Final Exam Flashcards
Type 1 Diabetes
loss of insulin production by pancreas
Type 2 Diabetes
Resistance to the actions of insulin
5 abnormalities due to insulin deficiency
- hyperglycemia
- increased lipolysis
- acidosis
- increased LDL; decreased HDL
- osmotic diuresis (increased urination)
Insulin replacement therapy
insulin associates as hexamer
rate limiting step for capillary absorption is the dissociation of hexamers into dimer and then monomers
5 different types of insulin
- ultra fast/ short acting: lispro
- short acting: regular
- intermediate acting: NPH
- long acting: lente /ultra lente
- ultra long acting: glargine
2 insulin treatment regimes
- Intensive insulin treatment (frequent monitoring of blood glucose, 3 or more daily injections of insulin)
- Continuous subcutaneous insulin infusion (insulin pump with lispro or regular insulin, allows control of dawn phenomenon, patient triggered bolus before meals)
4 adverse effects of insulin therapy
- hypoglycemia (especially dangerous in Type 1 diabetes)
- allergy and resistance to insulin
- lipohypertrophy
- lipoatrophy (due to impurities: switch to highly purified insulin)
Insulin resistance is due to?
decrease insulin receptor number
decrease insulin receptor kinase activity
post receptor defects
decrease GLUT4 translocation from impaired signalling (less glucose can be transported into cell)
Impaired islet function is due to?
loss of first phase insulin secretion
increase secretion of proinsulin
Treatment of type 2 diabetes
- diet and exercise: most effective, increase insulin sensitivity
- monotherapy with oral agent
Sulfonylureas (Glyburide)
Most effective when B cell function has not been severely compromised
Increased insulin secretion favors lipogenesis
inhibit voltage gated K channel -> activates voltage gated Ca channel -> more intracellular calcium -> cause insulin secretion
Repaglinide and Nateglinide
decrease ATP-sensitive K+ conductance
similar to sulfonylureas
maybe more specific for B-cell sulfonylurea receptor (fewer off targets effects)
action maybe glucose dependent
insulin release is rapid and brief
taken with meals for postprandial hyperglycemia
Repaglinide and Nateglinide
decrease ATP-sensitive K+ conductance
similar to sulfonylureas
maybe more specific for B-cell sulfonylurea receptor (fewer off targets effects)
action maybe glucose dependent
insulin release is rapid and brief
taken with meals for postprandial hyperglycemia
Biguanides (Metformin)
antihyperglycemic
inhibit gluconeogenesis
inhibit glucose-6-phosphatase activity -> glycogen sparing
decrease insulin resistance
mediated by activation of 5’AMP-activated protein kinase (AMPK) in hepatocytes and muscle
DO NOT INCREASE INSULIN SECRETION
NOT HYPOGLYCEMIC EVEN AT HIGH DOSES
Thiazolidinedione (Glitazones)
Activates peroxisome proliferator-activated receptor Y
increase adipose tissue -> weight gain
decrease TNFa
decrease leptin
increase lipoprotein lipase
increase GLUT4 and GLUT 1
a glucosidase inhibitors (Acarbose)
competitive and reversible inhibitors of a glucosidase
delay carbohydrate digestion and absorption
smaller rise in postprandial glucose
taken with first bit of meal
DO NOT PRODUCE HYPOGLYCEMIA, LACTIC ACIDOSIS or WEIGHT GAIN
effective regardless of age, genetic factor, body weight, duration or severity of the disease
PDGF receptors (platelet-derived growth factor)
activation: open c terminal loop, phosphorylation
involved in wound healing
released from activated platelets by degranulation
stimulates fibroblast migration, chemotactic and angiogenic
plays a role in arteriosclerosis (overactivity of PDGF)
blocking antibodies have been developed (problem: too much blockade will end up with bleeding disorder, no healing)
3 drugs that bind covalently to enzymes
- Acetylsalicylic acid (ASA, aspirin)
- Penicillin
- Phenelzine
Aspirin
irreversibly inactivates COX, inhibiting prostaglandin production
inflammation: due to prostaglandin E and F
ASA acetylates both COX1 and COX2, but COX2 is more important because it is inducible by inflammatory cytokines
antithrombotic: inhibition of COX1 leads to antithrombotic effect (prolonged bleeding)
analgesic: inhibition of prostaglandin synthesis decrease perception of pain
antipyretic: decrease prostaglandin synthesis in hypothalamus induce vasodilation and sweating, leads to decrease body temperature
COX2 selectivity for ASA
structural difference between the substrate binding channels in COX1 and 2
VAL434, ARG513, VAL532 side pocket absent in COX1
Penicillin
inhibit cross wall formation in bacteria -> abnormally elongated cells -> rupture and cell death
Transpeptidase cleaves terminal D-ala and connects it to m-dap, which is inhibited by penicillin
B-lactamase (decoy) give penicillin resistance to pathogenic bacteria
Phenelzine (Nardil)
antidepressant agent
mediates by 5-hydroxytryptamine (5-HT) and catecholamines (norepinephrine and dopamine)
inhibits monoamine oxidase (MAO) MAO has 2 isoforms A and B MAO A: 5-HT and norepinephrine MAO B: phenylethylamine MAO-A is more important for antidepressant effects
contains a hydrazine moiety similar to substrates of MAO
inactivates enzyme when covalently binds
non-selective MAO inhibitor
requires several weeks for onset for activity
food restriction for tyramine containing (cheese, red wine, beer) -> leads to hypertension
3 drugs that bind reversibly to enzymes
- Ramipril
- Sulfonamide
- Neostigmine
Ramipril
inhibit ACE enzyme
blood pressure control and congestive heart failure
reduce formation of angiotensin II, decrease blood pressure
adverse effect inhibit bradykinin metabolism, dry cough, throat irritation, dizziness, itching
Sulfonamide (antibiotic)
Interfere microbial folic acid biosynthesis
competes with para-aminobenzoic acid (PABA) substrate for dihydropteroate synthase (DHPS)
use in treatment of bacterial infection
resistance developed by overproduction of PABA or structural change to DHP enzyme
Neostigmine
muscle stimulant
inhibit hydrolysis of acetylcholine so acetylcholine cannot be metabolized
will release eventually
3 drug that mimic enzyme substrate (pseudosubstrate)
Zidovudine (AZT)
Acycloguanosine
Cytosine Arabinoside
Zidovudine (Retrovir, Azidothymidine AZT)
first approved drug for HIV treatment
nucleotide reverse transcriptase inhibitors (NRTIs)
site of action at RNA-directed DNA polymerase (reverse transcriptase) enzyme
inhibits reverse transcriptase in virus
lacks 3’ oxygen, cause DNA chain termination when incorporated into a growing DNA strand
Highly active anti-viral therapy (HAAT)
combinations of two or three drugs of different classes
AZT or another nucleoside mimics & non-nucleoside reverse transcriptase inhibitors
entry inhibitors = prevent virion from attaching to host cell membrane
integrate inhibitors = stop DNA incorporation into host DNA
decrease viral load
not curable of HIV but can improve quality of life
Acycloguanosine (acyclovir)
topical antiviral drug
treat symptoms of herpes simplex virus infections of the skin, mucous membrane and genitals
mimics deoxy guanosine
viral and host kinase convert acyclovir into Acycloguanosine triphosphate and used by viral DNA polymerase.
no tertiary hydroxyl group prevent binding of next nucleotide
Cytosine Arabinoside (cytarabine, araC)
pyrimidine analogue
cytotoxic
incorporation of AraCTP into DNA
mimics deoxycytidine
inhibit DNA polymerase activity, block DNA synthesis
inhibit topoisomerase I results in DNA supercoiling during synthesis
OH group modifies DNA structure inhibition of transcription factor binding to DNA
used in treatment of leukemia
3 types of natriuretic peptide
A type: 28 amino acid, secreted by myocyte in atria
B type: 32 amino acid, secreted by myocyte in ventricle
C type: 22 amino acid, secreted by vascular cells
3 effects of increased cGMP
- increase natriuresis (urination)
- decrease peripheral vascular pressure (decrease blood pressure)
- suppress renin-angiotensin
Mechanism of natriuresis (ANP)
ANP increase glomerular filtration
ANP stimulate phosphorylation of ENac (epithelial sodium channel) blocking Na reuptake
net increase excretion of water and sodium
Mechanism of muscle relaxation by Nitric oxide on soluble guanylyl cyclase
NO binds -> cGMP production -> cGMP binds to PKG -> PKG phosphorylates IP3 and L-type Ca channel -> decrease [Ca]
-> decrease MLCK activity -> decrease muscle contraction
Half life of nitroglycerin, isosorbide dinitrate and isosorbide mononitrate
Nitroglycerin: acute treatment, 2min
Isosorbide dinitrate: prophylactic (long-lasting) treatment, 1 hour
Isosorbide mononitrate: prophylactic treatment, 5 hours
release of NO (rapid dilation of blood vessels)
PDE inhibitor Methylxanthines
increased cortical arousal, more alert and deferral of fatigue myocardial contraction relaxation of smooth muscle increase gastric secretion increase digestive enzymes BRONCHODILATION
Theophylline
treats asthma bronchodilator agonist, inhibit PDE from turning cAMP to AMP decrease Ca smooth muscle relaxation
Rolipram
PDE4 inhibitor (cAMP selective)
treats depression
nausea GI disturbance and emesis
Roflumilast
PDE4 inhibitor
used in chronic obstructive pulmonary disease (COPD)
still upsets GI
Sildenafil (Viagra) and Tadalafil (longer halftime)
PDE5 inhibitor (cGMP specific)
inhibit breakdown of cGMP to GMP
higher cGMP concentration leads to muscle relaxation
leads to increase blood flow to corpus cavernosum of penis
erection restore
HYPOTENSIVE SHOCK if used with NITROGLYCERINE
Ligand binding domain of nuclear receptors
11-13 a helices arrange into a three layer antiparallel a-helical sandwich
long helices 3,7 and 10 form two outer layers
4,5,8,9 create ligand binding pockets
Agonists function of nuclear receptors
stabilize nuclear receptor formation and maintaining AF-2 helix 12 in the active conformation
Ligand binding pocket specificity is determined by?
- shape
- size
- plasticity
Ligand binding pocket specificity is determined by?
- shape
- size
- plasticity
Ligand binding of nuclear receptor triggers ? (6 steps)
- conformational change in LBD
- dismissal of corepressor
- recruitment of ubiquitylation leads to corepressor degradation
- enhanced affinity for co-activators
- recruit co-activator complex
- activation of gene transcription
Zinc finger domain in DNA binding domain (DBD)
P-box (proximal) domain: DNA binding in major groove
D-box (distal) domain: NR dimerization
nuclear receptors can bind to DNA as monomer, homodimers and heterodimers
Estrogen receptors
Type 1
activates gene containing estrogen response element (ERE)
can function as homodimers (a-a, b-b) or heterodimers (a-b)
ERa: breast, endometrial, ovarian and hypothalamus tissue (sex organs)
ERb: brain, bone, endothelial, heart, intestine, kidney, lung and prostate tissue (non-sex organs)
have overlapping and non-overlapping function, can oppose each other
What is the natural ligand of estrogen receptor?
17B- estradiol (estrogen) agonist induce puberty derived from cholesterol primarily produced in ovaries
Estrogen deficiency
menopause
ovarian insufficiency
hyperprolactinemia (elevated prolactin to enhance breast development during pregnancy and lactation)
Elevated estrogen level
weight gain liver toxicity breast hypertrophy thrombosis increase cancer risk endometrial cancer breast cancer
Tamoxifen
SERMs (selective estrogen receptor modulators)
derived from diethylstilbestrol
metabolized in liver by CYP2D6 and CYP3A4 into hydroxytamoxifen and N-desmethyl-4-hydroxytamoxifen
both have higher affinity for ER than tamoxifen
Tamoxifen is a mixed agonist/antagonist in what tissue?
Breast tissue: NCOR or SMRT corepressor highly expressed, antagonistic
Uterine tissue: SRC1 coactivator highly expressed, agonistic
Androgen Receptors
Steroid or Type 1 Receptors on X chromosome
2 isoforms, ARa and ARb
Natural ligands: 5a dihydrotestosterone and testosterone
Androgen receptors DNA binding conformation
Head to head homodimer
5’-AGAACAnnnAGAACA-3’
most stable conformation to the common hexameric “half site” DR3
Prostate cancer initiation
Overexpression of TMPRSS2-ERG (fusion protein) leading to cell cycle progression and overexpression of ETS transcription factor
Prostate cancer therapy
expectant management or active surveillance surgery radiation cryosurgery HORMONE therapy chemotherapy vaccine treatment bone-directed treatment
Androgen Deprivation Therapy (ADT)
tumor growth is initially androgen dependent androgen ablation (block the production of androgen) to cause regression of androgen-dependent tumors
Many men eventually fail this therapy and progress onto AIPC (androgen independent prostate cancer)
also called castration resistant prostate cancer (CRPC)
castration resistant prostate cancer (CRPC) treatment
development is inevitable
lethal
no longer respond to first-line androgen deprivation therapy
treat with CHEMOTHERAPY and anti-mitotic compound DOCETAXEL
4 possible mechanism for CPRC
- increased sensitivity of androgen receptors to its agonist
- AR mutation that render the receptor responsive to alternate non-androgen ligands
- ligand-independent AR activation (activation by kinase, phosphorylation)
- AR-independent mechanism (direct activation of TMPRESS2-ERG)
Retinoic acid receptors
Type 2 nuclear receptor
constant partner RXR and RAR
already binds to DNA
Acute Myeloid Leukemia (AML)
aggressive cancer of bone marrow affecting hematopoiesis
rapid accumulation of immature myeloid progenitors (leukemic blasts)
cytarabine and daunorubicin chemotherapy
Acute Promyelocytic Leukemia (APL)
Incidence highest in young adults
Presentation
Pancytopenia (Anemia, Neutropenia, Thrombocytopenia)
Coagulopathy
Promyelocytes in peripheral blood
most malignant form of AML
immediately start treatment even with suspicion
APL is now associated with the highest proportion of AML patients who are cured of their disease
APL pathogenesis
Translocation of retinoic acid receptor alpha
95% PML-RARa -t(15;17)
PML/RARa protein
dominant negative mutant forms homodimer (normally form heterodimer) repress target genes less responsive to agonist binds strongly to corepressors
ATRA (all-trans retinoic acid)
induce terminal myeloid differentiation
but cannot prevent the occurrence of malignant transformation in myeloid progenitor cells
combine with chemotherapy
Mechanism:
- bind ATRA to RAR cause ubiquitylation of PML-RARa protein
- CoR is dissociated from repressive complex and CoA is recruited.
- differentiation of promyelocytes is restored
Arsenic Trioxide (As2O3)
cause degradation of PML-RARa, promotes differentiation
APL cells extremely sensitive to arsenic trioxide
increase chance of survival with ATRA admission
Why choose DNA as drug targets?
- to a kill a cell by inducing DNA damage and apoptosis
2. to insert delete or edit aberrant genetic information causing disease
DNA-damage response proteins (DDR)
p53 activation
cell cycle arrest
apoptosis
selectivity achieved as cancerous cells proliferate faster than healthy cells
Cyclophosphamide
oral prodrug converted by CYP450 to active mustard
forms covalent purine (G) N7 adducts and N7-N7 crosslinks like cisplatin (not a prodrug delivered in active form)
treat cancers
side effects: teratogenic, immune suppression, alopecia, nausea, bladder and liver toxicity and cancer (induce mutation in DNA)
Doxorubicin and Actinomycin D
form covalent interactions with bases on opposing strands leading to inhibition of Topoisomerase I and replication stall
treat tumors
side effects : cancer (block repair machinery)
Gemcitabine
transported via SLC nucleoside transporters and gets phosphorylated (prodrug)
resembles deoxycytidine triphosphate
chain termination
treat leukemia and lung cancer
Acyclovir and Molnupiravir
block elongation of genetic DNA/RNA of virus, halts replication of host cell
prodrug: base is converted into nucleotide by viral kinase
inhibits HSV1/HSV2 herpes
Acyclovir and Molnupiravir
block elongation of genetic DNA/RNA of virus, halts replication of host cell
prodrug: base is converted into nucleotide by viral kinase
inhibits HSV1/HSV2 herpes
Gene augmentation
monogenic
copy of gene without mutation is cloned into a DNA plasmid
insert into cells
production of functional protein
if in somatic cell its called
somatic gene replacement therapy (SCRT)
Cystic fibrosis Duchenne muscle dystrophy hemophilia Huntington's Rett syndrome
Issue with delivering DNA into cells
small molecules that are hydrophobic can readily diffuse cell membrane
DNA Is impermeable to cell due to size and charge
Electroporation
use electrical charge to physically poke holes in cell membrane
no size limitation but organ aren’t accessible (ex vivo, because electrical charge maybe interrupt heart)
Gene gun
fires micro-projectiles containing DNA conjugated to heavy metal into cells
usually for plants
Problem with electroporation and gene gun
DNA still have to be transported to the correct compartment
random site integration
tissue must still be accessible
Chemical transfection of DNA into cells
Cationic lipid: interacts with negative charge on DNA, mixed with neutral lipids to form liposome
no size limitation but rapidly eliminated
Cationic polymers: cationic head interacts with DNA, forms condensed aggregates that stabilize DNA, can be attached to cell permeable peptides
no size limitation
Viral transduction of DNA into cells
Virus for in vivo modification
tropism: can be targeted to specific tissues
replication defective
replication occur in helper plasmid containing coding trans elements
Lentiviral vectors
RNA viruses Key proteins: GAG: capsid POL: protease, reverse transcriptase, integrase ENV: envelope glycoprotein TAT: nuclear import, transcription REV: nuclear export of unspliced RNA
enter via receptor mediated endocytosis
can infect non-dividing cells because TAT can bypass nuclear
most virus can only infect dividing cells because during division there is no nucleus so can access DNA directly
disadvantages: random integration, LIMITS ON SIZE (5kB)
AAV vectors
Two ORFS:
REP: regulatory proteins
CAP: encodes structural proteins/capsid
gene of interest insert between ITRs
enter via receptor mediated endocytosis
can deliver to nucleus
LIMITS ON SIZE (5kB)
ADA-SCID “Boy in the Bubble”
Adenosine deaminase deficiency, severe combined immunodeficiency) “Boy in bubble”
ADA catalyze conversion of adenosine to nucleoside inosine
impair lymphocyte development
immune system severely compromised
Treatment: ex vivo viral transduction of ADA gene into isolated bone marrow and lymphocytes that are reinjected
Hemophilia A
blood clotting disorder
mutations in factor 8 (85%) or factor 9 (15%)
internal or external bleeding
X-linked recessive
treatment: in vivo injection of pseudotyped AAV (target liver cells) containing F9 into blood
OTC deficiency
drawbacks of gene therapy delivery tools
- possible immunogenicity
- random insertion into genome
ornithine transcarbamylase deficiency: inability to metabolize ammonia
injected adenovirus carrying OTC gene
died of immune reaction to virus
Gene editing
advantages: can mimic healthy endogenous gene exactly, permanent cure
disadvantages: irreversibility, off target effects, stimulation of DNA damage (p53) when cutting DNA, immunogenicity
Zinc finger domains (ZF)
recognize triplets
can be linked linearly to form arrays to target larger sequences ( 3 ZFs target 9 bp)
Zinc finger nucleases (ZFNs)
two zinc finger arrays linked to subunits of the heterodimeric FOK1 endonucleases
FOK1 only active when heterodimer is formed
ZFNs bind to left and right sequences (Part A and Part B)
TALEs
transcription activator like effector
each TALE DOMAIN binds 1 bp of DNA can be linked to form arrays that target longer sequence
amino acids at position 12 and 13 of each TALE domain dictates which specific base is bound
amino acids 12 and 13 can be mutated to fit certain DNA sequence
TALE nucleases (TALENs)
Two TALE arrays linked to subunit of the heterodimeric FOK1 endonucleases
assembly cloning can be difficult
CRISPR/Cas9 4 step sequence
part of the prokaryotic immune system that defends against bacteriophages
- invasion
- adaptation
- production
- targeting
CRISPR/Cas9 mechanism
- Cas9 (endonuclease)
- crRNA contains 20 bp used to target
- trans-activating crRNA (tracrRNA)
Cas9 displays PAM sequence (‘5-NGG-3’) N=ACG or T
crRNA + tracrRNA = guide RNA
- Cas9 binds to PAM
- Cas9 uses 20 bp in the crRNA to recognize a match with DNA target
- If match, Cas9 activates its two nucleases which cut the top and bottom strands (double strand break)
2 DNA repair mechanisms
- non-homologous end joining (NHEJ): inactivation/knockout
2. homologous recombination (HR)/ homology directed repair (HDR): knock in or gene editing by supplying repair DNA
Homology directed repair (HDR) and PRIME editing
in addition to Cas9 and gRNA, supply a single stranded oligodeoxynucleotide with homology arms flanking the cut site for repair
PRIME editing: uses nCas9-RT (single strand break) and pegRNA (special type of guide RNA) that contains a template for RT which is used to fill in information repaired using exogenous enzymes
Base editing
dCas9 (dead Cas9) fused to a base modifying enzyme (cytidine deaminase)
endogenous DNA repair recognize damage base and repair it leading to gene conversion
dCas9 is catalytically inactive but still binds DNA
CRISPRi (inactivation) and gene silencing
dCas9 attached to transcriptional repressor domain such as KRAB (repressor)
- dCas9 targets and effector to a specific gene promoter
- blocks transcription or recruit other factors to turn gene off
Gene activation with CRISPRa
dCas9 attached to transcriptional activation domain such as VP64 (activator)
- dCas9 targets gene promoter (TATA box)
- recruit and stabilize transcription factor
Epigenome editing
dCas9 attached to DNA or histone modifying enzyme that induce epigenetic change (HERITABLE)
- dCas9 targets gene promoter
- cause activation or deactivation through methylation or acetylation
dCas9-p300 (histone acetyltransferase): activates gene
dCas9-Tet1 (DNA demethylase): activates gene
dCas9-Dnmt (DNA methyltransferase): silence gene
Ribonucleoprotein complex (RNP)
CRISPR/Cas9 can be delivered as RNP using a mixture of Cas9 protein and guide RNA in CATIONIC LIPID
can also be delivered using DNA PLASMID
Transthyretin amyloidosis (TTRA)
mutation of TTR gene made by liver
in vivo editing using lipid nanoparticle carrying mRNA encoding CRISPR/Cas9 and guide RNA targeting TTR
lipid goes straight to liver
knockout gene in liver decreased serum TTR production by mean of 50%
CAR-T cells
chimeric antigen receptor T-cell composed of extracellular antibody (scFv) domain artificially attached to intracellular T cell activation domain
editing T cell domain by CRISPR/Cas9
ex vivo
potential gene therapy to target cancer (lymphoma and myelomas)
CCR5 germline KO
CCR5 (HIV co-receptor) edits at embryonic stage
DNA antisense oligonucleotides (ASOs)
single stranded DNA that is complementary to a sequence contained within the gene being targeted (RNA)
enter nucleus and binds and targets pre-mRNA
generates a RNA-DNA heteroduplex
recognized by RNase H1 and targeted for degradation
ASO steric blockers
- block translation of mRNA
- alter splicing of pre-mRNA
- block adenylation (stability)
These ASOs are typically RNA or XNA based
do not activate RNase H
ASO drugs
enhance stability, delivery and efficacy
Kynmaro (Mipomersen): treat familiar hypercholesteremia, binds to mRNA of ApoB-100 (fat carrier) and initiates destruction of RNase H1
Vyondys (Golodirsen): treat DMD, works by inducing exon skipping, defective form of gene is not produced
RNAi (interference) - siRNA pathway
siRNA pathway
immune defense against double stranded RNA (virus)
siRNA is composed of guide and passenger strand
binds to RISC complex and directs slicing activity of Argonaute 2 (AGO2) target transcription or block
if match perfect = slice
if match imperfect = translational inhibition
RNAi - miRNA pathway
Pri-miRNAs cleaved by Drosha (enzyme)
contain hairpin structure
processed by Dicer to form 19-25 nt ds RNAs
binds to RISC/AGO complex
often partially complementary to target, act by binding to 3’UTR and blocking translation of multiple targets
Delivery of small RNAs into cells
Viral vectors: Lentivirus, adenovirus and AAV
Non-viral vectors: cationic polymer (PEI, cyclodextrins) or cationic lipids (DOTMA)
RNAi/miRNA Drugs
mi(micro)RNA perfect for multigenic disease such as cancer
si(small interfering)RNA for single gene (hemophilia)
Onpapttro siRNA based drug, treats TTRA
CRISPR/Cas 13
class II CRISPR system uses a single guide RNA and cleaves ssRNA but not dsDNA
contain 2 Higher Eukaryotes and Prokaryotes Nucleotide-binding (HEPN) domains, both RNase domains required for cleavage
Cas13 exhibits collateral RNA cleavage
Mechanism for Cas13 RNA cleavage
- binds to RNA and scans for protospacer flanking sequence (PFS) a non G-base
- test for annealing of 30 bp sequence to identify target RNA
- If match found, HEPN domains activates and cleaves sequence
- domain remains in active conformation and subsequently initiate trans cleavage, only observed in bacteria and in vitro
RNA base editing using dCas13
one or both HEPN domains are inactivated through mutation fusion of dCas13b to deaminase domain of ADAR2 enzyme purposely mismatch (A-C) to allow for deamination changing A to I which is actually G during translation
RNA methylation editing using dCas13
m6A catalyzed by METTL3/14 complex transfer of Me from SAM
modification alters RNA splicing, stability, export and translation efficiency
fusion of dCas13 to enzyme variants M3-M314 yield site specific m6A
Cas7-11
class 1 CRISPR system buy individual proteins are fused together (Cas7-11)
No PFS sequence and no collateral cleavage activity (trans)
No HEPN domains
Next generation nucleic acid vaccines
goal is to directly target APC cells so that proteins are expressed on their surface
SARS-COV-2 vaccines
ss(single stranded)RNA virus: use an RNA-dependent RNA-polymerase for replication
Spike glycoprotein binds to ACE-2 receptors on lung epithelial cells
Pfizer/Moderna: uses lipid nanoparticles to package modified RNA(pseudouridine)(less reactive to immune system) encoding
SPIKE PROTEIN
targets dendritic cells, present spike protein to B and T-cells to elicit immune response
Difference between Gram + and Gram negative bacteria
gram negative have 2 membrane while gram positive only have 1 thick peptidoglycan layer (membrane)
Penicillin antibiotic resistance
bacteria evolved thicker outer membrane so penicillin harder to penetrate
acquisition of penicillinase gene (breaks B-lactam ring to inactive penicillin)
Polymyxins (antibacterials)
amphipathic peptides attached to fatty acids- able to insert themselves into membrane
mechanism: directly binds to LPS (lipopolysaccharide) in outer cell membrane which leads to holes in membrane, leakage of cellular contents
BACTERIOCIDAL
Vancomycin (antibacterial)
Delivered intravenously
treatment for complicated skin infections, blood infections and meningitis
inhibit cell wall synthesis by directly binding to D-ALA-D-ALA precursors
prevent incorporation into growing peptide chain of cell wall, halts elongation and cross linking of peptidoglycan matrix
RESISTANCE: when bacteria change the precursor
Nystatin (Antifungals)
useful for candida infections such as thrush
not orally bioavailable
useful for topical and GI infections (not absorbed)
mechanism: binds to a fungal specific sterol called ergosterol in fungal cell membrane and cause leakage
Docosanol (antivirals)
used topically, poor oral bioavailability
mechanism: inhibit fusion of viral envelope with the host cell membrane; directly inserts into human cell membrane to protect from diffusion of virus
prevents viral replication
LJ-001 (Antivirals)
Blocks viral entry into host cell (after virus binding but before virus cell fusion)
poor stability
Mechanism: directly intercalates into viral membrane in irreversible manner, blocking fusion, only work if envelope is present
ONLY WORK ON ENVELOPED VIRUS such as HIV, influenza, filoviruses
Osmotic laxatives
treat constipation and digestive conditions
natural inorganic salts: MG-CITRATE which get partially absorbed or synthetic compounds that increase ions but aren’t absorbed (PEG 3350, lactulose)
Mechanism: Delivered into intestine orally, pulls water from surrounding tissue into intestine via OSMOSIS (from high to low), softer stools
Bulk-forming laxatives (Methylcellulose, Citrucel, psyllium fiber)
treat constipation
involve inert natural (psyllium fiber) or synthetic (polycarbophil) polymers that do not get absorbed but pass through digestive system
Mechanism: delivered into intestine orally, polymers absorb water creating a bulkier, liquid like stool that’s easier to pass
pH-modifiers
a) induce physiological effects in the stomach
b) re-absorption of drugs and mineral in the urine
Calcium carbonate (TUMS) or Magnesium hydroxide (milk of magnesia), neutralize H+ in stomach and increase pH
K-Phos (potassium acid phosphate) urine acidifier to keep calcium solubilized and prevent kidney stone formation
Metal Chelators
reduce amount of metal ions in the body
Desirox is an orally bioavailable iron chelator to treat iron overdose (or due to blood transfusions)
Drugs that target bone:
Biphosphonates
ALENDRONATE (FOSAMAX) and RISEDRONATE (ACTONEL)
Bisphosphonates are pyrophosphate analogues used to prevent and treat osteoporosis
converted into non-productive NTPs (nucleotide triphosphate) in cells
mechanism: attach to hydroxyapatite binding sites on bony surfaces, especially undergoing resorption, and kill osteoclasts (resorption cells)
