Medicinal Chemistry of Coronavirus Infections - I

Pál Perjési, PhD University of Pécs Institute of Pharmaceutical Chemistry May 05, 2020 The Coronavirus pandemic (May 5, 2020) https://coronavirus.jhu.edu/map.html The Coronavirus pandemic https://www.worldometers.info/coronavirus/?utm_campaign=h omeAdvegas1? The structure of the viruses

• Viruses are the smallest parasites, typically ranging from 0.02 to 0.4 micrometer, although several very large viruses up to 1 micrometer long (megavirus, pandoravirus) have recently been discovered. • Viruses depend completely on cells (bacterial, plant, or animal) to reproduce. • Viruses (virions) have an outer cover of protein (capsid) and sometimes lipid (envelope), an RNA or DNA core, and sometimes enzymes needed for the first steps of viral replication. The size of the viruses

SIB Swiss Institute of Bioinformatics (www.sib.swiss) Classification of Viruses

RNA Viruses DNA viruses • Contain an RNA genome. • Contain an DNA genome • Virus replication: • Virus replication: • RNA-dependent RNA polymerase • DNA-depndent DNA • Reverse transcriptase (Retroviruses) polymerase • Examples: • Examples: • Rubella virus • Herpes Virus • Dengue fever virus • Hepatitis B virus • Hepatitis A virus • Epstein-Barr virus • Hepatitis C virus • HIV • Influenza virus • Coronavirus Classification of Viruses The Baltimore Scheme

https://open.oregonstate.education/generalmicrobiology/chapter/the-viruses/ Replication of the double stranded DNA viruses – Replication of the genom DNA base pairing:

Key enzymes involved:

1. Helicase https://open.oregonstate.education/generalmicrobiology/ch 2. DNA dependent DNA polymerase apter/the-viruses/

Double-stranded DNA viruses usually must enter the host nucleus before they are able to replicate. Some of these viruses require host cell polymerases to replicate their genome, while others, such as adenoviruses or herpes viruses, encode their own replication factors. Most prominently, DNA-dependent DNA-polymerase synthesizes the new strands by adding nucleotides that complement each (template) strand. Polyomaviruses, adenoviruses, and herpesviruses are all nuclear-replicating DNA viruses. Replication of the double stranded DNA viruses - Transcription DNA-RNA base pairing:

Transcription is the first step in gene expression.It involves copying a gene's DNA sequence to make an RNA molecule. https://open.oregonstate.education/generalmicrobiology/ chapter/the-viruses// Transcription is performed by enzymes called DNA-dependent RNA polymerases, which link nucleotides to form an RNA strand (using a DNA strand as a template). In viruses and bacteria, the RNA transcripts act as messenger RNAs (mRNAs) right away. Replication of the dsRNA viruses

• Double-stranded RNA viruses, such as the rotavirus, cause diarrheal illness in humans.

• Cells have systems to destroy any dsRNA found in the cell. Thus the viral genome, in its dsRNA form, must be hidden or protected from the cell enzymes.

• Cells lack RNA-dependent RNA-polymerases, necessary for replication of the viral genome so the virus must have this enzyme itself. The viral RNA-dependent RNA polymerase acts as both a transcriptase to transcribe mRNA, as well as a replicase to replicate the RNA genome. Replication of the (+) sense ssRNA viruses

• Viruses with plus-strand RNA, such as coronaviruses (CoVs), can use their genome directly as mRNA with translation by the host ribosome occurring as soon as the unsegmented viral genome gains entry into the cell. • One of the viral genes expressed yields an RNA-dependent RNA-polymerase (or RNA replicase), which creates minus- strand RNA from the plus-strand genome.

• The minus-strand RNA can be used as a template for more plus-strand RNA, which can be used as mRNA or as genomes for the newly forming viruses. Negative-sense single-stranded RNA viruses ((-)ssRNA viruses)

• Negative sense ssRNA viruses, such as the Ebola virus and the influenza virus, need an RNA dependent RNA polymerase (RNA replicase) within its capside to form a positive sense RNA. • The positive-sense RNA acts as a viral mRNA, which is translated into proteins for the production of new virion materials. • When viral genomes are needed the plus-strand RNAs are used as templates to make minus-strand RNA. Replication of the (+) sense ssRNA viruses – Retroviruses -I

• Despite the fact that the retroviral genome is composed of +ssRNA, it is not used as mRNA. • Instead, the virus uses its RNA dependent DNA polymerase (reverse transcriptase) to synthesize a piece of ssDNA complementary to the viral genome.

• Because RNA transcription does not involve the same error-checking mechanisms as DNA transcription, RNA viruses, particularly retroviruses, are particularly prone to mutation. Replication of the (+) sense ssRNA viruses – Retroviruses-II

• Lastly, the reverse transcriptase is used as a DNA polymerase to make a complementary copy to the ssDNA, yielding a dsDNA molecule. • This allows the virus to insert its genome, in a dsDNA form, into the host chromosome, forming a provirus.

• A provirus can remain latent indefinitely or cause the expression of viral genes, leading to the production of new viruses. Excision of the provirus does not occur for gene expression. (e.g. HIV; human T-lymphotropic virus type 1 and 2 (HTLV-1 and HTLV-2)) Coronaviridae

• Coronaviruses are involved in human and vertebrate's diseases. Coronaviruses are members of the subfamily Orthocoronavirinae in the family Coronaviridae and the order Nidovirales

The particles are typically decorated with large (appr. 20 nm), club- or petal-shaped surface projections (the "peplomers" or "spikes"), which in electron micrographs of spherical particles create an image reminiscent of the solar corona. Taxonomy of Coronaviridae (according to the International Committee on Taxonomy of Viruses)

https://www.mdpi.com/2076-0817/9/3/186/htm Origin of evolution of human-pathogen Coronaviruses

2002

2012

2019

SARS: Severe Acute Respiratory Syndrome MARS: Middle East Respiratory Syndrome https://www.mdpi.com/2076-0817/9/3/186/htm COVID-19 (SARS-CoV-2)

• COVID-19 is a spherical or pleomorphic enveloped particles containing single-stranded (positive-sense) RNA associated with a nucleoprotein (N) within a capsid comprised of matrix protein. The envelope bears club-shaped glycoprotein (S) projections. Some coronaviruses also contain a hem agglutinin- esterase protein (HE)4. https://doi.org/10.1016/j.jmii.2020.03.022 REPLICATION OF COVID19

1. Attachment of the virus to receptors on the host cell surface; 2. Entry of the virus through the host cell membrane; 3. Uncoating of viral nucleic acid; 4. Replication Synthesis of early regulatory proteins, eg, nucleic acid polymerases; Synthesis of new viral RNA or DNA; Synthesis of late, structural proteins 5. Assembly (maturation) of viral particles; 6. Release from the cell Potential anti-viral therapeutics used in patients with SARS and MERS infections The role of replication process in pathogenicity • SARS-CoV-2 (COVID-19) binds to ACE2 (the angiotensin- converting enzyme 2) by its S (Spike) protein and allows COVID-19 to enter and infect cells. • In order to attach the virus receptor (spike protein) to its cellular ligand (ACE2), activation by the serine protease TMPRSS2 is needed.

https://doi.org/10.1016/j.jmii.2020.03.022 Inhibition of TMPRSS2 by Camostat Mesylate (NI-03) Thank you for your attention!