30 - herpes i

Question 1

what is herpes and what are the two types

Answer 1

• family of viruses that causes chronic recurrent infections
• HSV-1
  
  • mouth and nose infections
• HSV-2
  
  • genital infection
  • Other sub-types less prevalent

Question 2

where does herpes reside

Answer 2

Herpees resides in neurons

When the virus is latent its just sitting there, but every so often something will stimulate it into become active again

Question 3

describe HSV-1 including the symptoms, % of many people are infected, what triggers it, and what type of infection it is

Answer 3

• Cold sores and fever blisters on the mouth and nose, sometimes eye
• More than 80% of population is infected
  
  • acquired at a young age and you carry it throughout the rest of your life
• Only 10 to 20% experience outbreaks
  
  • every so often the virus will leave the nerve cells and go to other ares in your body
• Virus escapes eradication by latency inside neurons
  
  • Inaccessible to immune system
    
    • how it persists throughout your lifetime
  • Stress, sunlight, immune suppression trigger outbreaks
  • Virus travels down axions of nerve cells to epithelial cells
• Lytic infection
  
  • Only in epithelial cells, does not damage neurons

Question 4

describe HSV-1 in terms of its viral activity, the damage, what causes the damage, and drug administration

Answer 4

• Lytic infection
  
  • Viral activity is short (less than 24 hours)
    
    • last about a week
    • the immune system is primed to get rid of it quickly
  • Viral damage is minimal
  • Most damage is caused by the immune system
    
    • Over-stimulated and destroys most of the tissue
    • immune system damage causes the damage
    • Drug must be administered quickly
      
      • need to shut down viral activity within the first few hours of the outbreak (when you feel a tingly sensation)

Question 5

describe HSV-2 in terms of its viral activity, the damage, what causes the damage, and drug administration

Answer 5

• Sores and fever blisters on the anus and genitals
• Infects 15 to 20% of population
• Infection is much more virulent than HSV-1
  
  • Painful
  • only 1 or 2 outbreaks per year
• Usually one outbreak per year
• Most common type of STD
• Viral activity is short
  
  • Viral damage is minimal
• Most damage by immune system
  
  • Drug must be administered quickly
  • if you have a prescription you have to administer it fast

Question 6

what is being seen recently with respect to HSV-1 and HSV-2 and the regions they are being found in

Answer 6

recently, you see HSV-1 in the lower regions, it it no longer just confined to the upper region
and, you see HSV-2 in the upper regions, it it no longer just confined to the bottom region

Question 7

describe the herpes virus structure

Answer 7

• Genetic information is double stranded DNA
• Very complex virus
  
  • More than 70 genes
  • Most viruses have less than 10
  • Virus has it’s own polymerase
    
    • DRUG TARGET
    • polymerase is an enzyme used to copy nucleic acid

Question 8

describe the components of nucleic acid

Answer 8

• polymerases assemble the components of nucleic acids together to make DNA or RNA
• Nucleosides (no phosphate)
  
  • base - N containing heterocycles
• Sugar (2-deoxyribose in DNA or ribose in RNA)
  
  • RNA has an extra OH
• sugar and the nucleosides stay the same, what differs is the base
• Base – nitrogen containing aromatic heterocycle
  
  • Heterocycles are ring structures incorporating heteroatoms

Question 9

what are the four different bases and what makes them recognizable to other molecules

Answer 9

• Four different bases (ATCG)
  
  • RNA is AUCG
• Each base is “recognized” by other molecules because of its shape and hydrogen bonding pattern
• Enables binding of only certain structures to each base

Question 10

describe the structure of nucleic acid including what the units are called and what the backbone is composed of

Answer 10

• Polymers formed by connecting nucleosides together using phosphate esters
• The individual units are now called nucleotides (phosphate containing)
• Forms a long strand
  
  • units are linked one after another
• Backbone of sugars and phosphates
• One base per sugar

Question 11

how does nucleic acid encode information and what is the information stored as

Answer 11

• Nucleic acid encodes information in its structure
  
  • structure is read out by molecules
• Info is stored as the sequence of bases

Question 12

what are the positives of double strands for nucleic acids

Answer 12

• Stabilize the molecules
  
  • double strands reinforce each other and stabilize the structure
  • Long term info storage (DNA)
• Second strand provides an easy way to replicate or read information
• Error checking
  
  • second strand acts as a proof reading system

Question 13

describe the process of polymerase copying nucleic acids

Answer 13

• Use one strand as a template to make another strand
• Nucleotides are added one at a time, matching each added base against its compliment on the other strand
  
  • once it makes sure that the nucleotides match up, it then connects them together
  • polymerase starts from the primer and moves from the 3’ to the 5’ of the template strand
  • as the polymerases add bases, they are being added to the 3’ end that is being synthesized
  • 3’ OH and 5’ OH
    
    • 3’ OH is used as a nucleophile to add the next piece to the growing strand

Question 14

describe how polymerase creates a new strand of DNA

Answer 14

• Uses the 3’-OH as a nucleophile
• check the base and choose its complementary base, put that into place and does a chemical reaction
• 3’ OH on the template acts as a nucleophile and donates electrons to the electrophile (phosphorus of the phosphate group on the complementary base) and leaving group (two phosphate groups on the complementary base) leaves
• gives you a brand new base in the sequence, joined together with the phosphate = brand new 3’ OH that you can use to add the next piece

Question 15

how does polymerase add bases

Answer 15

one at a time. after each bases is added, a new 3’ OH nucleophile is available for next addition

Question 16

how does rational drug design relate to the viral replication of nucleic acid

Answer 16

• Use knowledge of enzyme mechanism and substrate(s) to design a drug
• we know the mechanism of the reaction and the structure of the substrate in detail
• allows us to prevent the viral replication of this nucleic acid

Question 17

what is the selectivity problem with nucleic acids?

Answer 17

• Must block viral enzyme without blocking host enzyme
• nucleotides that the virus uses are the exact same as the human cells
• product of the virus are the exact same as the human cells
• want to prevent the viral polymerase from functioning = no viral protein = no viral infection = virus dies
• do not want the drug to target the host polymerase, only the viral polymerase

Question 18

what will happen if there is poor selectivity

Answer 18

• toxicity

- interference with normal cell function creates problems

Question 19

what is strategy 1 in increasing selectivity of an antiviral

Answer 19

non-natural base

Question 20

explain the process of adding a non-natural base to your antiviral

Answer 20

• you have a patten of H bonds for the base on the template strand, come up with a molecule that has the same patterns of H-bonds in the drug
• if the enzyme is a little bit sloppy, this drug can get incorporated into the growing chain = binds to the letter in the growing chain
• if you are lucky nucleic displacement will occur = adding the base into the growing strand in of the nucleic acid
• results in the growing strand not being readable by the enzyme

Question 21

what is the effect of a non-natural base in your antiviral

Answer 21

• Substrate structure disrupted, polymerase cannot function
• once the drug gets incorporated to the growing strand, the structure is messed up so the polymerase is no longer able to add anything to the growing strand = strand is too short, termination of virus replication
• Nucleic acid not readable by other enzymes
  
  • Spelling mistake
  • if the polymerase is sloppy and continues adding bases, you will end up with a DNA stand that cannot be read by other enzymes = preventing replication of the virus

Question 22

what are the three requirements for a non-natural base

Answer 22

• Drug is a substrate for kinase
  
  • kinase is an enzyme that adds phosphates
    
    • Host
      
      • most common
    • Virus (rare)
• Drug is a substrate for viral polymerase
  
  • Gets incorporated into viral nucleic acid
  • Create an “unreadable” strand
• Drug must NOT be a substrate for host polymerase
  
  • Side effects!

Question 23

describe the selectivity requirements for a non-natural base in a virally infected cell vs a healthy cell

Answer 23

viral cell:
- first step is your drug gets phosphorylated inside a virally infected cell
- once the drug is phosphorylated, it must become a substrate for the viral polymerase
- having the drug be a substrate for the viral polymerase = defective viral nucleic acid = stops viral replication = infected cell death
healthy cell:
- need to make sure the healthy drug stays healthy
- first issue is that the drug can be phosphorylated by the host = pretty likely to get phosphorylated drug bound to healthy cell
- need to make sure it is not a substrate for the host polymerase and that it doesn’t cause problems as it builds up in the cell