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Article ; Online: A Biochemical Perspective of the Nonstructural Proteins (NSPs) and the Spike Protein of SARS CoV-2.

Yoshimoto, Francis K

2021 Volume 40, Issue 3, Page(s) 260–295

Abstract: The global pandemic that shut down the world in 2020 was caused by the virus, SARS CoV-2. The chemistry of the various nonstructural proteins (NSP3, NSP5, NSP12, NSP13, NSP14, NSP15, NSP16) of SARS CoV-2 is discussed. Secondly, a recent major focus of ... ...

Abstract	The global pandemic that shut down the world in 2020 was caused by the virus, SARS CoV-2. The chemistry of the various nonstructural proteins (NSP3, NSP5, NSP12, NSP13, NSP14, NSP15, NSP16) of SARS CoV-2 is discussed. Secondly, a recent major focus of this pandemic is the variant strains of SARS CoV-2 that are increasingly occurring and more transmissible. One strain, called "D614G", possesses a glycine (G) instead of an aspartate (D) at position 614 of the spike protein. Additionally, other emerging strains called "501Y.V1" and "501Y.V2" have several differences in the receptor binding domain of the spike protein (N501Y) as well as other locations. These structural changes may enhance the interaction between the spike protein and the ACE2 receptor of the host, increasing infectivity. The global pandemic caused by SARS CoV-2 is a rapidly evolving situation, emphasizing the importance of continuing the efforts to interrogate and understand this virus.
MeSH term(s)	COVID-19/genetics ; COVID-19/metabolism ; COVID-19/pathology ; Humans ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; Viral Nonstructural Proteins ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-02-24
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-021-09967-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19.

Yoshimoto, Francis K

The protein journal

2020 Volume 39, Issue 3, Page(s) 198–216

Abstract: The devastating effects of the recent global pandemic (termed COVID-19 for "coronavirus disease 2019") caused by the severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) are paramount with new cases and deaths growing at an exponential rate. In ... ...

Abstract	The devastating effects of the recent global pandemic (termed COVID-19 for "coronavirus disease 2019") caused by the severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) are paramount with new cases and deaths growing at an exponential rate. In order to provide a better understanding of SARS CoV-2, this article will review the proteins found in the SARS CoV-2 that caused this global pandemic.
MeSH term(s)	Amino Acid Sequence ; Betacoronavirus/chemistry ; Betacoronavirus/genetics ; Betacoronavirus/physiology ; COVID-19 ; Coronavirus Envelope Proteins ; Coronavirus Infections/drug therapy ; Coronavirus Infections/metabolism ; Coronavirus Infections/virology ; Coronavirus Nucleocapsid Proteins ; Drug Discovery/methods ; Genome, Viral ; Host-Pathogen Interactions/drug effects ; Humans ; Nucleocapsid Proteins/chemistry ; Nucleocapsid Proteins/genetics ; Nucleocapsid Proteins/metabolism ; Pandemics ; Phosphoproteins ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/metabolism ; Pneumonia, Viral/virology ; Polyproteins ; Protein Interaction Maps/drug effects ; SARS-CoV-2 ; Sequence Alignment ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; Viral Envelope Proteins/chemistry ; Viral Envelope Proteins/genetics ; Viral Envelope Proteins/metabolism ; Viral Matrix Proteins/chemistry ; Viral Matrix Proteins/genetics ; Viral Matrix Proteins/metabolism ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism ; Viral Proteins/chemistry ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Viral Regulatory and Accessory Proteins/chemistry ; Viral Regulatory and Accessory Proteins/genetics ; Viral Regulatory and Accessory Proteins/metabolism ; Viroporin Proteins
Chemical Substances	Coronavirus Envelope Proteins ; Coronavirus Nucleocapsid Proteins ; NSP1 protein, SARS-CoV-2 ; Nucleocapsid Proteins ; ORF1ab polyprotein, SARS-CoV-2 ; ORF3a protein, SARS-CoV-2 ; ORF6 protein, SARS-CoV-2 ; Phosphoproteins ; Polyproteins ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins ; Viral Matrix Proteins ; Viral Nonstructural Proteins ; Viral Proteins ; Viral Regulatory and Accessory Proteins ; Viroporin Proteins ; envelope protein, SARS-CoV-2 ; membrane protein, SARS-CoV-2 ; nucleocapsid phosphoprotein, SARS-CoV-2 ; spike protein, SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-05-24
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-020-09901-4
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Article ; Online: Synthesis of menarandroside A from dehydroepiandrosterone.

Offei, Samuel D / Arman, Hadi D / Yoshimoto, Francis K

Organic & biomolecular chemistry

2023 Volume 21, Issue 15, Page(s) 3172–3176

Abstract: Menarandroside A, which bears a 12α-hydroxypregnenolone steroid backbone, was isolated from the plant, ...

Abstract	Menarandroside A, which bears a 12α-hydroxypregnenolone steroid backbone, was isolated from the plant,
MeSH term(s)	Humans ; Diabetes Mellitus, Type 2 ; Steroids ; Glucagon-Like Peptide 1/metabolism ; Oxidation-Reduction ; Dehydroepiandrosterone/metabolism
Chemical Substances	Steroids ; Glucagon-Like Peptide 1 (89750-14-1) ; Dehydroepiandrosterone (459AG36T1B)
Language	English
Publishing date	2023-04-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2097583-1
ISSN	1477-0539 ; 1477-0520
ISSN (online)	1477-0539
ISSN	1477-0520
DOI	10.1039/d3ob00054k
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Article ; Online: Synthesis of hyocholic acid and its derivatization with sodium periodate to distinguish it from cholic acid by mass spectrometry.

Ho, Tu M / Arman, Hadi D / Yoshimoto, Francis K

Steroids

2023 Volume 197, Page(s) 109260

Abstract: Low concentrations of hyocholic acid in human serum has been linked to diabetes. Due to its important role in human health, we were interested in synthesizing hyocholic acid to explore potential biochemical properties of this bile acid. Here, a synthesis ...

Abstract	Low concentrations of hyocholic acid in human serum has been linked to diabetes. Due to its important role in human health, we were interested in synthesizing hyocholic acid to explore potential biochemical properties of this bile acid. Here, a synthesis of hyocholic acid is reported from chenodeoxycholic acid. The key step was a Rubottom oxidation of a silyl enol ether intermediate to directly incorporate the oxygen at C6. Furthermore, the synthesized hyocholic acid product was treated with NaIO
MeSH term(s)	Humans ; Cholic Acid ; Cholic Acids ; Bile Acids and Salts ; Mass Spectrometry
Chemical Substances	Cholic Acid (G1JO7801AE) ; muricholic acid (39016-49-4) ; metaperiodate (B45A1BUM4Q) ; Cholic Acids ; Bile Acids and Salts
Language	English
Publishing date	2023-06-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	80312-1
ISSN	1878-5867 ; 0039-128X
ISSN (online)	1878-5867
ISSN	0039-128X
DOI	10.1016/j.steroids.2023.109260
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Article ; Online: Update and Supplementary Articles Proteins of SARS CoV-2, Which Causes COVID-19, and the Interacting Proteins.

Yoshimoto, Francis K / Berliner, Lawrence J

The protein journal

2021 Volume 40, Issue 3, Page(s) 255–259

Abstract: Coronavirus disease 2019 (COVID-19), which is the pandemic caused by the virus, severe acute respiratory syndrome coronavirus-2 (SARS CoV-2), first appearing in December 2019, continues to confound the world. In this update we provide insights into how ... ...

Abstract	Coronavirus disease 2019 (COVID-19), which is the pandemic caused by the virus, severe acute respiratory syndrome coronavirus-2 (SARS CoV-2), first appearing in December 2019, continues to confound the world. In this update we provide insights into how some of the new mutant variant strains of SARS CoV-2 have evolved to be more infective. We also introduce our supplement of the special issue on the topic of the proteins of SARS CoV-2 in the Protein Journal, which follows this introduction.
MeSH term(s)	COVID-19/genetics ; COVID-19/metabolism ; Humans ; Mutation ; Protein Binding ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism
Language	English
Publishing date	2021-05-21
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-021-10000-1
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Article: The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19

Yoshimoto, Francis K

Protein J

Abstract	The devastating effects of the recent global pandemic (termed COVID-19 for "coronavirus disease 2019") caused by the severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) are paramount with new cases and deaths growing at an exponential rate. In order to provide a better understanding of SARS CoV-2, this article will review the proteins found in the SARS CoV-2 that caused this global pandemic.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #342993
Database	COVID19

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Article ; Online: Synthesis of 6β-hydroxy androgens from a 3,5-diene steroid precursor to test for cytochrome P450 3A4-catalyzed hydroxylation of androstenedione.

Yoshimoto, Francis K / Guerrero, Samantha Q / Ho, Tu M / Arman, Hadi D

Steroids

2023 Volume 199, Page(s) 109298

Abstract: 6β-Hydroxytestosterone is a biomarker for the activity of human cytochrome P450 3A4 (P450 3A4), the major drug metabolizing cytochrome P450 enzyme. Despite its significance, efficient routes for the chemical synthesis of 6β-hydroxytestosterone are rare. ... ...

Abstract	6β-Hydroxytestosterone is a biomarker for the activity of human cytochrome P450 3A4 (P450 3A4), the major drug metabolizing cytochrome P450 enzyme. Despite its significance, efficient routes for the chemical synthesis of 6β-hydroxytestosterone are rare. In this study, 6β-hydroxytestosterone was synthesized through the oxidation of a 3,5-diene precursor under the Uemura-Doyle reaction conditions using a dirhodium catalyst in the presence of tert-butylhydroperoxide. Mechanistic studies showed that some oxygen is incorporated from molecular oxygen and CH abstraction is partially rate-limiting. This reaction was used to synthesize 6β-hydroxyandrostenedione, which was used as a standard to test the hypothesis of whether P450 3A4 catalyzes the hydroxylation of androstenedione. Upon incubation of P450 3A4 with androstenedione, a hydroxylated product was formed, which matched the retention time of synthetic 6β-hydroxyandrostenedione. This reaction can be exploited to study other biochemical processes involving compounds with a 6 β -hydroxy-3-keto-Δ
Language	English
Publishing date	2023-08-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	80312-1
ISSN	1878-5867 ; 0039-128X
ISSN (online)	1878-5867
ISSN	0039-128X
DOI	10.1016/j.steroids.2023.109298
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Article ; Online: Pyridine-containing substrate analogs are restricted from accessing the human cytochrome P450 8B1 active site by tryptophan 281.

Liu, Jinghan / Offei, Samuel D / Yoshimoto, Francis K / Scott, Emily E

The Journal of biological chemistry

2023 Volume 299, Issue 4, Page(s) 103032

Abstract: The human oxysterol 12α-hydroxylase cytochrome P450 8B1 (CYP8B1) is a validated drug target for both type 2 diabetes and nonalcoholic fatty liver disease, but effective selective inhibitors are not yet available. Herein, steroidal substrate-mimicking ... ...

Abstract	The human oxysterol 12α-hydroxylase cytochrome P450 8B1 (CYP8B1) is a validated drug target for both type 2 diabetes and nonalcoholic fatty liver disease, but effective selective inhibitors are not yet available. Herein, steroidal substrate-mimicking compounds with a pyridine ring appended to the C12 site of metabolism were designed as inhibitors, synthesized, and evaluated in terms of their functional and structural interactions with CYP8B1. While the pyridine nitrogen was intended to coordinate the CYP8B1 active site heme iron, none of these compounds elicited shifts in the CYP8B1 Soret absorbance consistent with this type of interaction. However, when CYP8B1 was cocrystallized with the pyridine-containing compound with the 3-keto-Δ4 steroid backbone most similar to the endogenous substrate, it was apparent that this ligand was bound in a channel leading to the active site, instead of near the heme iron. Inspection of this structure suggested that tryptophan 281 directly above the heme might restrict active site binding of potential inhibitors with this design. This hypothesis was supported when a CYP8B1 W281F mutation did allow all three compounds to coordinate the heme iron as designed. These results indicated that the design of next-generation CYP8B1 inhibitors should be compatible with the low-ceiling tryptophan immediately above the heme iron.
MeSH term(s)	Humans ; Steroid 12-alpha-Hydroxylase/metabolism ; Cytochrome P-450 Enzyme System/metabolism ; Catalytic Domain ; Tryptophan ; Diabetes Mellitus, Type 2 ; Steroids ; Pyridines/pharmacology ; Heme/metabolism ; Iron/metabolism
Chemical Substances	Steroid 12-alpha-Hydroxylase (EC 1.14.18.8) ; Cytochrome P-450 Enzyme System (9035-51-2) ; Tryptophan (8DUH1N11BX) ; Steroids ; Pyridines ; Heme (42VZT0U6YR) ; Iron (E1UOL152H7)
Language	English
Publishing date	2023-02-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.103032
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Article ; Online: Copper oxidation chemistry using a 19-iminopyridine-bearing steroidal ligand: (i) C5-C6 olefin difunctionalization and (ii) C1β-hydroxylation/C19-peroxidation.

Offei, Samuel D / Arman, Hadi D / Yoshimoto, Francis K

Steroids

2022 Volume 186, Page(s) 109088

Abstract: The Schönecker oxidation involves the 12beta-hydroxylation of 17-imino pyridine DHEA derivatives using copper and either molecular oxygen or hydrogen peroxide as the oxidant. In this study, a 19-imino pyridine DHEA derivative was synthesized and was ... ...

Abstract	The Schönecker oxidation involves the 12beta-hydroxylation of 17-imino pyridine DHEA derivatives using copper and either molecular oxygen or hydrogen peroxide as the oxidant. In this study, a 19-imino pyridine DHEA derivative was synthesized and was treated with copper nitrate and hydrogen peroxide. Our results showed the difunctionalization of an olefin for delta-5 steroid substrates to yield a 5beta-hydroxylated 6alpha-nitrate ester product. In contrast, for 19-imino pyridine precursors with a 5alpha-androstane steroid backbone: a 1beta-hydroxylation and 19-peroxidation occurred to yield a 1beta-hydroxylated 19-imidoperoxoic acid product. In conclusion, new Schönecker oxidation chemistry was discovered (C5-C6 olefin difunctionalization and C1beta-hydroxylation/C19-peroxidation) when a 19-imino pyridine DHEA derivative was used as the substrate.
MeSH term(s)	Alkenes ; Copper ; Dehydroepiandrosterone/chemistry ; Hydrogen Peroxide ; Hydroxylation ; Ligands ; Nitrates ; Oxidation-Reduction ; Steroids/chemistry
Chemical Substances	Alkenes ; Ligands ; Nitrates ; Steroids ; Dehydroepiandrosterone (459AG36T1B) ; Copper (789U1901C5) ; Hydrogen Peroxide (BBX060AN9V)
Language	English
Publishing date	2022-07-11
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	80312-1
ISSN	1878-5867 ; 0039-128X
ISSN (online)	1878-5867
ISSN	0039-128X
DOI	10.1016/j.steroids.2022.109088
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Zs.A 87: Show issues

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Article ; Online: Editorial: Proteins of SARS CoV-2, the Cause of COVID-19, and the Proteins that Interact with Them.

Yoshimoto, Francis K / Berliner, Lawrence J

The protein journal

2020 Volume 39, Issue 6, Page(s) 599

MeSH term(s)	COVID-19/epidemiology ; COVID-19/metabolism ; COVID-19/virology ; Host-Pathogen Interactions ; Humans ; Protein Interaction Maps ; SARS-CoV-2/physiology ; Viral Proteins/metabolism
Chemical Substances	Viral Proteins
Language	English
Publishing date	2020-12-05
Publishing country	Netherlands
Document type	Editorial ; Introductory Journal Article
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-020-09947-4
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