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Article ; Online: Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals.

Kottur, Jithesh / White, Kris M / Rodriguez, M Luis / Rechkoblit, Olga / Quintana-Feliciano, Richard / Nayar, Ahana / García-Sastre, Adolfo / Aggarwal, Aneel K

PLoS pathogens

2023 Volume 19, Issue 7, Page(s) e1011546

Abstract: The RNA N7-methyltransferase (MTase) activity of SARS-CoV-2's nsp14 protein is essential for viral replication and is a target for the development of new antivirals. Nsp14 uses S-adenosyl methionine (SAM) as the methyl donor to cap the 5' end of the SARS- ...

Abstract	The RNA N7-methyltransferase (MTase) activity of SARS-CoV-2's nsp14 protein is essential for viral replication and is a target for the development of new antivirals. Nsp14 uses S-adenosyl methionine (SAM) as the methyl donor to cap the 5' end of the SARS-CoV-2 mRNA and generates S-adenosyl homocysteine (SAH) as the reaction byproduct. Due to the central role of histone MTases in cancer, many SAM/SAH analogs with properties of cell permeability have recently been developed for the inhibition of these MTases. We have succeeded in identifying two such compounds (SGC0946 and SGC8158) that display significant antiviral activity and bind to the SARS-CoV-2 nsp14 N7-MTase core. Unexpectedly, crystal structures of SGC0946 and SGC8158 with the SARS-CoV-2 nsp14 N7-MTase core identify them as bi-substrate inhibitors of the viral MTase, co-occupying both the SAM and RNA binding sites; positing novel features that can be derivatized for increased potency and selectivity for SARS-CoV-2 nsp14. Taken together, the high-resolution structures and the accompanying biophysical and viral replication data provide a new avenue for developing analogs of SGC0946 and SGC8158 as antivirals.
MeSH term(s)	Humans ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Antiviral Agents/pharmacology ; SARS-CoV-2/genetics ; Viral Nonstructural Proteins/metabolism ; COVID-19 ; S-Adenosylmethionine/metabolism ; RNA ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Exoribonucleases/genetics ; Histone-Lysine N-Methyltransferase ; Protein-Arginine N-Methyltransferases
Chemical Substances	Methyltransferases (EC 2.1.1.-) ; Antiviral Agents ; Viral Nonstructural Proteins ; S-Adenosylmethionine (7LP2MPO46S) ; RNA (63231-63-0) ; RNA, Viral ; Exoribonucleases (EC 3.1.-) ; DOT1L protein, human (EC 2.1.1.-) ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; PRMT7 protein, human (EC 2.1.1.319) ; Protein-Arginine N-Methyltransferases (EC 2.1.1.319)
Language	English
Publishing date	2023-07-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1011546
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Article ; Online: Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase.

Journal of medicinal chemistry

2023 Volume 66, Issue 12, Page(s) 7785–7803

Abstract: An under-explored target for SARS-CoV-2 is ... ...

Abstract	An under-explored target for SARS-CoV-2 is the
MeSH term(s)	Humans ; Methyltransferases ; SARS-CoV-2/genetics ; Viral Nonstructural Proteins/genetics ; COVID-19 ; RNA, Viral/genetics ; Exoribonucleases
Chemical Substances	Methyltransferases (EC 2.1.1.-) ; Viral Nonstructural Proteins ; RNA, Viral ; Exoribonucleases (EC 3.1.-)
Language	English
Publishing date	2023-06-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.2c02120
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Article ; Online: Controversial Dietary Patterns: A High Yield Primer for Clinicians.

Aggarwal, Monica / Ros, Emilio / Allen, Kathleen / Sikand, Geeta / Agarwala, Anandita / Aspry, Karen / Kris-Etherton, Penny / Devries, Stephen / Reddy, Koushik / Singh, Tamanna / Litwin, Sheldon E / Keefe, James O' / Miller, Michael / Andrus, Bruce / Blankstein, Ron / Batiste, Columbus / Belardo, Danielle / Wenger, Christopher / Batts, Travis /

Barnard, Neal D / White, Beth A / Ornish, Dean / Williams, Kim A / Ostfeld, Robert J / Freeman, Andrew M

The American journal of medicine

2022 Volume 135, Issue 6, Page(s) 680–687

Abstract: In cardiology clinic visits, the discussion of optimal dietary patterns for prevention and management of cardiovascular disease is usually very limited. Herein, we explore the benefits and risks of various dietary patterns, including intermittent fasting, ...

Abstract	In cardiology clinic visits, the discussion of optimal dietary patterns for prevention and management of cardiovascular disease is usually very limited. Herein, we explore the benefits and risks of various dietary patterns, including intermittent fasting, low carbohydrate, Paleolithic, whole food plant-based diet, and Mediterranean dietary patterns within the context of cardiovascular disease to empower clinicians with the evidence and information they need to maximally benefit their patients.
MeSH term(s)	Cardiovascular Diseases/prevention & control ; Diet, Mediterranean ; Fasting ; Humans
Language	English
Publishing date	2022-02-05
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	80015-6
ISSN	1555-7162 ; 1873-2178 ; 0002-9343 ; 1548-2766
ISSN (online)	1555-7162 ; 1873-2178
ISSN	0002-9343 ; 1548-2766
DOI	10.1016/j.amjmed.2022.01.028
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Article: SARS-CoV-2 Inhibitors Identified by Phenotypic Analysis of a Collection of Viral RNA-Binding Molecules.

Simba-Lahuasi, Alvaro / Cantero-Camacho, Ángel / Rosales, Romel / McGovern, Briana Lynn / Rodríguez, M Luis / Marchán, Vicente / White, Kris M / García-Sastre, Adolfo / Gallego, José

Pharmaceuticals (Basel, Switzerland)

2022 Volume 15, Issue 12

Abstract: Antiviral agents are needed for the treatment of SARS-CoV-2 infections and to control other coronavirus outbreaks that may occur in the future. Here we report the identification and characterization of RNA-binding compounds that inhibit SARS-CoV-2 ... ...

Abstract	Antiviral agents are needed for the treatment of SARS-CoV-2 infections and to control other coronavirus outbreaks that may occur in the future. Here we report the identification and characterization of RNA-binding compounds that inhibit SARS-CoV-2 replication. The compounds were detected by screening a small library of antiviral compounds previously shown to bind HIV-1 or HCV RNA elements with a live-virus cellular assay detecting inhibition of SARS-CoV-2 replication. These experiments allowed detection of eight compounds with promising anti-SARS-CoV-2 activity in the sub-micromolar to micromolar range and wide selectivity indexes. Examination of the mechanism of action of three selected hit compounds excluded action on the entry or egress stages of the virus replication cycle and confirmed recognition by two of the molecules of conserved RNA elements of the SARS-CoV-2 genome, including the highly conserved S2m hairpin located in the 3'-untranslated region of the virus. While further studies are needed to clarify the mechanism of action responsible for antiviral activity, these results facilitate the discovery of RNA-targeted antivirals and provide new chemical scaffolds for developing therapeutic agents against coronaviruses.
Language	English
Publishing date	2022-11-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph15121448
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Article ; Online: The IRE1α-XBP1 arm of the unfolded protein response is a host factor activated in SARS-CoV-2 infection.

Fernández, Jose Javier / Marín, Arturo / Rosales, Romel / Penrice-Randal, Rebekah / Mlcochova, Petra / Alvarez, Yolanda / Villalón-Letelier, Fernando / Yildiz, Soner / Pérez, Enrique / Rathnasinghe, Raveen / Cupic, Anastasija / Kehrer, Thomas / Uccellini, Melissa B / Alonso, Sara / Martínez, Fernando / McGovern, Briana Lynn / Clark, Jordan J / Sharma, Parul / Bayón, Yolanda /

Alonso, Andrés / Albrecht, Randy A / White, Kris M / Schotsaert, Michael / Miorin, Lisa / Stewart, James P / Hiscox, Julian A / Gupta, Ravindra K / Irigoyen, Nerea / García-Sastre, Adolfo / Crespo, Mariano Sánchez / Fernández, Nieves

Biochimica et biophysica acta. Molecular basis of disease

2024 Volume 1870, Issue 5, Page(s) 167193

Abstract: SARS-CoV-2 infection can cause severe pneumonia, wherein exacerbated inflammation plays a major role. This is reminiscent of the process commonly termed cytokine storm, a condition dependent on a disproportionated production of cytokines. This state ... ...

Abstract	SARS-CoV-2 infection can cause severe pneumonia, wherein exacerbated inflammation plays a major role. This is reminiscent of the process commonly termed cytokine storm, a condition dependent on a disproportionated production of cytokines. This state involves the activation of the innate immune response by viral patterns and coincides with the biosynthesis of the biomass required for viral replication, which may overwhelm the capacity of the endoplasmic reticulum and drive the unfolded protein response (UPR). The UPR is a signal transduction pathway composed of three branches that is initiated by a set of sensors: inositol-requiring protein 1 (IRE1), protein kinase RNA-like ER kinase (PERK), and activating transcription factor 6 (ATF6). These sensors control adaptive processes, including the transcriptional regulation of proinflammatory cytokines. Based on this background, the role of the UPR in SARS-CoV-2 replication and the ensuing inflammatory response was investigated using in vivo and in vitro models of infection. Mice and Syrian hamsters infected with SARS-CoV-2 showed a sole activation of the Ire1α-Xbp1 arm of the UPR associated with a robust production of proinflammatory cytokines. Human lung epithelial cells showed the dependence of viral replication on the expression of UPR-target proteins branching on the IRE1α-XBP1 arm and to a lower extent on the PERK route. Likewise, activation of the IRE1α-XBP1 branch by Spike (S) proteins from different variants of concern was a uniform finding. These results show that the IRE1α-XBP1 system enhances viral replication and cytokine expression and may represent a potential therapeutic target in SARS-CoV-2 severe pneumonia.
Language	English
Publishing date	2024-04-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	60-7
ISSN	1879-260X ; 1879-2596 ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-260X ; 1879-2596 ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbadis.2024.167193
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Article ; Online: Passenger Mutations Confound Phenotypes of SARM1-Deficient Mice.

Uccellini, Melissa B / Bardina, Susana V / Sánchez-Aparicio, Maria Teresa / White, Kris M / Hou, Ying-Ju / Lim, Jean K / García-Sastre, Adolfo

Cell reports

2020 Volume 31, Issue 1, Page(s) 107498

Abstract: The Toll/IL-1R-domain-containing adaptor protein SARM1 is expressed primarily in the brain, where it mediates axonal degeneration. Roles for SARM1 in TLR signaling, viral infection, inflammasome activation, and chemokine and Xaf1 expression have also ... ...

Abstract	The Toll/IL-1R-domain-containing adaptor protein SARM1 is expressed primarily in the brain, where it mediates axonal degeneration. Roles for SARM1 in TLR signaling, viral infection, inflammasome activation, and chemokine and Xaf1 expression have also been described. Much of the evidence for SARM1 function relies on SARM1-deficient mice generated in 129 ESCs and backcrossed to B6. The Sarm1 gene lies in a gene-rich region encompassing Xaf1 and chemokine loci, which remain 129 in sequence. We therefore generated additional knockout strains on the B6 background, confirming the role of SARM1 in axonal degeneration and WNV infection, but not in VSV or LACV infection, or in chemokine or Xaf1 expression. Sequence variation in proapoptotic Xaf1 between B6 and 129 results in coding changes and distinct splice variants, which may account for phenotypes previously attributed to SARM1. Reevaluation of phenotypes in these strains will be critical for understanding the function of SARM1.
MeSH term(s)	Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Apoptosis/genetics ; Apoptosis Regulatory Proteins/metabolism ; Armadillo Domain Proteins/genetics ; Armadillo Domain Proteins/metabolism ; Axons/metabolism ; Brain/metabolism ; Cytoskeletal Proteins/genetics ; Cytoskeletal Proteins/metabolism ; Encephalitis, California/genetics ; Eye Diseases, Hereditary ; Female ; La Crosse virus ; Male ; Mice ; Mice, 129 Strain ; Mice, Inbred C57BL ; Mice, Knockout ; Mutation/genetics ; Phenotype ; Receptors, Interleukin-1/metabolism ; Retinal Degeneration ; Signal Transduction/genetics ; Toll-Like Receptors/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; Vision Disorders ; West Nile Fever/genetics
Chemical Substances	Adaptor Proteins, Signal Transducing ; Apoptosis Regulatory Proteins ; Armadillo Domain Proteins ; Cytoskeletal Proteins ; Receptors, Interleukin-1 ; SARM1 protein, mouse ; Toll-Like Receptors ; Tumor Necrosis Factor-alpha ; XAF1 protein, mouse
Language	English
Publishing date	2020-04-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2020.03.062
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Article ; Online: Trending Nutrition Controversies #3: Top Controversies in 2021.

Aggarwal, Monica / Freeman, Andrew M / Ros, Emilio / Allen, Kathleen / Sikand, Geeta / Aspry, Karen / Kris-Etherton, Penny / Devries, Stephen / Reddy, Koushik / Singh, Tamanna / Litwin, Sheldon E / O'Keefe, James / Miller, Michael / Andrus, Bruce / Blankstein, Ron / Batiste, Columbus / Belardo, Danielle / Wenger, Christopher / Batts, Travis /

Barnard, Neal D / White, Beth A / Ornish, Dean / Williams, Kim A / Ostfeld, Robert J

The American journal of medicine

2021 Volume 135, Issue 2, Page(s) 146–156

Abstract: Each year, patients are bombarded with diverging and even contradictory reports concerning the impact of certain additives, foods, and nutrients on cardiovascular health and its risk factors. Accordingly, this third review of nutrition controversies ... ...

Abstract	Each year, patients are bombarded with diverging and even contradictory reports concerning the impact of certain additives, foods, and nutrients on cardiovascular health and its risk factors. Accordingly, this third review of nutrition controversies examines the impact of artificial sweeteners, cacao, soy, plant-based meats, nitrates, and meats from grass compared to grain-fed animals on cardiovascular and other health outcomes with the goal of optimizing clinician-led diet counseling.
MeSH term(s)	Cardiovascular Physiological Phenomena/drug effects ; Diet/standards ; Food Analysis ; Humans ; Nutritional Physiological Phenomena ; Nutritional Sciences
Language	English
Publishing date	2021-09-09
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	80015-6
ISSN	1555-7162 ; 1873-2178 ; 0002-9343 ; 1548-2766
ISSN (online)	1555-7162 ; 1873-2178
ISSN	0002-9343 ; 1548-2766
DOI	10.1016/j.amjmed.2021.07.046
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Article: Influenza B virus reverse genetic backbones with improved growth properties in the EB66® cell line as basis for vaccine seed virus generation

White, Kris M / Ayllon, Juan / García-Sastre, Adolfo / Krammer, Florian / Mena, Ignacio / Potenski, Anna

Vaccine. 2018 Feb. 21, v. 36, no. 9

2018

Abstract: Vaccination remains the best available prophylaxis to prevent influenza virus infections, yet current inadequacies in influenza virus vaccine manufacturing often lead to vaccine shortages at times when the vaccine is most needed, as it was the case ... ...

Abstract	Vaccination remains the best available prophylaxis to prevent influenza virus infections, yet current inadequacies in influenza virus vaccine manufacturing often lead to vaccine shortages at times when the vaccine is most needed, as it was the case during the last influenza virus pandemic. Novel influenza virus vaccine production systems will be crucial to improve public health and safety. Here we report the optimization of influenza B virus growth in the proprietary EB66® cell line, currently in use for human vaccine production. To this end, we collected, curated and sequenced 71 influenza B viruses selected for high diversity in date of isolation and lineage. This viral collection was tested for ability to enter and replicate within EB66® cells in a single cycle assay and appears to readily infect these cells. When the collection was tested for viral progeny production in a multi-cycle assay, we found a large variation from strain to strain. The strains with the top growth characteristics from the B/Victoria and B/Yamagata lineages were selected for vaccine backbone generation using a reverse genetics system. We then showed that these backbones maintain their desirable growth within EB66® cells when the HA and NA from poorly growing strains were substituted for the parental segments, indicating that the selected backbones are viable options for vaccine production in EB66®. Finally, we show that compounds previously reported to enhance influenza virus growth in cell culture also increase virus production in the EB66® cell line.
Keywords	cell culture ; cell lines ; disease control ; humans ; Influenza B virus ; influenza vaccines ; manufacturing ; pandemic ; production technology ; progeny ; public health ; reverse genetics ; vaccination ; viral growth ; viruses
Language	English
Dates of publication	2018-0221
Size	p. 1146-1153.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2018.01.050
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Article ; Online: Influenza B virus reverse genetic backbones with improved growth properties in the EB66® cell line as basis for vaccine seed virus generation.

White, Kris M / Ayllon, Juan / Mena, Ignacio / Potenski, Anna / Krammer, Florian / García-Sastre, Adolfo

Vaccine

2018 Volume 36, Issue 9, Page(s) 1146–1153

Abstract	Vaccination remains the best available prophylaxis to prevent influenza virus infections, yet current inadequacies in influenza virus vaccine manufacturing often lead to vaccine shortages at times when the vaccine is most needed, as it was the case during the last influenza virus pandemic. Novel influenza virus vaccine production systems will be crucial to improve public health and safety. Here we report the optimization of influenza B virus growth in the proprietary EB66® cell line, currently in use for human vaccine production. To this end, we collected, curated and sequenced 71 influenza B viruses selected for high diversity in date of isolation and lineage. This viral collection was tested for ability to enter and replicate within EB66® cells in a single cycle assay and appears to readily infect these cells. When the collection was tested for viral progeny production in a multi-cycle assay, we found a large variation from strain to strain. The strains with the top growth characteristics from the B/Victoria and B/Yamagata lineages were selected for vaccine backbone generation using a reverse genetics system. We then showed that these backbones maintain their desirable growth within EB66® cells when the HA and NA from poorly growing strains were substituted for the parental segments, indicating that the selected backbones are viable options for vaccine production in EB66®. Finally, we show that compounds previously reported to enhance influenza virus growth in cell culture also increase virus production in the EB66® cell line.
MeSH term(s)	Animals ; Cell Line ; Ducks ; Hemagglutination, Viral ; Influenza B virus/genetics ; Influenza B virus/growth & development ; Influenza Vaccines ; Reverse Genetics
Chemical Substances	Influenza Vaccines
Language	English
Publishing date	2018-02-01
Publishing country	Netherlands
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2018.01.050
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Article ; Online: Hepatitis C virus drugs that inhibit SARS-CoV-2 papain-like protease synergize with remdesivir to suppress viral replication in cell culture.

Bafna, Khushboo / White, Kris / Harish, Balasubramanian / Rosales, Romel / Ramelot, Theresa A / Acton, Thomas B / Moreno, Elena / Kehrer, Thomas / Miorin, Lisa / Royer, Catherine A / García-Sastre, Adolfo / Krug, Robert M / Montelione, Gaetano T

Cell reports

2021 Volume 35, Issue 7, Page(s) 109133

Abstract: ... similarity of the substrate binding clefts of SARS-CoV-2 main protease (M ...

Abstract	Effective control of COVID-19 requires antivirals directed against SARS-CoV-2. We assessed 10 hepatitis C virus (HCV) protease-inhibitor drugs as potential SARS-CoV-2 antivirals. There is a striking structural similarity of the substrate binding clefts of SARS-CoV-2 main protease (M
MeSH term(s)	Adenosine Monophosphate/analogs & derivatives ; Adenosine Monophosphate/pharmacology ; Alanine/analogs & derivatives ; Alanine/pharmacology ; Antiviral Agents/pharmacology ; COVID-19/virology ; Cell Culture Techniques ; Cell Line ; Coronavirus Papain-Like Proteases/antagonists & inhibitors ; Coronavirus Papain-Like Proteases/metabolism ; Drug Repositioning/methods ; Drug Synergism ; Hepacivirus/drug effects ; Hepatitis C/drug therapy ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protease Inhibitors/pharmacology ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; Virus Replication/drug effects ; COVID-19 Drug Treatment
Chemical Substances	Antiviral Agents ; Protease Inhibitors ; remdesivir (3QKI37EEHE) ; Adenosine Monophosphate (415SHH325A) ; Coronavirus Papain-Like Proteases (EC 3.4.22.2) ; papain-like protease, SARS-CoV-2 (EC 3.4.22.2) ; Alanine (OF5P57N2ZX)
Language	English
Publishing date	2021-04-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2021.109133
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