Molecular Biology of SARS-CoV-2. Opportunities for Antivirus Drug Development

Preface
Acknowledgments
1 Origin, Evolution, Structure, and Life Cycle of SARS-CoV-2
Origin and Evolution of SARS-CoV-2
Virion Structure, Genome, and Life Cycle of SARS-CoV-2
2 SARS-CoV-2 Attachment and Penetration
Introduction
Spike (S) Protein Structure, Priming by Host Proteases, and Fusion
Glycosylation of S and Cell Entry, Immune Evasion, and Pathogenesis
Phosphorylation as a Potential Regulator of S Expression and Furin Cleavage
ACE2 Receptor as Cellular Receptor for S
ACE2 as Determinant of Host, Tissue, and Cell Ranges
Structural and Functional Features of ACE2
Host Molecules Other Than ACE2 Involved in S-Mediated Entry or Pathogenesis
The Lysosomal Transmembrane Protein TMEM106B
Kringle Containing Transmembrane Protein 1 and Asialoglycoprotein Receptor-1
Heparan Sulfate Proteoglycans and Sialic Acid–Containing Glycolipids
Integrins α5β3 and α5β1
CD147/Basigin2/EMMPRIN
Membrane-Type MMPs
C-Lectin Type, Toll-Like, and Mannose Receptors
Neuropilin-1/VEGF165R
Nonimmune Receptor Glucose-Regulated Protein 78 (GRP78)
CD209L/L-SIGN and CD209/DC-SIGN
Estrogen Receptor Alpha
Anti-S Neutralizing Antibodies Can Replace ACE2 for Viral Entry
Tyrosine Protein Kinase Receptor AXL as Low-Affinity Receptor for S
Host Factors Involved in Viral Entry Restriction
Mucins
Changes in Host Cell Membrane
Leucine-Rich Repeat–Containing Protein 15 (LRRC15)
3 Translation of SARS-CoV-2 Early Proteins
Role of the 5′-Untranslated Region in Initial Translation of Genomic Viral RNA
Translation of ORF1a and ORF1b and −1 Programmed Ribosomal Frameshift
Posttranslational Processing of Early ORF1a and ORF1b Viral Polyproteins
NSP5 (Main Protease [Mpro], 3CLpro)
NSP3 (Papain-Like Protease [PLpro])
4 SARS-CoV-2 Biosynthesis
Compartmentalization of Viral Replication to Shield Viral Molecules
Nucleocapsid Protein: Phase Separation Into Membraneless Organelles
NSPs 3/4/6: Generation of Double-Membrane Vesicles and Convoluted Membranes
Viral Genome Replication and Transcription
The 5′-Untranslated Region
The 3′-Untranslated Region
Long-Range RNA-RNA Interactions
Synthesis of Viral Genomic and Subgenomic RNAs
Replication-Transcription Complex
NSP8
NSP12
TRS-Dependent Template Switching
TRS-Independent Template Switching
Intragenomic Rearrangements Possibly Secondary to Template Switching
m7G 5′-Capping and 3′-Polyadenylation of Viral RNAs
NSP12 and NSP9
NSP14
NSP16 and NSP10
SARS-CoV-2 RNA Translation: Switching by NSP1 from Host to Viral Translation
5 SARS-CoV-2 Assembly and Release
Nucleocapsid (N)
ORF9b as a Viral Assembly Protein Generated by Leaky Ribosome Scanning
Envelope (E) and ORF3a Viroporins
Envelope (E)
ORF3a
Membrane (M) Protein
Endosomal Release of the Virus
6 SARS-CoV-2 Transmission and COVID-19 Susceptibility and Severity
7 Evasion of Innate Host Defenses by SARS-CoV-2 and Its Pathogenic Correlates
The Interferon Response in Innate Immunity
Modulation of Interferon Response in Immune Evasion and Pathogenesis by SARS-CoV-1, MERS-CoV, and HIV-1
Modulation of Interferon Response and Other Host Defenses in Immune Evasion and Pathogenesis by SARS-CoV-2
SARS-CoV-2 Proteins in Immune Evasion and Pathogenesis
Accessory Proteins (Open Reading Frames 3a, 3b, 6, 7a, 7b, 8, 9b, 9c, 10)
ORF3a
ORF3b
ORF6
ORF7a
ORF7b
ORF8
ORF9b
ORF9c
ORF10
Nonstructural Proteins (NSPs 1, 2, 3, 4, 5, 6, 9, 10/14/16, 12, 13, and 15)
NSP1
NSP2
NSP3 (PLpro)
NSP4
NSP5 (Mpro, 3CLpro)
NSP6
NSP9
NSP10, NSP14, and NSP16
NSP12
NSP13
NSP15
Structural Proteins (Nucleocapsid, Membrane, Envelope, Spike)
Nucleocapsid (N)
Membrane (M)
Envelope (E)
Spike (S)
SARS-CoV-2 Micrornas and Immune Evasion and Pathogenesis
Concluding Remarks
8 SARS-CoV-2 Variation and Its Effects on Virulence and Pathogenicity
9 Potential Treatments for SARS-CoV-2 Beyond Current and Related New-Generation Antivirals and Monoclonal Antibodies
Nucleic Acid–Based Therapeutics
XNAzymes
CRISPR-Cas13d
Ribonuclease Targeting Chimeras
Locked Nucleic Acid–Containing ASOs
Small Interfering RNAs
Host Circular RNAs
Repurposed Drugs
The Antineoplastic Obatoclax
The Antihelminthic and Molluscicide Niclosamide
The Antihypertensive Carvedilol and the Antineoplastic Toremifene
The Antidepressant Fluoxetine
Ursodeoxycholic Acid and z-Guggulsterone
The Antibiotics Ceftaroline and Ceftriaxone
The Phosphorylation Inhibitors Alectinib and Berzosertib
The Hippo Pathway Inhibitor Verteporfin
The Antineoplastic Selinexor
The Metformin Derivative Supformin to Reduce Inflammation
New Pharmacotherapies Excluding New Generations of Approved Ones
Quinolizidine Aloperine Derivative Compound 5
Serine Protease Inhibitor Nafamostat
The KCB261770 Antibacterial
4E2RCat and the Potential Chemotherapy Adjunct Silmitasertib
The Glycogen Synthase Kinase-3 Inhibitor T-1686568
The Viral Entry Inhibitor Picolinic Acid
The Broad-Spectrum Antiviral Protein Griffithsin
Peptidomimetic Oligomers Targeting Membrane Phosphatidylserine
α1-Adrenergic Receptor Antagonists
Androgen Receptor Antagonists
Other Potential Therapeutic Approaches
ACE2-Fc Decoys
Soluble ACE2, ADAM17 Inhibition, and Angiotensin I Enhancement
Monoclonal Antibodies Against ACE2
Nuclear ACE2 Inhibitor
Methyltransferase Phosphorylated CTD-Interacting Factor (PCIF)1 as the Target
Replication-Transcription Complex–Specific T Cells as Vaccine Targets
Inactivation of RNA Helicase NSP13
NSP16-Defective SARS-CoVs or NSP16-Interacting Domain of NSP10
OAS-RNase L Pathway Activation and Complement System Attenuation
NLRP3 Inflammasome Inhibitors
Potential Viral Exit Inhibitors
Bivalent Monoclonal Antibodies Against Viral Spike
Tetravalent Bispecific Nanobody-Based Immunoglobulins Against Viral Spike
Multi-specific, Multi-affinity Antibody Platform Targeting Viral Spike
Viral Entry Inhibitors Based on the Ankyrin Repeat Fold
Non-neutralizing Antibodies Against Spike
Monoclonal Antibodies Targeting SARS-CoV-2 Proteins Other Than Spike
Mesenchymal Stem Cells With Macropore-Deficient Mitochondria
Concluding Remarks
10 Long COVID
Long COVID in the Context of Post-Acute Infection Syndromes
Definition
Prevalence
Risk Factors
Pathogenesis
Persistence of SARS-CoV-2
Reactivation of Viruses
Immune Activation/Dysregulation
Autoimmunity
Microvascular Dysfunction
Dysregulation of the Microbiota-Gut-Brain Axis
Pathophysiology
Systemic
Cardiovascular
Neurologic
Respiratory
Endocrine
Hepatic
Health-Related Quality of Life, Health Care Costs, and Disability
Treatment
Concluding Remarks
Coda
Index

Offering a thorough, accessible overview of the basic science and clinical data regarding the virus that causes COVID-19, Molecular Biology of SARS-CoV-2 is an excellent resource for researchers, clinical scientists, physicians, and students. This volume offers in-depth, extended content that originated with Drs. Roberto Patarca’s and William A. Haseltine’s chapter in The COVID-19 Textbook, edited by Dr. Haseltine and Dr. Patarca. The greatly expanded material in this text provides a much-needed primer in this complex area. 

• Reviews the basic science, clinical data and various perspectives on how SARS-CoV-2 infects cells, replicates, manipulates cellular machinery, evades host defenses, and is transmitted to other hosts
• Covers the origin and structure of SARS-CoV-2, followed by chapters based on the life cycle of the virus
• Provides a thorough review of what is known for each molecular component of the viral life cycle while incorporating information on pertinent prevention and therapeutic interventions 

Roberto Patarca, MD, PhD
 
Dr. Patarca is the Chief Medical Officer at ACCESS Health International and a former pharmaceutical and medical device company executive and faculty at Harvard Medical School and the University of Miami. His research has focused on the AIDS virus, microbial replication regulation, adoptive cellular immunotherapy, drug resistance testing, cardiovascular interventions, and chronic fatigue syndrome.
 
He served on Advisory Committees to two U.S. Secretaries of Health and Human Services, was elected to the Academy of Sciences of Latin America; worked with the World Health Organization on standardization of cytokine level measurements, and has been published widely.

William A. Haseltine, PhD
 
In Dr. Haseltine’s career at the forefront of medical research and application, he has educated a generation of doctors at Harvard Medical School, designed the strategy to develop the first treatment for HIV/AIDS, is well-known for his groundbreaking work on cancer, and led the team that pioneered the development of new drugs based on information from the human genome.
 
He is the author of more than two hundred peer-reviewed manuscripts and fifteen books. As Chair and CEO of ACCESS Health International, Dr. Haseltine is dedicated to ensuring that advances in medical technology translate to improved health outcomes worldwide.