Pharmacogenomics Flashcards
What is a drug?
a medicine or substance which has a physiological effect when ingested or otherwise introduced into the body
What is a drug target?
a protein, cell or organ affected by a specific drug
What are two characteristics of good drugs?
potent and specific
-strong effects on specific biological target (pathway) and minimal effects on all other targets (pathways)
What are three examples of targets?
human
bacteria
virus
What are four examples of drugs?
small molecule
antibodies
vaccines
oligos
What are the steps involved in the pre-clinical part of drug development?
first step: target selection
second step: lead discovery
third step: lead expansion
–>development candidates
What are the steps in drug development?
discovery: target identification, validation and lead discovery
- > 10 to the 4 compounds
preclinical: laboratory and animal testing
-250 lead compounds
phase 1: safety and dosage
-20 to 80 healthy volunteers, 5 drug candidates
phase 2: efficacy and side effects
-100 to 300 patient volunteers
phase 3: adverse reactions
-1000-5000 patients
approval: 1 drug
post-marketing surveillance
What is the success rate of drug development?
1 in 5,000
-4% of drug development processes yield licensed drugs
What is the cost to bring a new drug to market?
> $1.5 billion
What are the reasons for drug development failure?
flawed biological hypothesis
-wrong target chosen
lack of understanding of fundamental molecular mechanisms underlying pathophysiology
lack of efficacy in clinical studies
What are the challenges of drug development?
identify all proteins/genes that can be a potential target
identify all compounds that can be used as drugs
confirmation that a compound inhibits the intended target
identification of undesirable secondary effects
What are solutions to the challenges of drug development?
rational use of drugs in clinical and community settings
identification of novel drug targets
understanding of effects of modulation of targets
-molecular mechanism, protein interactions & networks
What are the approaches to target identification?
data-mining approaches
-identification of proteins that play an important role in disease-associated pathway
genetic/genomic approaches
-identification of genes that cause disorder or increase risk of disorder
-show changes in expression levels in disease states
in vitro approaches
-identification of targets by chemogenomic screening of small-molecule tools
What is data-mining?
looking into the literature to find associations between genes and disease
What is the use of knockout, knock-in, and knock-down?
reduce expression of protein to assess involvement/toxicity
Differentiate between the two types of chemogenomic screens.
forward chemical genetics (FCG)
-start with compound library which is administered to wild type or engineered yeast cells expressing a protein of interest
-hits are selected based on phenotypic readout
-targets identified by treating genetic libraries with the identified hits
reverse chemical genetics (RCG)
-start with selection of a target of interest which is treated with a compound library in vivo
-wild type cells or genetic libraries are treated with the selected hits to identify a phenotype and/or target
What are the two main targets of drugs?
enzyme
GPCR
What is meant by drug target network?
one drug can hit multiple proteins
protein can be hit by multiple drugs
What is meant by disease gene network?
one gene can cause many different diseases
What is druggability?
ability of a protein to be modulated by a drug-like small molecule
What are the desired properties of the protein binding site for binding drugs?
binding site with complimentary properties
-appropriate size to accommodate a drug-like ligand
-buried (increase interaction surface)
What are the methods for assessing drugability?
sequence-based
-predict druggable based on sequence features
structure-based
-protein structures contain drug-like pockets
ligand-based
-high affinity drug-like compounds available
precedence-based
-protein is an established small molecule drug target
increasing confidence in druggability as you go down this list
What is key in the process of structure-based drug design?
identification and characterization of binding sites
-in some cases there may not be information about the binding site, in other cases a putative binding site has been identified by computational or experimental means but druggability is unknown
What might be considered when a site for a given target is known?
finding additional sites whose targeting could produce a desired biological response
True or false: there has been a steady increase in drug development of antimicrobial drugs
false
Why are we not seeing very many new antimicrobial drugs coming to market?
pressure on healthcare to curtail unnecessary use
most are for short courses of therapy
-chronic disease drugs are most cost effective
they are considered life saving (subject to price control)
risk of obsolescence (resistance)
How can we try encourage bringing new antimicrobials to market?
rational use of antimicrobials in community and clinic
development and use of alternative therapies for prevention of bacterial infections and evolution of resistance
new drugs
-identify targets using genome data
-drug repositioning
Pasteur Act
What is the Pasteur Act?
novel financing mechanism to revitalize antibiotic R&D
-fed gov would pay for the value the drug provides to society rather than paying for the volume prescribed
What are the key components of target identification in bacteria?
essential
selective
mutagenesis
What constitutes a good drug that targets bacteria?
injure target organism without affecting the host
How can a drug target the desired organism without affecting the host?
attacking processes that are critical to microbial well-being but dont affect mammals
-bacterial cell wall
-inhibition of enzyme unique to bacteria
-disruption of bacterial protein synthesis
-other: essential, non-human, choke point
What is the K-value paradox? C-value paradox? N-value paradox?
complexity does not correlate with:
-chromosome number (K-value paradox)
-genome size (C-value paradox)
-gene number (N-value paradox)
Which animal is the model of choice for pre-clinical drug discovery?
mice
-similar to human genome
Differentiate pharmacogenetics and pharmacogenomics.
pharmacogenetics:
-study of variability in drug response determined by single gene
pharmacogenomics:
-study of variability in drug response determined by multiple genes within the genome
What is the ultimate goal of pharmacogenetics/genomics?
understand how someone’s genetic make-up determines how well a medicine works in his or her body, as well as what side effects are likely to occur
=right medicine for the right patient
Why does drug response vary?
genetic differences
-SNPs
ethnicity
age
pregnancy
disease
drug interactions
What are SNPs?
single base differences in DNA sequences
-most genetic variations between individuals are due to SNPs
What is the frequency at which SNPs occur?
1 per 300-1000 base pairs
What is warfarin used for?
prevent blood clotting (DVT, PE, stroke prevention)
-interferes with production of vitamin K and other proteins required for blood clotting
-less proteins=ability to clot is reduced
Which drug causes the most emergency deparment visits?
warfarin
What is the role of CYP 2C9 in relation to warfarin?
tells the body to make an enzyme to metabolize warfarin
What occurs to warfarin when the CYP 2C9 gene is changed?
lower the ability to metabolize or clear warfarin from the body
-warfarin overdose due to build up
-people with CYP 2C9 variants need lower doses
What is the role of CYP 4F2?
reduces blood clotting by reducing the amount of vitamin K
What can occur if there is a variant in CYP 4F2?
higher vitamin K levels
-need higher warfarin doses
What is the role of the VKORC1 gene?
holds the instructions for making an enzyme called vitamin K epoxide reductase (VKOR)
-this enzyme helps in recycling vitamin K
What can occur if there is a variant in VKORC1?
reduced vitamin K recycling
-may need lower dose of warfarin
What is the role of CFTR protein?
chloride channel
What occurs when there is a mutation in the CF gene?
reduction/elimination/loss function
-decrease in chloride transport into and out of cells create an imbalance of water movement causing the body to produce thick sticky mucus
What is the correlation between CFTR gene and gentamicin?
translational read through
What occurs with a class I CFTR mutation?
introduces a premature termination codon (stop codon) into the mRNA sequence
-the stop codon should normally be the last instruction in the CFTR gene
What is the mechanism of ataluren?
read through nonsense mutations
-structurally similar but chemically distinct from gentamicin
What is one of the first successful medications produced by genomic medicine?
Kalydeco (ivacaftor)
What occurs with the G551D mutation in the CFTR gene?
channels present but fail to open correctly
What is the triple combination therapy for CF?
Trikafta
-elexacaftor/ivacaftor/tezacaftor + ivacaftor)
What is Trikafta used for?
patients 12 and older with at least one F508 deletion mutation in the CFTR gene
What is an ASO?
single-stranded nucleic acid that hybridizes with the complementary mRNA in a sequence-specific manner
-hybridization of the ASO to the target mRNA can result in specific inhibition of gene expression resulting in reduced levels of translation of the target transcript
What is the terminology for ASOs?
-rsen
What is Duchenne muscular dystrophy?
disease caused by mutations in the dystrophin gene
-characterized by progressive muscle weakness
-one of the largest genes identified (79 exons)
-mutations in DMD due to large deletions and single point mutations
-usually affects males
What is the role of Exondys 51 (eteplirsen)?
exon skipping therapy for DMD patients ammendable to exon 51 skipping
What is SMA?
spinal muscular atrophy
-neurodegenerative disease primarily characterized by loss of spinal motor neurons (SMN) leading to paralysis and premature death
What are the two identical genes that code for SMN?
SMN1 and SMN2
-most of the functional protein from SMN1
-SMN2 lacks exon 7=unstable and less functional proteins
What is Spinraza (nusinersen)?
ASO that targets splicing of SMN2 leading to increased SMN protein levels, capable of improving clinical phenotypes in many patients
What are molecular glues?
molecules that encourage two proteins to come together that normally wouldnt interact
What is targeted therapy?
targeting specific genes or proteins to help stop cancer from growing and spreading
-less side effects than chemotherapy and radiation
-find a molecule present more frequently in cancer cells than in normal cells (difficult as cancer cells evolve from normal cells)
What are the hallmarks of cancer cells?
resisting cell death
inducing angiogenesis
enabling replicative immortality
sustaining proliferative signaling
evading growth suppressors
activating invasion and metastasis
What are the drugs that can be used in targeted therapies for cancer?
small molecule
antibodies
vaccine
ASO
Describe small molecule drugs.
can easily travel across cell membranes
act outside or inside the cell
interact with specific areas of target protein and modify its enzyme activity or its interaction with other molecules
interact with receptors outside the cell to activate pathways inside the cell OR diffuse through the plasma membrane and interact with intracellular receptors
What are the BCR-ABL dependent and independent mechanisms of resistance?
BCR-ABL duplication: oncogene amplification
BCR-ABL mutations
-T315I mutation
-P loop mutations
increase in the expression of P-glycoprotein efflux pump
drug import by OAT 1
alternative signaling pathway activation
What are cancer vaccines typically used for?
treatment not prevention
-enhance immune response against cancer
Differentiate the front end and back end of an antibody.
front end
-binds target
-variable region
back end
-binds other immune cells
-constant region
Can can occur once the cancer cell has been targeted by the antibody?
binding to the antibody can elicit an immune response
-body is killing the cancer cells
drugs (toxins, radio isotopes) can be attached to the antibody and delivered specifically to the cancer cell
-leading to cell death
-radiation also kills neighboring cells
What is HER2?
cell transmembrane surface bound tyrosine kinase normally involved in signal transduction for cell growth and differentiation
What happens when HER2 receptor undergoes homodimerization or heterodimerization?
activation of downstream signaling pathways promoting cell growth, proliferation, and survival
-increase in receptor mediated signalling leads to uncontrolled proliferation
What is Herceptin?
trastuzumab
-MAB that works on extracellular and intracellular domain of HER2 receptors
-also flags for the cells for killing by the immune system
What does pertuzumab do differently than trastuzumab?
inhibits HER2 forming dimer pairs
What is Avastin?
bevacizumab
-binds VGEF
=blocks angiogenesis for cancer therapy
What are the roles of VGEF?
promotes tumor vessel survival
increasing tumor vessel permeability
stimulating new tumor vessel growth
What is the correlation between tumor cells and T cells?
T cells have an innate ability to target tumor cells
-can lead to tumor cell lysis
-requires cell to cell contact
tumor cells can evade destruction by cytotoxic T cells
What are bispecific antibodies?
enhance therapeutic potential of antibodies
bring target cells or tissue (one antigen binding site) in contact with other structures (second antigen binding site)
the second antigen binding site can bind to effector cells via cytotoxicity triggering molecules
as a result, a cytolytic synapse is created between T cell and cancer cell
What is BiTE Antibodies?
bispecific T cell engager to bridge cancer cells to T cells
one domain is designed to target an antigen on the surface of a cancer cell whereas the other is designed to engage CD3 on the surface of a T cell
What is a major role of CYP 2D6?
metabolism of antidepressants, antihypertensives, and chemo
How is codeine activated?
CYP 2D6
How is ticagrelor metabolized?
CYP 3A4/5
How is clopidogrel metabolized?
CYP 2C19
How is prasugrel metabolized?
CYP 3A4 and 2B6
lesser extent: 2C9 and 2C19
What are the emerging hallmarks of cancer?
avoiding immune destruction
tumor-promoting inflammation
genome instability and mutation
deregulating cellular energetics
What are the factors that interfere with successful targeting of drugs to tumor cells?
tumor heterogeneity
antigen shedding
antigen modulation
evading immune response
Describe tumor heterogeneity.
the surface make-up of tumor cells in a tumor is not consistent
-there are many different sub-populations of cells and they express different surface molecules
this heterogeneity means that not all cells in the tumor are of one type and hence will not interact with one, single targeted drug or drug conjugated
How does tumor heterogeneity limit the ability of genomic approaches to capture therapeutically relevant information?
tumor sampling is invasive and sometimes not feasible
may not be contemporaneous to the clinically significant disease process
may derive from an uninformative part of the tumor deposit
some technologies may not be sensitive to detect low frequency and primary resistance mutations or secondary mutations arise under the selection pressure of treatment
same mutation in different tumor may produce an unexpected response to treatment
Describe EV and antigen shedding.
EV–>drug exportation
shedding of antigens means the antigens are released from the surface of the tumor
-they can then interact with circulating immunoconjugates and neutralize the targeting potential of the conjugates
=specificity is lost
What is antigen modulation?
phenomenon that upon endocytosis of the surface antigen-immunoconjugate complex, some of these antigens are not exposed anymore on the surface; there is no replenishment of endocytosed surface antigens
=antibody is no longer recognized by the tumor
What are the challenges in cancer vaccine development?
cancer cells suppress the immune system
cancer cells start from a persons own healthy cells
larger or more advanced tumors are hard to get rid of using only a vaccine
people who are sick or older can have weak immune systems
each individuals tumor is in some sense unique and has its own antigens
abnormal signatures can help distinguish them
What are some cancers that have preventive vaccines?
liver (Hep B) and cervical (HPV)
What is another name for therapeutic cancer vaccines?
immunotherapy
-boost the immune system to fight cancer
-given to people who already have cancer
What are the many different ways that cancer vaccines work?
keep the cancer from coming back
destroy any cancer cells still in the body after treatment ends
stop a tumor from growing or spreading
What are examples of therapeutic cancer vaccines?
BCG
Sipuleucel-T (Provenge)
CAR-T cell therapy
immune check point inhibitors
personalized neoantigen vaccines
Describe BCG.
intravesical immunotherapy
made from mycobacterium bovis
-weakened to reduce harm to body
given after TURBT
What are two enzymes that are specific to prostate cancer?
PAP and PSA
-enzymes made by prostate cells that are often overproduced by prostate tumors
What is the vaccine for prostate cancer?
Sipuleucel-T (Provenge)
What are CAR-T cells?
cytotoxic T cells engineered to specifically kill cancer cells expressing specific target receptor(s)
-CD8 T-cells: bind and kill infected cells and cancer cells
What are the two components of CAR?
antigen recognition region
-antigen binding site
intracellular signaling domain
What is the aim with CAR T-cell therapy?
make the cytotoxic T cells to express CAR
CAR should bind the antigens over-expressed only in cancer cells
TCR-MHC1 interaction should not be disturbed
cytotoxic T cells should be stimulated and kill cancer cells
What is one of the most frequent side effects of CAR T-cell therapy?
cytokine release syndrome (CRS)
-rapid and massive release of cytokines into the bloodstream which can lead to high fever and low blood pressure
What are the challenges of CAR T cell therapy?
autologous nature
time consuming
cost
What are immune checkpoint inhibitors?
these drugs take the “brakes” off the immune system to help it recognize and attack cancer cells
What is the molecule which cancer cells have that can allow them to be disguised and go undetected?
PD-L1/PD-L2
What is the mechanism of PD-1 receptors?
found on T cells and downregulate the immune system
-suppress T-cell activity
-prevent damage from inflammatory response
binding of PD-L1 or PD-L2 results in:
-T cell apoptosis
-downregulation of cytokine production
-suppression of anti-tumor response
What are the targets of the following drugs?
-nivolimumab
-pembrolizumab
-ipilimumab
nivolimumab and pembrolizumab: anti-PD-1
ipilimumab: anti-CTLA-4
