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Article ; Online: SARS-CoV and SARS-CoV-2 main protease residue interaction networks change when bound to inhibitor N3.

Griffin, Jeddidiah W D

2020 Volume 211, Issue 3, Page(s) 107575

Abstract: COVID-19 is a respiratory disease caused by the coronavirus SARS-CoV-2. SARS-CoV-2 has many similarities with SARS-CoV. Both viruses rely on a protease called the main protease, or ... ...

Abstract	COVID-19 is a respiratory disease caused by the coronavirus SARS-CoV-2. SARS-CoV-2 has many similarities with SARS-CoV. Both viruses rely on a protease called the main protease, or M
MeSH term(s)	Antiviral Agents/pharmacology ; Betacoronavirus/enzymology ; COVID-19 ; Catalytic Domain ; Cluster Analysis ; Coronavirus 3C Proteases ; Coronavirus Infections/drug therapy ; Cysteine Endopeptidases ; Drug Design ; Enzyme Inhibitors/pharmacology ; Humans ; Pandemics ; Pneumonia, Viral/drug therapy ; Polyproteins ; Protein Binding ; SARS Virus/enzymology ; SARS-CoV-2 ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Proteins/antagonists & inhibitors
Chemical Substances	Antiviral Agents ; Enzyme Inhibitors ; ORF1ab polyprotein, SARS-CoV-2 ; Polyproteins ; Viral Nonstructural Proteins ; Viral Proteins ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Keywords	covid19
Language	English
Publishing date	2020-07-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2020.107575
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Article ; Online: SARS-CoV and SARS-CoV-2 main protease residue interaction networks change when bound to inhibitor N3

Griffin, Jeddidiah W.D.

Journal of Structural Biology

2020 Volume 211, Issue 3, Page(s) 107575

Keywords	Structural Biology ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2020.107575
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: SARS-CoV and SARS-CoV-2 main protease residue interaction networks change when bound to inhibitor N3

Griffin, Jeddidiah W D

J Struct Biol

Abstract: COVID-19 is a respiratory disease caused by the coronavirus SARS-CoV-2. SARS-CoV-2 has many similarities with SARS-CoV. Both viruses rely on a protease called the main protease, or Mpro, for replication. Therefore, inhibiting Mpro may be a successful ... ...

Abstract	COVID-19 is a respiratory disease caused by the coronavirus SARS-CoV-2. SARS-CoV-2 has many similarities with SARS-CoV. Both viruses rely on a protease called the main protease, or Mpro, for replication. Therefore, inhibiting Mpro may be a successful strategy for treating COVID-19. Structures of the main proteases of SARS-CoV and SARS-CoV-2 with and without inhibitor N3 are available in the Protein Data Bank. Comparing these structures revealed residue interaction network changes associated with N3 inhibition. Comparing network clustering with and without inhibitor N3 identified the formation of a cluster of residues 17, 18, 30-33, 70, 95, 98, 103, 117, 122, and 177 as a network change in both viral proteases when bound to inhibitor N3. Betweenness and stress centrality differences as well as differences in bond energies and relative B-factors when comparing free Mpro to inhibitor-bound Mpro identified residues 131, 175, 182, and 185 as possibly conformationally relevant when bound to the inhibitor N3. Taken together, these results provide insight into conformational changes of betacoronavirus Mpros when bound to an inhibitor.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #640251
Database	COVID19

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Article ; Online: Residue Interaction Network Analysis Predicts a Val24-Ile31 Interaction May be Involved in Preventing Amyloid-Beta (1-42) Primary Nucleation.

Griffin, Jeddidiah W D / Bradshaw, Patrick C

The protein journal

2021 Volume 40, Issue 2, Page(s) 175–183

Abstract: Alzheimer's disease (AD) patients could benefit from a more effective treatment than the current FDA-approved options. Because amyloid-beta (Aβ) is thought to play a central role in AD pathogenesis, many experimental drugs attempt to reduce Aβ-induced ... ...

Abstract	Alzheimer's disease (AD) patients could benefit from a more effective treatment than the current FDA-approved options. Because amyloid-beta (Aβ) is thought to play a central role in AD pathogenesis, many experimental drugs attempt to reduce Aβ-induced pathology. Preventing amyloid accumulation may be a more effective strategy than clearing Aβ plaques after they form. If preventing Aβ accumulation can treat or prevent AD, then understanding Aβ primary nucleation may aid rational drug design. This study examines Aβ residue interaction networks and reports network and structural observations that may provide insight into primary nucleation. While many studies identify structural features of Aβ that promote aggregation, this study reports features that may resist primary nucleation by examining Aβ42 studies in more and less polar solvents. In Aβ42 in a less polar solvent (PDB ID: 1IYT), Val24 and Ile31 have higher betweenness and residue centrality values. This may be due to a predicted interaction between Val24 and Ile31. Residues in the central hydrophobic cluster (CHC) of Aβ40 and Aβ42 had significantly higher betweenness values compared to the average betweenness of the structures, highlighting the CHC's reported role in oligomerization. The predicted interaction between Val24 and Ile31 may reduce the likelihood of primary nucleation of Aβ.
MeSH term(s)	Alzheimer Disease ; Amyloid beta-Peptides/chemistry ; Amyloid beta-Peptides/metabolism ; Databases, Protein ; Humans ; Hydrophobic and Hydrophilic Interactions ; Isoleucine/chemistry ; Isoleucine/metabolism ; Models, Molecular ; Peptide Fragments/chemistry ; Peptide Fragments/metabolism ; Protein Aggregation, Pathological/metabolism ; Protein Stability ; Valine/chemistry ; Valine/metabolism
Chemical Substances	Amyloid beta-Peptides ; Peptide Fragments ; amyloid beta-protein (1-42) ; Isoleucine (04Y7590D77) ; Valine (HG18B9YRS7)
Language	English
Publishing date	2021-02-10
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-021-09965-w
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Article ; Online: Effects of a high protein diet and liver disease in an in silico model of human ammonia metabolism

Jeddidiah W. D. Griffin / Patrick C. Bradshaw

Theoretical Biology and Medical Modelling, Vol 16, Iss 1, Pp 1-

2019 Volume 14

Abstract: Abstract Background After proteolysis, the majority of released amino acids from dietary protein are transported to the liver for gluconeogenesis or to peripheral tissues where they are used for protein synthesis and eventually catabolized, producing ... ...

Abstract	Abstract Background After proteolysis, the majority of released amino acids from dietary protein are transported to the liver for gluconeogenesis or to peripheral tissues where they are used for protein synthesis and eventually catabolized, producing ammonia as a byproduct. High ammonia levels in the brain are a major contributor to the decreased neural function that occurs in several pathological conditions such as hepatic encephalopathy when liver urea cycle function is compromised. Therefore, it is important to gain a deeper understanding of human ammonia metabolism. The objective of this study was to predict changes in blood ammonia levels resulting from alterations in dietary protein intake, from liver disease, or from partial loss of urea cycle function. Methods A simple mathematical model was created using MATLAB SimBiology and data from published studies. Simulations were performed and results analyzed to determine steady state changes in ammonia levels resulting from varying dietary protein intake and varying liver enzyme activity levels to simulate liver disease. As a toxicity reference, viability was measured in SH-SY5Y neuroblastoma cells following differentiation and ammonium chloride treatment. Results Results from control simulations yielded steady state blood ammonia levels within normal physiological limits. Increasing dietary protein intake by 72% resulted in a 59% increase in blood ammonia levels. Simulations of liver cirrhosis increased blood ammonia levels by 41 to 130% depending upon the level of dietary protein intake. Simulations of heterozygous individuals carrying a loss of function allele of the urea cycle carbamoyl phosphate synthetase I (CPS1) gene resulted in more than a tripling of blood ammonia levels (from roughly 18 to 60 μM depending on dietary protein intake). The viability of differentiated SH-SY5Y cells was decreased by 14% by the addition of a slightly higher amount of ammonium chloride (90 μM). Conclusions Data from the model suggest decreasing protein consumption may be one simple strategy to decrease blood ammonia levels and minimize the risk of developing hepatic encephalopathy for many liver disease patients. In addition, the model suggests subjects who are known carriers of disease-causing CPS1 alleles may benefit from monitoring blood ammonia levels and limiting the level of protein intake if ammonia levels are high.
Keywords	Ammonia ; Hepatic encephalopathy ; Liver cirrhosis ; Carbamoyl phosphate synthetase 1 ; Nitrogen ; Urea cycle ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effects of a high protein diet and liver disease in an in silico model of human ammonia metabolism.

Griffin, Jeddidiah W D / Bradshaw, Patrick C

Theoretical biology & medical modelling

2019 Volume 16, Issue 1, Page(s) 11

Abstract: Background: After proteolysis, the majority of released amino acids from dietary protein are transported to the liver for gluconeogenesis or to peripheral tissues where they are used for protein synthesis and eventually catabolized, producing ammonia as ...

Abstract	Background: After proteolysis, the majority of released amino acids from dietary protein are transported to the liver for gluconeogenesis or to peripheral tissues where they are used for protein synthesis and eventually catabolized, producing ammonia as a byproduct. High ammonia levels in the brain are a major contributor to the decreased neural function that occurs in several pathological conditions such as hepatic encephalopathy when liver urea cycle function is compromised. Therefore, it is important to gain a deeper understanding of human ammonia metabolism. The objective of this study was to predict changes in blood ammonia levels resulting from alterations in dietary protein intake, from liver disease, or from partial loss of urea cycle function. Methods: A simple mathematical model was created using MATLAB SimBiology and data from published studies. Simulations were performed and results analyzed to determine steady state changes in ammonia levels resulting from varying dietary protein intake and varying liver enzyme activity levels to simulate liver disease. As a toxicity reference, viability was measured in SH-SY5Y neuroblastoma cells following differentiation and ammonium chloride treatment. Results: Results from control simulations yielded steady state blood ammonia levels within normal physiological limits. Increasing dietary protein intake by 72% resulted in a 59% increase in blood ammonia levels. Simulations of liver cirrhosis increased blood ammonia levels by 41 to 130% depending upon the level of dietary protein intake. Simulations of heterozygous individuals carrying a loss of function allele of the urea cycle carbamoyl phosphate synthetase I (CPS1) gene resulted in more than a tripling of blood ammonia levels (from roughly 18 to 60 μM depending on dietary protein intake). The viability of differentiated SH-SY5Y cells was decreased by 14% by the addition of a slightly higher amount of ammonium chloride (90 μM). Conclusions: Data from the model suggest decreasing protein consumption may be one simple strategy to decrease blood ammonia levels and minimize the risk of developing hepatic encephalopathy for many liver disease patients. In addition, the model suggests subjects who are known carriers of disease-causing CPS1 alleles may benefit from monitoring blood ammonia levels and limiting the level of protein intake if ammonia levels are high.
MeSH term(s)	Ammonia/blood ; Ammonia/metabolism ; Ammonium Chloride/pharmacology ; Carbamoyl-Phosphate Synthase (Ammonia)/metabolism ; Cell Differentiation/drug effects ; Cell Line, Tumor ; Cell Survival/drug effects ; Computer Simulation ; Diet, High-Protein/adverse effects ; Humans ; Kinetics ; Liver/metabolism ; Liver Diseases/blood ; Liver Diseases/etiology ; Liver Diseases/metabolism ; Male ; Models, Biological ; Nitrogen/metabolism ; Tretinoin/pharmacology ; Urea/metabolism
Chemical Substances	Ammonium Chloride (01Q9PC255D) ; Tretinoin (5688UTC01R) ; Ammonia (7664-41-7) ; Urea (8W8T17847W) ; Carbamoyl-Phosphate Synthase (Ammonia) (EC 6.3.4.16) ; Nitrogen (N762921K75)
Language	English
Publishing date	2019-07-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2156462-0
ISSN	1742-4682 ; 1742-4682
ISSN (online)	1742-4682
ISSN	1742-4682
DOI	10.1186/s12976-019-0109-1
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Article ; Online: In silico prediction of novel residues involved in amyloid primary nucleation of human I56T and D67H lysozyme.

Griffin, Jeddidiah W D / Bradshaw, Patrick C

BMC structural biology

2018 Volume 18, Issue 1, Page(s) 9

Abstract: Background: Amyloidogenic proteins are most often associated with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, but there are more than two dozen human proteins known to form amyloid fibrils ... ...

Abstract	Background: Amyloidogenic proteins are most often associated with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, but there are more than two dozen human proteins known to form amyloid fibrils associated with disease. Lysozyme is an antimicrobial protein that is used as a general model to study amyloid fibril formation. Studies aimed at elucidating the process of amyloid formation of lysozyme tend to focus on partial unfolding of the native state due to the relative instability of mutant amyloidogenic variants. While this is well supported, the data presented here suggest the native structure of the variants may also play a role in primary nucleation. Results: Three-dimensional structural analysis identified lysozyme residues 21, 62, 104, and 122 as displaced in both amyloidogenic variants compared to wild type lysozyme. Residue interaction network (RIN) analysis found greater clustering of residues 112-117 in amyloidogenic variants of lysozyme compared to wild type. An analysis of the most energetically favored predicted dimers and trimers provided further evidence for a role for residues 21, 62, 104, 122, and 112-117 in amyloid formation. Conclusions: This study used lysozyme as a model to demonstrate the utility of combining 3D structural analysis with RIN analysis for studying the general process of amyloidogenesis. Results indicated that binding of two or more amyloidogenic lysozyme mutants may be involved in amyloid nucleation by placing key residues (21, 62, 104, 122, and 112-117) in proximity before partial unfolding occurs. Identifying residues in the native state that may be involved in amyloid formation could provide novel drug targets to prevent a range of amyloidoses.
MeSH term(s)	Computer Simulation ; Humans ; Models, Molecular ; Muramidase/chemistry ; Muramidase/genetics ; Mutation ; Protein Conformation ; Protein Folding
Chemical Substances	Muramidase (EC 3.2.1.17)
Language	English
Publishing date	2018-07-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2050440-8
ISSN	1472-6807 ; 1472-6807
ISSN (online)	1472-6807
ISSN	1472-6807
DOI	10.1186/s12900-018-0088-1
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Article ; Online: Amino Acid Catabolism in Alzheimer's Disease Brain: Friend or Foe?

Griffin, Jeddidiah W D / Bradshaw, Patrick C

Oxidative medicine and cellular longevity

2017 Volume 2017, Page(s) 5472792

Abstract: There is a dire need to discover new targets for Alzheimer's disease (AD) drug development. Decreased neuronal glucose metabolism that occurs in AD brain could play a central role in disease progression. Little is known about the compensatory neuronal ... ...

Abstract	There is a dire need to discover new targets for Alzheimer's disease (AD) drug development. Decreased neuronal glucose metabolism that occurs in AD brain could play a central role in disease progression. Little is known about the compensatory neuronal changes that occur to attempt to maintain energy homeostasis. In this review using the PubMed literature database, we summarize evidence that amino acid oxidation can temporarily compensate for the decreased glucose metabolism, but eventually altered amino acid and amino acid catabolite levels likely lead to toxicities contributing to AD progression. Because amino acids are involved in so many cellular metabolic and signaling pathways, the effects of altered amino acid metabolism in AD brain are far-reaching. Possible pathological results from changes in the levels of several important amino acids are discussed. Urea cycle function may be induced in endothelial cells of AD patient brains, possibly to remove excess ammonia produced from increased amino acid catabolism. Studying AD from a metabolic perspective provides new insights into AD pathogenesis and may lead to the discovery of dietary metabolite supplements that can partially compensate for alterations of enzymatic function to delay AD or alleviate some of the suffering caused by the disease.
MeSH term(s)	Alzheimer Disease/metabolism ; Amino Acids/metabolism ; Animals ; Brain/metabolism ; Homeostasis/physiology ; Humans ; Metabolism ; Neurons/metabolism
Chemical Substances	Amino Acids
Language	English
Publishing date	2017
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1942-0994
ISSN (online)	1942-0994
DOI	10.1155/2017/5472792
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Article ; Online: In Silico Preliminary Association of Ammonia Metabolism Genes GLS, CPS1, and GLUL with Risk of Alzheimer's Disease, Major Depressive Disorder, and Type 2 Diabetes.

Griffin, Jeddidiah W D / Liu, Ying / Bradshaw, Patrick C / Wang, Kesheng

Journal of molecular neuroscience : MN

2018 Volume 64, Issue 3, Page(s) 385–396

Abstract: Ammonia is a toxic by-product of protein catabolism and is involved in changes in glutamate metabolism. Therefore, ammonia metabolism genes may link a range of diseases involving glutamate signaling such as Alzheimer's disease (AD), major depressive ... ...

Abstract	Ammonia is a toxic by-product of protein catabolism and is involved in changes in glutamate metabolism. Therefore, ammonia metabolism genes may link a range of diseases involving glutamate signaling such as Alzheimer's disease (AD), major depressive disorder (MDD), and type 2 diabetes (T2D). We analyzed data from a National Institute on Aging study with a family-based design to determine if 45 single nucleotide polymorphisms (SNPs) in glutaminase (GLS), carbamoyl phosphate synthetase 1 (CPS1), or glutamate-ammonia ligase (GLUL) genes were associated with AD, MDD, or T2D using PLINK software. HAPLOVIEW software was used to calculate linkage disequilibrium measures for the SNPs. Next, we analyzed the associated variations for potential effects on transcriptional control sites to identify possible functional effects of the SNPs. Of the SNPs that passed the quality control tests, four SNPs in the GLS gene were significantly associated with AD, two SNPs in the GLS gene were associated with T2D, and one SNP in the GLUL gene and three SNPs in the CPS1 gene were associated with MDD before Bonferroni correction. The in silico bioinformatic analysis suggested probable functional roles for six associated SNPs. Glutamate signaling pathways have been implicated in all these diseases, and other studies have detected similar brain pathologies such as cortical thinning in AD, MDD, and T2D. Taken together, these data potentially link GLS with AD, GLS with T2D, and CPS1 and GLUL with MDD and stimulate the generation of testable hypotheses that may help explain the molecular basis of pathologies shared by these disorders.
MeSH term(s)	Alzheimer Disease/genetics ; Ammonia/metabolism ; Carbamoyl-Phosphate Synthase (Ammonia)/genetics ; Depressive Disorder, Major/genetics ; Diabetes Mellitus, Type 2/genetics ; Glutamate-Ammonia Ligase/genetics ; Glutaminase/genetics ; Humans ; Polymorphism, Single Nucleotide
Chemical Substances	Ammonia (7664-41-7) ; Glutaminase (EC 3.5.1.2) ; Glutamate-Ammonia Ligase (EC 6.3.1.2) ; Carbamoyl-Phosphate Synthase (Ammonia) (EC 6.3.4.16)
Language	English
Publishing date	2018-02-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	1043392-2
ISSN	1559-1166 ; 0895-8696
ISSN (online)	1559-1166
ISSN	0895-8696
DOI	10.1007/s12031-018-1035-0
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Zs.A 3006: Show issues

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Article ; Online: Hepatitis C virus-induced myeloid-derived suppressor cells regulate T-cell differentiation and function via the signal transducer and activator of transcription 3 pathway.

Ren, Jun P / Zhao, Juan / Dai, Jun / Griffin, Jeddidiah W D / Wang, Ling / Wu, Xiao Y / Morrison, Zheng D / Li, Guang Y / El Gazzar, Mohamed / Ning, Shun B / Moorman, Jonathan P / Yao, Zhi Q

Immunology

2016 Volume 148, Issue 4, Page(s) 377–386

Abstract: T cells play a pivotal role in controlling viral infection; however, the precise mechanisms responsible for regulating T-cell differentiation and function during infections are incompletely understood. In this study, we demonstrated an expansion of ... ...

Abstract	T cells play a pivotal role in controlling viral infection; however, the precise mechanisms responsible for regulating T-cell differentiation and function during infections are incompletely understood. In this study, we demonstrated an expansion of myeloid-derived suppressor cells (MDSCs), in particular the monocytic MDSCs (M-MDSCs; CD14(+) CD33(+) CD11b(+) HLA-DR(-/low) ), in patients with chronic hepatitis C virus (HCV) infection. Notably, HCV-induced M-MDSCs express high levels of phosphorylated signal transducer and activator of transcription 3 (pSTAT3) and interleukin-10 (IL-10) compared with healthy subjects. Blocking STAT3 signalling reduced HCV-mediated M-MDSC expansion and decreased IL-10 expression. Importantly, we observed a significant increase in the numbers of CD4(+) CD25(+) Foxp3(+) regulatory T (Treg) cells following incubation of healthy peripheral blood mononuclear cells (PBMCs) with MDSCs derived from HCV-infected patients or treated with HCV core protein. In addition, depletion of MDSCs from PBMCs led to a significant reduction of Foxp3(+) Treg cells developed during chronic HCV infection. Moreover, depletion of MDSCs from PBMCs significantly increased interferon-γ production by CD4(+) T effector (Teff) cells derived from HCV patients. These results suggest that HCV-induced MDSCs promote Treg cell development and inhibit Teff cell function, suggesting a novel mechanism for T-cell regulation and a new strategy for immunotherapy against human viral diseases.
MeSH term(s)	Cell Proliferation ; Cells, Cultured ; Chronic Disease ; Forkhead Transcription Factors/metabolism ; Hepacivirus/immunology ; Hepatitis C/immunology ; Hepatitis C Antigens/immunology ; Humans ; Interferon-gamma/metabolism ; Interleukin-10/metabolism ; Interleukin-2 Receptor alpha Subunit/metabolism ; Myeloid-Derived Suppressor Cells/physiology ; Myeloid-Derived Suppressor Cells/virology ; STAT3 Transcription Factor/metabolism ; T-Lymphocytes, Helper-Inducer/immunology ; T-Lymphocytes, Helper-Inducer/virology ; T-Lymphocytes, Regulatory/immunology ; T-Lymphocytes, Regulatory/virology ; Viral Core Proteins/immunology
Chemical Substances	FOXP3 protein, human ; Forkhead Transcription Factors ; Hepatitis C Antigens ; IL10 protein, human ; Interleukin-2 Receptor alpha Subunit ; STAT3 Transcription Factor ; STAT3 protein, human ; Viral Core Proteins ; Interleukin-10 (130068-27-8) ; Interferon-gamma (82115-62-6)
Language	English
Publishing date	2016
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80124-0
ISSN	1365-2567 ; 0019-2805 ; 0953-4954
ISSN (online)	1365-2567
ISSN	0019-2805 ; 0953-4954
DOI	10.1111/imm.12616
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