abstract: RNA interference (RNAi) constitutes a major target in drug discovery. Recently, we reported that the Argonaute protein 2 (Ago2) PAZ domain selectively binds with all ribonucleotides except adenine and poorly recognizes deoxyribonucleotides. The binding ... ...

Abstract	RNA interference (RNAi) constitutes a major target in drug discovery. Recently, we reported that the Argonaute protein 2 (Ago2) PAZ domain selectively binds with all ribonucleotides except adenine and poorly recognizes deoxyribonucleotides. The binding properties of the PAZ domain with polynucleotides and the molecular mechanisms of substrates' selectivity remains unclear. In this study, the binding potencies of polynucleotides and the associated conformational and dynamic changes in PAZ domain are investigated. Coinciding with nucleotides' binding profile with the PAZ domain, polyuridylate (PolyU) and polycytidylate (PolyC) were potent binders. However, K
MeSH term(s)	Argonaute Proteins/chemistry ; Argonaute Proteins/metabolism ; Ligands ; Molecular Dynamics Simulation ; Polynucleotides/metabolism ; Protein Domains ; Protein Structure, Secondary ; Substrate Specificity ; Thermodynamics
Chemical Substances	Argonaute Proteins ; Ligands ; Polynucleotides
Language	English
Publishing date	2018-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2017.10.145
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Article: Repurposing FDA-approved phytomedicines, natural products, antivirals and cell protectives against SARS-CoV-2 (COVID-19) RNA-dependent RNA polymerase.

Kandeel, Mahmoud / Kitade, Yukio / Almubarak, Abdullah

PeerJ

2020 Volume 8, Page(s) e10480

Abstract: Following the recent emergence of SARS-CoV-2 or coronavirus disease 2019 (COVID-19), drug discovery and vaccine design to combat this fatal infection are critical. In this study, an essential enzyme in the SARS-CoV-2 replication machinery, RNA-dependent ... ...

Abstract	Following the recent emergence of SARS-CoV-2 or coronavirus disease 2019 (COVID-19), drug discovery and vaccine design to combat this fatal infection are critical. In this study, an essential enzyme in the SARS-CoV-2 replication machinery, RNA-dependent RNA polymerase (RDRP), is targeted in a virtual screening assay using a set of 1,664 FDA-approved drugs, including sets of botanical and synthetic derivatives. A set of 22 drugs showed a high docking score of >-7. Notably, approximately one-third of the top hits were either from natural products or biological molecules. The FDA-approved phytochemicals were sennosides, digoxin, asiaticoside, glycyrrhizin, neohesperidin, taxifolin, quercetin and aloin. These approved natural products and phytochemicals are used as general tonics, antioxidants, cell protectives, and immune stimulants (nadid, thymopentin, asiaticoside, glycyrrhizin) and in other miscellaneous systemic or topical applications. A comprehensive analysis was conducted on standard precision and extra precision docking, two-step molecular dynamics simulations, binding energy calculations and a post dynamics analysis. The results reveal that two drugs, docetaxel and neohesperidin, showed strong binding profiles with SARS CoV-2 RdRP. These results can be used as a primer for further drug discovery studies in the treatment of COVID-19. This initiative repurposes safe FDA-approved drugs against COVID-19 RdRP, providing a rapid channel for the discovery and application of new anti-CoV therapeutics.
Language	English
Publishing date	2020-11-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.10480
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Article ; Online: A Diversifiable Synthetic Platform for the Discovery of New Carbasugar SGLT2 Inhibitors Using Azide-Alkyne Click Chemistry.

Kitamura, Yoshiaki / Kandeel, Mahmoud / Oba, Erina / Iwai, Chiori / Iritani, Keitaro / Nagaya, Nanako / Namura, Reo / Katagiri, Hiroshi / Ueda, Hiroshi / Kitade, Yukio

Chemical & pharmaceutical bulletin

2023 Volume 71, Issue 3, Page(s) 240–249

Abstract: Sodium-glucose cotransporter 2 (SGLT2) inhibitors are clinically available to control blood glucose levels in diabetic patients via an insulin-independent mechanism. It was found that some carbasugar analogs of known SGLT2 inhibitors exert a high ... ...

Abstract	Sodium-glucose cotransporter 2 (SGLT2) inhibitors are clinically available to control blood glucose levels in diabetic patients via an insulin-independent mechanism. It was found that some carbasugar analogs of known SGLT2 inhibitors exert a high inhibiting ability toward SGLT2 and have a prolonged blood glucose lowering effect. In this study, we designed new candidates of carbasugar SGLT2 inhibitor that can be synthesized using copper-catalyzed azide-alkyne cycloaddition (CuAAC) into an aromatic ring, which is a part of the pharmacophore at the final stage in the synthetic protocol for the easier discovery of superior SGLT2 inhibitors. Based on the results of molecular docking studies, some selected compounds have been synthesized. Evaluation of these compounds using a cell-based assay revealed that the majority of these compounds had SGLT2 inhibitory activity in a dose-dependent manner. The SGLT2 inhibitory activity of 7b and 7c was almost equal to that of SGLT2 inhibitors in current use. Furthermore, molecular dynamics simulations also revealed that 7c is a promising novel SGLT2 inhibitor.
MeSH term(s)	Humans ; Alkynes ; Azides ; Blood Glucose ; Carbasugars ; Click Chemistry ; Molecular Docking Simulation ; Sodium-Glucose Transporter 2 ; Sodium-Glucose Transporter 2 Inhibitors ; Cycloaddition Reaction
Chemical Substances	Alkynes ; Azides ; Blood Glucose ; Carbasugars ; Sodium-Glucose Transporter 2 ; Sodium-Glucose Transporter 2 Inhibitors
Language	English
Publishing date	2023-03-01
Publishing country	Japan
Document type	Journal Article
ZDB-ID	213307-6
ISSN	1347-5223 ; 0009-2363
ISSN (online)	1347-5223
ISSN	0009-2363
DOI	10.1248/cpb.c22-00841
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Article ; Online: Antiviral drug discovery by targeting the SARS-CoV-2 polyprotein processing by inhibition of the main protease

Mahmoud Kandeel / Jinsoo Kim / Mahmoud Fayez / Yukio Kitade / Hyung-Joo Kwon

PeerJ, Vol 10, p e

2022 Volume 12929

Abstract	The spread of SARS-CoV-2, the causative agent for COVID-19, has led to a global and deadly pandemic. To date, few drugs have been approved for treating SARS-CoV-2 infections. In this study, a structure-based approach was adopted using the SARS-CoV-2 main protease (Mpro) and a carefully selected dataset of 37,060 compounds comprising Mpro and antiviral protein-specific libraries. The compounds passed two-step docking filtration, starting with standard precision (SP) followed by extra precision (XP) runs. Fourteen compounds with the highest XP docking scores were examined by 20 ns molecular dynamics simulations (MDs). Based on backbone route mean square deviations (RMSD) and molecular mechanics/generalized Born surface area (MM/GBSA) binding energy, four drugs were selected for comprehensive MDs analysis at 100 ns. Results indicated that birinapant, atazanavir, and ritonavir potently bound and stabilized SARS-CoV-2 Mpro structure. Binding energies higher than −102 kcal/mol, RMSD values <0.22 nm, formation of several hydrogen bonds with Mpro, favourable electrostatic contributions, and low radii of gyration were among the estimated factors contributing to the strength of the binding of these three compounds with Mpro. The top two compounds, atazanavir and birinapant, were tested for their ability to prevent SARS-CoV-2 plaque formation. At 10 µM of birinapant concentration, antiviral tests against SARS-CoV-2 demonstrated a 37% reduction of virus multiplication. Antiviral assays demonstrated that birinapant has high anti-SARS-CoV-2 activity in the low micromolar range, with an IC50 value of 18 ± 3.6 µM. Therefore, birinapant is a candidate for further investigation to determine whether it is a feasible therapy option.
Keywords	SARS-CoV-2 ; COVID-19 ; Main protease ; Molecular modeling ; Drug discovery ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	540
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
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Article: A pilot study on the pharmacokinetics of a single intramuscular injection of cefquinome in Arabian camel calves.

Altayban, Abdullah / Kandeel, Mahmoud / Kitade, Yukio / Al-Nazawi, Mohammed

Acta veterinaria Hungarica

2020 Volume 68, Issue 1, Page(s) 59–64

Abstract: This study was conducted to evaluate the pharmacokinetics of cefquinome in camel calves after a single intramuscular injection in a dose of 2 mg/kg body weight (kg b. w.). Cefquinome concentrations were measured by ultra-high performance liquid ... ...

Abstract	This study was conducted to evaluate the pharmacokinetics of cefquinome in camel calves after a single intramuscular injection in a dose of 2 mg/kg body weight (kg b. w.). Cefquinome concentrations were measured by ultra-high performance liquid chromatography-mass spectrometry (UPLC-MS/MS). A non-compartmental pharmacokinetic model was used to fit the time-concentration curve and estimate the pharmacokinetic parameters. The peak serum concentration (Cmax) was 28.4 μg/mL at the time of maximum concentration (Tmax) of 25 min. The elimination half-life (t1/2) was 17.4 h. The area under the concentration-time curve (AUC0-∞) was 103.7 μg/ml-1h and the mean residence time (MRT0-∞) was 21.3 h. In comparison with other animal species, the pharmacokinetics of cefquinome in Arabian camel calves showed faster absorption from the site of injection and slower elimination. Since cefquinome, as other beta-lactams, is a time-dependent antimicrobial agent, a single dose of 2 mg/kg b. w. might be sufficient against the most sensitive organisms in camel calves owing to its prolonged elimination phase. However, dose readjustment is required for cases needing concentrations above 2 µg/mL for 12 h or above 1 µg/mL for 24 h.
MeSH term(s)	Animals ; Anti-Bacterial Agents/administration & dosage ; Anti-Bacterial Agents/pharmacokinetics ; Camelus/metabolism ; Cephalosporins/administration & dosage ; Cephalosporins/pharmacokinetics ; Injections, Intramuscular/veterinary ; Male ; Pilot Projects
Chemical Substances	Anti-Bacterial Agents ; Cephalosporins ; cefquinome (Z74S078CWP)
Language	English
Publishing date	2020-05-08
Publishing country	Hungary
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605742-1
ISSN	1588-2705 ; 0236-6290 ; 0365-8198
ISSN (online)	1588-2705
ISSN	0236-6290 ; 0365-8198
DOI	10.1556/004.2020.00008
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Article ; Online: Synthesis of cationic glucosamino nucleic acids for stabilizing oligonucleotides.

Kitamura, Yoshiaki / Moribe, Shuichi / Kitade, Yukio

Bioorganic & medicinal chemistry letters

2018 Volume 28, Issue 19, Page(s) 3174–3176

Abstract: Glucosamino nucleic acids (GANAs) bearing a β-N-glycoside bond between carbon 1 of the glucosamine and the nucleobase nitrogen were synthesized and incorporated into oligonucleotides (4',6'-GANA and 3',6'-GANA). The thermal stability of oligonucleotide ... ...

Abstract	Glucosamino nucleic acids (GANAs) bearing a β-N-glycoside bond between carbon 1 of the glucosamine and the nucleobase nitrogen were synthesized and incorporated into oligonucleotides (4',6'-GANA and 3',6'-GANA). The thermal stability of oligonucleotide duplexes containing the GANA zwitterionic nucleotides was also investigated.
MeSH term(s)	Base Pairing ; Biochemical Phenomena ; Cations ; Glucosamine/chemistry ; Hot Temperature ; Nucleic Acid Hybridization ; Nucleic Acids/chemical synthesis ; Nucleic Acids/chemistry ; Oligonucleotides/chemistry
Chemical Substances	Cations ; Nucleic Acids ; Oligonucleotides ; Glucosamine (N08U5BOQ1K)
Language	English
Publishing date	2018-08-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2018.08.024
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Article ; Online: The emerging SARS-CoV-2 papain-like protease: Its relationship with recent coronavirus epidemics.

Kandeel, Mahmoud / Kitade, Yukio / Fayez, Mahmoud / Venugopala, Katharigatta N / Ibrahim, Abdelazim

Journal of medical virology

2020 Volume 93, Issue 3, Page(s) 1581–1588

Abstract: The papain-like protease ( ... ...

Abstract	The papain-like protease (PL
MeSH term(s)	Amino Acid Sequence ; COVID-19/pathology ; Catalytic Domain/physiology ; Coronavirus Papain-Like Proteases/metabolism ; Humans ; Middle East Respiratory Syndrome Coronavirus/enzymology ; Models, Molecular ; Polyproteins/biosynthesis ; Polyproteins/genetics ; SARS Virus/enzymology ; SARS-CoV-2/enzymology ; Sequence Alignment ; Severe Acute Respiratory Syndrome/pathology ; Ubiquitin/metabolism ; Viral Proteins/biosynthesis ; Viral Proteins/genetics
Chemical Substances	Polyproteins ; Ubiquitin ; Viral Proteins ; Coronavirus Papain-Like Proteases (EC 3.4.22.2)
Keywords	covid19
Language	English
Publishing date	2020-09-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.26497
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Article: Molecular dynamics and binding selectivity of nucleotides and polynucleotide substrates with EIF2C2/Ago2 PAZ domain

Kandeel, Mahmoud / Yukio Kitade

International journal of biological macromolecules. 2018 Feb., v. 107

2018

Abstract	RNA interference (RNAi) constitutes a major target in drug discovery. Recently, we reported that the Argonaute protein 2 (Ago2) PAZ domain selectively binds with all ribonucleotides except adenine and poorly recognizes deoxyribonucleotides. The binding properties of the PAZ domain with polynucleotides and the molecular mechanisms of substrates’ selectivity remains unclear. In this study, the binding potencies of polynucleotides and the associated conformational and dynamic changes in PAZ domain are investigated. Coinciding with nucleotides’ binding profile with the PAZ domain, polyuridylate (PolyU) and polycytidylate (PolyC) were potent binders. However, KdPolyU and KdPolyC were 15.8 and 9.3μM, respectively. In contrast, polyadenylate (PolyA) binding was not detectable. Molecular dynamics (MD) simulation revealed the highest change in root mean square deviation (RMSD) with ApoPAZ or PAZ domain bound with experimentally approved, low affinity substrates, whereas stronger binding substrates such as UMP or PolyU showed minimal RMSD changes. The loop between α3 and β5 in the β-hairpin subdomain showed the most responsive change in RMSD, being highly movable in the ApoPAZ and PAZ-AMP complex. Favorable substrate recognition was associate with moderate change in secondary structure content. In conclusion, the PAZ domain retains differential substrate selectivity associated with corresponding dynamic and structural changes upon binding.
Keywords	adenine ; binding properties ; drugs ; molecular dynamics ; polynucleotides ; ribonucleotides ; RNA interference ; uridine monophosphate
Language	English
Dates of publication	2018-02
Size	p. 2566-2573.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2017.10.145
Database	NAL-Catalogue (AGRICOLA)

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