antiviral (Dr. Cochrane) Flashcards
1
Q
What is CC50?
A
Drug concentration at which reduces cell viability by 50%
2
Q
How to find selectivity (SI) or therapeutic index (TI)?
A
CC50/IC50
3
Q
What does a high TI/SI indicate?
A
drug is more selective to the virus targeted
4
Q
what is drug clearance affected by?
A
i) metabolism in liver
ii) excretion through kidney/gut
5
Q
Factors to consider when developing antivirals
A
i) toxicity of drug (try to minimize)
ii) efficacy of drug (better if done in low conc)
iii) drug delivery (how is the drug delivered to site of infection)
iv) drug clearance
v) how quick does drug resistance occur in virus?
6
Q
Ways to deliver drug to targeted site
A
i) gut
ii) IV, inhalation, topical
iii) directly to site of infection (reduce toxicity while maximize drug efficacy)
7
Q
What happens after pattern recognition receptors are activated?
A
signaling induced through IRF3/7 or NFkB
–> express interferons + proinflammatory cytokines
8
Q
Pattern recongition receptors found on cell surface
A
TLR2,4,6
9
Q
Pattern recongition receptors found on endosome
A
TLR3,7,8,9
10
Q
Pattern recongition receptors found in cytoplasm
A
RIG-1, cGAS
11
Q
What does TLR2,4 detect?
A
viral coat proteins
12
Q
What does TLR7,8 detect?
A
ssRNA
13
Q
What does TLR3, MDA5, RIG-1 detect
A
dsRNA
14
Q
What does cGAS detect?
A
DNA
15
Q
What does TRL9 detect?
A
hypomethylated CpG DNA
16
Q
what PRR detects dsRNA?
A
TLR3, MDA5, RIG-1
17
Q
what PRR detects DNA?
A
cGAS
18
Q
what PRR detect viral coat proteins?
A
TLR2,4
19
Q
What PRR detect hypomethylated CpG DNA?
A
TLR9
20
Q
What PRR detect ssRNA?
A
TLR7,8
21
Q
What happens after interferon interacts with its receptor?
A
signalling –> increase interferon-stimulated genes (ISG) expression
–> increase the cells’ ability to repsond and block virus replication
22
Q
Types of interferon present
A
i) type I
ii) type II
iii)type III
23
Q
examples of type 1 interferon
A
interferon alpha, beta
24
Q
examples of type II interferon
A
interferon gamma
25
examples of type III interferon
interferon pheta
26
where are type I interferons found?
all nucleated cells
27
Where are type II interferons made?
T helper cells, NK cells, CD8 killer cells after they are activated
28
Examples where immune system leads to serious clinical outcomes
immune system hyperactivated (too much cytokines)
--> systemic inflammatory response syndrome (SIRS) or ARDS in Covid
--> multi-organ failure, systemic damage
29
Where is interferon treatment applied to?
hepatitus B, C with interferon alpha
--> more than 24 weeks
30
possible side effects of interferon treatment
have significant side effect reducing quality of life
31
Alternative approach to using interferon
activate innate immune system with TLR7/8 agonist (Imiquimod)
--> treat warts (HPV)
32
drugs that inhibit viral entry
i)Miraviroc
ii)T20
iii)Sunitinib (inhibits AAK1, GAK)
iv) lenacapavir (HIV-1, by binding to capsid)
33
How does Miraviroc work?
binds to CCR5 coreceptor --> compete with HIV-1 Gp120
34
How does T20 work?
mimic one of helical bundles
--> prevent six helical bundle from forming
35
Drugs that inhibit endosome release
i) chloroquine
ii) amantidine
36
How does chloroquine work?
prevent acidification of endosome needed for many virus
--> absorb protons to prevent pH change
37
How does amantidine work?
bind to M2 ion channel on influenza A virus
--> block ion flow
38
Why amantidine no longer recommmended for treatment?
lots of resistant virus formed
39
Drugs that inhibit viral genome replication
acyclovir
40
How does acyclovir work?
recognize and phosphorylate thymidine kinase of herpes virus
41
What viruses do acyclovir work on?
herpes virus
42
Herpes inhibitors present
i) Acyclovir (phosphorylate thymidine kinase)
ii) other chain terminators (e.g. famciclovir and other drugs with -vir)
iii)Foscarnet
43
How does Foscarnet work?
block PPi binding site in polymerase
--> prevent PPi being cleaved from deoxynucleotide triphosphate
44
Concentration of foscarnet needed to inhibit viral polymerase
100 fold lower than cellular DNA polymerase is inhibited
45
How do drugs inhibit viral reverse transcription in HIV-1?
i) these drugs lack 3'OH in ribose
--> cannot add next base
ii) induce conformational change by binding to other sites on RT
--> affect polymerization site
46
Why are inhibitors for viral reverse transcription able to incorporate in DNA?
lack 3' to 5' exonuclease in reverse transcriptase
47
other infections where HIV-1 NRTi inhibitors are used on
HBV (lamuvidine, tenofovir)
48
How does tenofovir work?
also facilitate chain termination even tho it has 3'OH
49
How does non-nucleoside reverse transcriptase inhibitors (NNRTi) work?
bind to other site
--> induce conformational change in RT that changes polymerase active site
50
Drugs that inhibits integration of HIV-1
i) dolutegravir
ii) cabotegravir
51
why does dolutegravir have high barrier to drug resistance?
i) long plasma half-life
ii) slow dissociation rate
52
what's special abt cabotegravir?
long half life
--> can be formulated as nanoparticle injection
53
drugs that inhibit HIV-1 capsid interaction
lenacapavir
54
How does lenacapavir work?
bind to HIV capsid in a pocket between capsid protein in hexamers
55
Effect of using lenacapvir in HIV-1 life cycle
i) Viral entry -- by interacting with sites that help traffick viral core to nucleus
--> virus stay in cytoplasm
ii) Viral core assembly
--> interfere with capsid-capsid interaction of Gag
--> prevent viral particle assembly + release
56
How does inhibitors to HIV-1 protease work
bind to catalytic site of HIV-1 protease
--> mimic transition state of substrate during rxn
57
Describe HIV-1 treatment evolution
i) first used AZT, not effective after couple of months
ii) combine multiple drugs to lower the chance of virus obtaining resistance on all of the drugs
58
Standard therapy for HCV?
interferon + ribavirin
59
newer treatment for HCV
combination of drugs that target different virus coded proteins (NS3 protease, replicase)
60
What does the newer treatment for HCV target
NS3 protease, NS5A&B replicase
61
What is targeted within SARS-Cov2?
i) viral protease
ii) viral replicase
62
how does viral protease affected by drug?
prevent processing of viral polyprotein precursors needed for viral replication
63
Drugs that target viral protease of SARS-Cov2
Paxlovid
--> nirmatrelvir + rotonavir
64
Strategies used to target viral replicase of SARS Cov-2
i) stalling by replacing ATP with RTP -- elongation barrier after three nt added -- RdRp stalling
ii)induce hypermutation (increase rate of forming defective viral genome)
65
Drugs used to target viral replicase of SARS-Cov2
remdesivir --> stalling
molnupiravir, favipiravir
--> hypermutation
66
How does molnupiravir and favipiravir work?
induce hypermutation (increase rate of forming defective viral genome)
67
How does remdesivir work?
stalling by replacing ATP with RTP -- elongation barrier after three nt added -- RdRp stalling
68
How is viral release inhibited by drugs?
i)target neuraminidase by mimicking its substrate
--> unable to cleave sialic acid
--> cannot leave the cell and infect others
ii) lenacapavir by binding to capsid that prevent virus assembly and release
iii) Nilotinib --> prevent assembly plus release of Ebola
69
Function of viral neuraminidase
cleaves terminal sialic acid from surface glycoprotein
--> prevent re-infection + allow virus to leave and infect others
70
When can inhibitors for neuraminidase be used?
i) 36 to 48 hrs after onset of illness
ii) can be used before or after exposure of influenza A and B (prevent disease)
71
Alternate approaches to drug development
i) re-purpose FDA approved drugs
ii) develop compounds that prevent virus to use cellular processes
72
Examples of drugs being re-purposed
i) Lamuvidine --> HIV-1, HBV
ii) Cyclosporine A
iii) Nilotinib
73
What virus can ribavarin be used in?
HCV, RSV
74
What are the proposed mechanisms for ribavirin?
i) Inhibit inosine monophosphate dehydrogenase (IMPDH)
--> reduce GTP available
ii) modulate immune function thru T helper type 1
iii) inhibit RNA 5' capping --> recognized by immune system
iv) inhibit viral RNA polymerase
v) increase mutation frequency
75
the effect of inhibiting RNA 5' capping to virus
less stable RNA, get recognized by immune system
75
Original function of cyclosporin A
as a calcineurin inhibitor that act on T cells
--> immunosuppressive drug to block t cell proliferation
76
What does cyclosporin A act on
cycophilin A --> proline cis0trans isomerase
77
Which viruses do cyclosporin A act on?
HCV, HIV
78
How does cyclosporin A act on HCV?
dissociate cyclophilin A from replicase
--> stop replication
79
How does cyclosporin A act on HIV?
destabilize capsid
--> stop nuclear import of viral genome, block viral infection
80
Where is cyclophilin A found in HCV?
part of replicase complex
81
Where is cyclophilin A found in HIV?
binds to incoming viral capsid
--> stabilize it to allow import into nucleus
82
Drug that target viral glycoprotein maturation
castanospermine
83
How does castanospermine work?
inhibits ER alpha-glucosidase I
--> stop removal of terminal glucose on N-linked glycans
--> disrupt folding of viral proteins
84
What does castanospermine act on
ER alpha-glucosidase I
85
Which virus does castanospermine act on?
Dengue virus (all 4 serotypes)
--> no effect on yellow fever, west nile virus
86
Original purpose of nilotinib
cancer drug through inhibiting ABL of BCR-ABL involved in modulating cell signalling
87
What is nilotinib re-purposed to?
Ebola virus --> reduce production of viral particles
88
How does nilotinib help to stop virual growth?
ABL phosphorylation needed on VP40 of Ebola
--> bind to ABL portion will stop viral particles from leaving
89
What are the targets for drugs that inhibit membrane trafficking
AAK1, GAK
90
How does inhibitors of AAK1 and GAK have an effect on virus?
affect virus entry and release
--> affect intracellular trafficking of viral particle
91
What does AAK1 and GAK help virus?
acts as kinase regulators for AP1 and 2
--> essential for HCV infection
92
Which viruses do inhibitors on AAk1 and GAK work?
HCV, West nile, Zika, dengue, ebola
93
What happens if inhibitors for membrane trafficking are added post-infeciton?
no effect on viral RNA replication
94
A host mechanism where durgs can use to manipualte
RNA splicing
95
Viruses that uses alternative RNA splicing
HIV-1, adenovirus, influenza, papilloma, herpes
96
Drugs tested to alter RNA processing
digoxin
97
Original purpose of digoxin
inhibit Na+/K+ ATPase
--> more Ca2+ accumulate
==> stronger contractions
98
Why is digoixn not a viable treatment
limited therapeutic index
--> need high dosages for it to work
99
Which virusesis digoxin effective on?
HIV, adenovirus, SARS-Cov2
100
Strategies to prepare for future pandemic
i) vaccine
ii) virus-directed antiviral
iii) host-directed antivirals
101
Advantage of using host-directed antivirals
i) resistance not as worried as interaction with host is crucial
ii) broad-spectrum
102
Problems of using vaccine
short shelf-life may limit ability to store vaccines
103
How to develop host-directed antivirals
i) generate population of cells with CRISPR with one gene disrupted in each cell
ii) infect cells with virus --> virus kill susceptible cells
iii) harvest surviving cells, isolate DNA
--> identify the killssgRNA sequence
iv) identify antiviral properties of known inhibitors of identified proteins
104
Issue of using virus-directed antiviral
specificty of antivirals might limit effectiveness of treatment
--> use combination of drugs to slow down buildup of resistance
