Antivirals

Lecture 20
Biology 3310/4310
Virology
Spring 2017

You can’t go back and you can’t stand

still. If the thunder don’t get you, then the
lightning will.
JERRY GARCIA
The Wheel (lyrics by Robert Hunter)
 Vaccines can prevent viral disease

• But they have modest or no therapeutic effect if an individual is

already infected (exception?)
• Our second arm of antiviral defense is antivirals
• Can stop infection once it has started
Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University
 Despite 50 years of research,
our arsenal of antiviral drugs remains dangerously small

Only about 100 antiviral drugs are available on the US market

Most against HIV, HCV, herpesviruses - Persistent infections

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Why are there so few antiviral drugs?

• Compounds interfering with virus growth can adversely affect the host cell
- Side effects are common (unacceptable)

- Every step in viral life cycle engages host functions

• Some medically important viruses can’t be propagated, have no animal model,

or are dangerous
- HBV, HPV

- Smallpox

- Ebola, Lassa

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 An unappreciated third reason may be the most important

• A compound must block virus replication completely! It must be

potent
• Many standard pharmaceuticals can be effective if enzyme activity is
partially blocked
• Partial inhibition is not acceptable for an antiviral drug - resistant
mutants will arise
• Makes drug discovery expensive

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Another serious problem for antiviral discovery:

Many acute infections are of short duration

• By the time the patient feels ill, it is too late to impact clinical disease
• Antiviral drugs for these viruses must be given early in infection or prophylactically to
populations at risk
- Safety issues; giving drugs to healthy people not wise (exception: PrEP)
• No broad-spectrum antiviral agents are currently available
• Lack of rapid diagnostic reagents has hampered development of antiviral drugs

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 LJ1001, a broad spectrum antiviral

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University http://www.ncbi.nlm.nih.gov/pubmed/20133606

 LJ1001, a broad spectrum antiviral

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Antiviral history

• The first modest search for antiviral drugs occurred in the early 1950s
- Chemists looked at derivatives of the sulfonamide antibiotics

- Synthesis of thiosemicarbazones active against poxviruses

- Smallpox was still a major threat after WWII

• 1960s and 1970s: “blind screening” programs to find chemicals with antiviral
activity
- Spurred on by successes in the treatment of bacterial infections with antibiotics

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Blind screening

• No attempt to focus discovery on a virus or a virus-specific mechanism

• Random chemicals and natural product mixtures tested for ability to block replication
of a variety of viruses in cell culture systems

• Hits, compounds or mixtures that block in vitro viral replication; purified and fractions
tested in various cell culture and animal models for safety and efficacy

• Promising molecules called leads were modified systematically by medicinal chemists

- To reduce toxicity, increase solubility and bioavailability

- To improve other pharmacokinetic properties

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Thousands of molecules were made and screened before a
specific antiviral was even tested in humans

• Considerable effort, very little success

• One exception: Symmetrel (amantadine)
- Approved late 1960s for treatment of influenza A virus infections

- One of three drugs now available for influenza

• Mechanism of action was often unknown or speculative

- Mechanism of action of Symmetrel deduced early 1990s

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Antiviral discovery today

• Recombinant DNA technology & sophisticated chemistry make targeted discovery

possible
• Essential viral genes cloned, expressed in genetically tractable organisms, purified,
analyzed in atomic detail
• Life cycles of most viruses known, targets for intervention can be generalized
• Modern technology allows inhibitors to be found even for viruses that cannot be
propagated in cell culture
• Blind screening procedures are dead

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 The path of drug discovery

•Will the compound get to the right place in the body at

the right concentration? (bioavailability)
Proof of principle •Will the compound persist in the body long enough to be
effective? (pharmacokinetics)
•Will the compound be safe? (toxicity and specificity)
Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Significant hurdles stand in the way of finding effective
antiviral drugs

It is not unusual for the cost to bring an antiviral drug to market to exceed $100-200 million dollars!
Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 From drug discovery to the clinic

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Mechanism-based screens

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Cell-based screen

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Antiviral screening

• High-throughput: 10,000 compounds/day

• Chemical libraries
• Natural products
• Combinatorial chemistry
• Structure-based design
• In silico screening

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 High throughput screening

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

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room number: virus

We have many antibiotics, but fewer antivirals. What is a reason for the
difference?

A. Robotic screening is slow

B. There are few serious viral infections
C. Resistance is a problem
D. Antivirals must be potent
E. All of the above

1
 Resistance to antiviral drugs

• Resistance to any antiviral drug must be anticipated

- Viruses replicate efficiently

- Modest to high mutation frequencies

• Special concern during extended therapy for chronic infections (HIV, HBV, HCV)
• Viral mutants resistant to every antiviral drug in arsenal have been detected
• Disconcerting because antiviral arsenal is small

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Dangers of drug resistance

• Patient cannot be treated with same drug

• If no other drug is available, infection cannot be stopped
• Genetic analysis of resistance provides insight into antiviral mechanism
• May reveal new strategies to reduce or circumvent problem

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Mechanisms of drug resistance

• RNA viruses: error prone RNA polymerase, no correction mechanism

• One misincorporation in 104 - 105 nucleotides polymerized (106
greater than host DNA genome)
• In RNA viral genome of 10 kb, this frequency leads to one mutation in
1-10 genomes

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Mechanisms of drug resistance

• DNA viruses: most DNA polymerases can excise and replace

misincorporated nucleotides
• DNA viruses evolve more slowly than RNA viruses because they have
less diversity

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Acyclovir, a highly effective,
anti-herpes simplex virus drug
A prodrug; a nucleoside analog

Many antiviral compounds are nucleoside and nucleotide analogs

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Acyclovir mechanism of action

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Improving acyclovir
• Valacyclovir (valatrex), an L-valyl ester derivative of acyclovir, has markedly
improved bioavailability
• Ester is taken up after oral administration, acyclovir is released when the ester is
cleaved by cellular enzymes

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Acyclovir-resistant HSV

• Arise spontaneously during virus replication

• Some mutants cannot phosphorylate the pro-drug
- Mutations are in viral thymidine kinase gene

• Some mutants cannot incorporate phosphorylated drug into DNA

- Mutations are in viral DNA polymerase gene

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Acyclovir-resistant HSV

• TK mutants can be devastating in AIDS patients

- May cause disseminated disease
- Often resistant to other nucleoside analogs that require viral TK (cross-
resistance)
- Treat with Foscarnet, DNA polymerase inhibitor (side effects)

• DNA polymerase mutants may also be resistant to Foscarnet: no

treatment options left

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Symmetrel (Amantadine)

• Interacts with influenza viral M2 protein (ion channel)

• Blocks entry of protons into virion, prevents uncoating

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
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Resistance to which antiviral would involve amino acid changes in a viral enzyme?

A. Acyclovir
B. Amantadine
C. LJ001
D. Penicillin
E. All of the above

2
 Influenza virus NA inhibitors

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

Principles of Virology, ASM Press
 Influenza virus NA inhibitors

Zanamivir Oseltamivir
(Relenza) (Tamiflu)

• Designed to mimic natural ligand, sialic acid

• Closer inhibitor to natural compound, less likely target can change to
avoid binding drug while maintaining viable function

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 How inhibitors of NA (Tamiflu, Relenza) work

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Circulating H1N1 and H3N2 viruses are largely resistant to Adamantanes,
not recommended for use
http://www.cdc.gov/flu/weekly/index.htm
Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University
 WIN compounds

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Inhibitors of picornavirus uncoating

Pharmac. Ther.
Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University
29:287, 1985
 New HCV drugs

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 HCV new drug pipeline

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University http://www.hcvdrugs.com/ Principles of Virology, ASM Press
 Targets for intervention: HIV replication

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 The problem with AIDS therapy:
relentless viral replication for years

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Azido-deoxythymidine (AZT) - first HIV drug

• Initially discovered during screens for anti-tumor cell compounds

• Phosphorylated to active form by cellular kinases
• Chain terminator
• Not good substrate for most cellular polymerases, better for HIV RT

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 AZT

• Substantial side effects (unlike acyclovir)

• Can be given orally, is absorbed rapidly, but half-life is ~1 hr (degraded
by liver enzymes)
• Consequently patients dosed 2-3x daily
• Short half-life, multiple dose regimen problematic: resistant mutants
will be selected

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Resistance to AZT

• Mutants resistant to AZT arose immediately after drug was licensed

• Single aa changes at one of four sites in RT
• Altered RT do not bind phosphorylated AZT
• New nucleoside analogs developed: Didanosine (ddI), Zalcitabine (ddC),
Stavudine (d4T), Lamivudine (3TC)
• This lead to combination therapy, use of two antiviral drugs to combat
resistance
• Mutants resistant to two drugs arose <1 yr

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Non-nucleoside RT inhibitors (NNRTI)

nevirapine (Viramune) delavirdine efavirenz

11-cyclopropyl-4-methyl-5,11-dihydro-6H- dipyrido[3,2-b:2′,3′-e][1,4]diazepin-6-one
Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Resistance to NNRTIs

• Resistant mutants are selected rapidly

• Amino acid substitutions in any of seven residues that line binding
sites on enzyme confer resistance
• Cannot be used alone for treatment of AIDS
• Now used largely in combination therapy

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Antiviral drugs that target HIV protease
HIV protease absolutely required for production of infectious virions

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Antiviral drugs that target HIV protease
Key finding: HIV protease recognizes and cleaves small synthetic peptides

Peptidomimetic

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 IN inhibitors

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Maraviroc: CCR5 inhibitor

gp120
Free binding site
wt
gp120
receptor on CCR5

High affinity

Binding site
Disrupted

•
MVC ( ) by MVC

Bound Very low affinity

to CCR5

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Go to:

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Which of the following HIV antivirals inhibits the earliest stage of infection?

A. Nucleoside inhibitors
B. NNRTIs
C. CCR5 inhibitors
D. Integrase inhibitors
E. Fusion inhibitors

3
 Combination therapy

• HAART: HIV can be treated as a chronic disease

• Target different mechanisms
• One pill containing three inhibitors

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Mathematics of drug resistance

• Assume one mutation needed for drug resistance

• Mutation rate 1 every 104 bases polymerized
• Each base is substituted in every 104 viruses
• Each person makes 1010 new viruses/day
• 1010/104 = 106 viruses will be produced each day with resistance to
one drug

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

 Mathematics of drug resistance

• Developing resistance to two drugs: 104 x 104 = 108

• 1010/108 = 100 viruses resistant to two drugs per day
• Resistance to three drugs: 104 x 104 x 104 = 1012 viruses needed
• Remember replication is suppressed by drugs

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Complera (Efavirenz, emtricitabine, rilpivirine) 2011, Stribild (Efavirenz, emtricitabine, cobicistat) 2012
 ART saves
lives

Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University Principles of Virology, ASM Press
 Pre-exposure prophylaxis (PrEP)
ARE YOU
READY FOR
PrEP Access
?
How Can I Start PrEP?
Talk with your doctor or health care provider
to determine if PrEP is right for you

• Daily double therapy (tenofovir and emtricitabine) If you and your health
care provider agree

for those at high risk for HIV infection

that PrEP might
reduce your risk of
getting HIV, he or she Your health care
will test you for HIV provider will
and other sexually also test to see if
transmitted diseases your kidneys are

• Reduces risk of sexual transmission of HIV-1 by

working well

If PrEP is a good option for you, your health

>90% care provider will give you a prescription

How Do I Pay for PrEP?

• Reduces risk of transmission by IVDU by >70% PrEP is covered by most You can also contact
your local health
insurance programs

• No resistance in trials, but real world?

department and
HIV/AIDS service
organizations for
more information
If you do not have
insurance, your health
care provider can direct

• https://www.ncbi.nlm.nih.gov/pubmed/27391094
you to medication
assistance programs that
may help pay for PrEP

Start Talking. Stop HIV.

Follow us online at facebook.com/StartTalkingHIV and @TalkHIV

 There are 1016 HIV genomes on the planet today

With this number of genomes, it is highly probable that HIV genomes exist that are resistant to every one of the antiviral drugs that we have now,
or EVER WILL HAVE!
Virology Lectures 2017 • Prof. Vincent Racaniello • Columbia University