Unit 2 Flashcards
1
Q
What are Natural Products?
A
Compounds produced by organisms that provide them with an evolutionary advantage (protect them from attacks, predators, etc.)
2
Q
Where do we find natural products?
A
- can be isolated from any organism
- usually plants, fungi, bacteria, and marine organisms
- explore ecosystems
- natural products from defensive symbiosis
3
Q
Why natural products over synthetic drugs?
A
- usually common in nature
- complex structures that are difficult to replicate and have unique properties
- interact with specific targets
- very diverse
4
Q
Natural Product Discovery (4)
A
Extraction
Fraction
Bioassay screening
Bioactive Natural Products
5
Q
Requirements for Field Collection
A
- Easily collected
- Get them back
- Easily stored
- Can be grown in lab
6
Q
Biopiracy
A
The stealing of biodiversity or indigenous knowledge (take back to your own country and make money from it)
7
Q
Difficulties Obtaining Natural Products
A
- Need a lot
- Lots of wasted solvents and chromatography
8
Q
Chromatography/Isolation
A
- stationary phase (solid, can be liquid)
- mobile phase - solvents or buffers (liquid, can be gas)
- scale
-dry
9
Q
Testing for bioactivity
A
- must be easily tested
- specific targets
- phenotype
- scale
10
Q
Structure Elucidation
A
- solve structure by NMR or X-ray crystallization
- can use mass spectrometry, UV, IR
11
Q
X-ray Crystallography
A
describes where electron density is located by scattering x-rays and interactions with electrons
- must be a crystallized product
12
Q
Infrared Spectroscopy measures
A
functional groups and bond flexibility
13
Q
Mass Spectrometry measures
A
molecular weight and molecular formula
14
Q
Ultraviolet Spectroscopy measures
A
bond conjugation and aromaticity
15
Q
Genomics
A
DNA sequencing and bioinformatics have allowed the mapping and annotation of organism genomes and BGCs
16
Q
Metabolomics
A
use of large LC-MS/MS data sets gas allowed comparative analyses of produced compounds across organisms
17
Q
Updated Central Dogma
A
DNA - predict genes that eventually produce final product
RNA
Protein - enzymes used to make the natural products
Natural Product
18
Q
Biosynthetic Gene Clusters (BGCs)
A
groups of genes that encode the enzymes that synthesize compounds like antibiotics
- many are not always expressed (“silent”)
19
Q
Discovering Antibiotics from Genomes
A
Bacteria BGCs are studied in silico on the computer - bioinformatics
20
Q
Bioinformatics to Predict Function
A
- Enzymes have reaction specificity and are encoded in the genome
- Similar enzymes will have similar reaction specificities and encode similar genes
- used to predict function of other enzymes
21
Q
Bioinformatics to Predict Structures
A
BGCs are used to predict function and using bioinformatics online in databases, the structure can be predicted
22
Q
Liquid Chromatography Mass Spectrometry (LC-MS) or Mass Spectrometry (MS)
A
- use databases
- use intrinsic properties that won’t change in experimental conditions
- LC-MS/MS based fragmentation patterns work well
23
Q
Natural Product Classification
A
- used to be by chemical class (plant natural products still are)
- now by biosynthetic pathway
- natural products built using smaller organic products used for identification
24
Q
Organic molecules used to build natural products (6)
A
- acetates
- sugars
- amino acids
- isoprene
- shikimate
- lipid
25
Ribosomally Encoded and Post-Translationally Modified Peptides (RiPPs)
- peptide natural products
- sequence found in genome
- found in plants and fungi
- proteases free the sequence from a larger one
26
Non-ribosomal Peptides
- production encoded by non-ribosomal peptide synthetases (NRPS)
- often contain non-proteinogenic amino acids
- can hybridize with polyketide natural products
27
Polyketides
- production encoded by polyketide synthetases (PKS)
- modular enzyme structure (AT, KS, T, TE, KR, DH, ER)
- ketide units usually obvious or reduced to alcohols, or -enes
28
Terpenes
- composed of isoprene units (5 carbon structure)
29
alkaloids
- basic nitrogen containing compound (nitrogens)
- bitter
- bioactive
- many known toxins are alkaloids
30
Lead Compound
a compound that has the desired effect on a drug target and is the starting point for designing a new drug
31
Chemical Synthesis of Drugs
- use molecule with know drug target
- modify to increase potency, efficacy, and bioavailability
32
Arylomycin
- natural product originally isolated from an actinobacteria off the coast of Nigeria
- inhibits signal peptidase in gram + bacteria and not gram -
33
Drug Leads
- natural products
- natural ligands
- enzyme substrates (kinases)
34
Biological Screening
Testing tens of thousands of drugs to determine what can bind to desired target using natural product libraries and synthetic chemical libraries
35
Natural Product Libraries
can use purified compounds or natural product extracts - usually more diverse library
36
Synthetic Chemical Libraries
Many Pharma companies have the same massive synthetic libraries that they screen for drug leads
37
High Throughput Screening
- usually done robotically
- used to test on a target and see what hits
- does not tell pharmacokinetics
38
What do we want out of our drugs?
- Interact with target (potency, efficacy, and selectivity)
- Reach target (selectivity and bioavailability)
39
Bioavailability
proportion of the drug that enters circulation and can therefore have an effect on the target
40
Importance of hydrophobicity and hydrophilicity...
- too hydrophobic - the drug won't enter the blood stream to enter circulation (need to bind to serum proteins)
- too hydrophilic - the drug won't cross membranes or interact well with targets (has more H-bonds)
41
Lipinski's Rule of 5
Predict the oral bioavailability of the drug
1. No more than 5 H-bond donors (NH or OH)
2. No more than 10 H-bond acceptors (N or O)
3. Molecular Weight less than 500 Da (must be small)
4. LogP less than 5 (tells hydrophobicity)
42
Why use a smaller compound?
if too big, it is less likely to passively diffuse across membranes
- bigger usually means less soluble
- bigger = harder to synthesize
43
LogP
how hydrophobic is the compound
>1 hydrophobic
<1 hydrophilic
44
Exceptions to Lipinski's rule of 5
~mostly just guidelines~
many natural products break these rules but in general these rules assume passive diffusion and determine bioavailability
45
Privileged Structures
- can break Lipinski's rules
- can be capable of binding to many targets
- often aromatic rings with side chains
46
Toxicophoric Groups
- groups that cause toxicity
- include overly electrophilic groups, metal chelating groups, metabolized into electrophilic groups
47
False Positive in Screening
- compounds that aggregate on drug targets without binding specifically (no specificity)
48
PAINS compound
Pan-Assay Interference Compounds
- quinones, catechols, enones, curcumin
49
Fragment Based Screening - De Novo Synthesis
- looks for several small molecules that bind and then links them
- use NMR or X-ray Crystallography to identify fragments that bind to target
50
Virtual Screening
Use computers, interactions between targets and digital libraries can be modeled
- complex computational tools
51
Targets Computed
- Protein Data Bank
- crystallized structures
- computed structures using software
52
Digital Compounds
- line structure can be produced by digital libraries
53
Computational High Throughput Screening
Software used to match 3D compound shapes into protein active sites
54
Pharmacophore
- Active Center of a Drug
- most important interactions between drug and target
55
Modify and Optimize the compound
- add functional groups
- remove functional groups
- open rings
- close rings
56
If modifications result in lower potency...
- most of the molecule is the pharmacophore (important)
57
Add groups to...
optimize pharmacokinetics and stabilization of pharmacophore
58
Why modify?
- change potency
- change selectivity
- change activity
- can make it easier to make
59
Structure-Activity Relationships (SAR)
structure is directly related to activity
60
Homologation
- increases lipophilicity by adding CH2
- better passage through membranes
- more flexibility
61
Ring Formation
- increase lipophilicity and constrain flexibility
- better bioavailability (more soluble)
- constrain pharmacophoric groups into optimal positions
62
Bioisosterism
- swap functional groups but maintain or amplify biological activity/interactions
- alleviate toxicity/off target effects
- decrease susceptibility to metabolism
- potentially simplify synthesis
63
Lipophilicity Effects on PK and PD
- high lipophilicity = poor oral absorption and easy metabolism
- low lipophilicity = no passive diffusion
64
Drug Action Depends on:
1. drug has to reach site of action (PK)
2. drug has to interact with the site of action (PD)
65
Blood-brain barrier
surrounds capillaries of circulatory system in brain
- protects CNS from undesirable polar molecules in blood
- difficult to pass
66
Special Membranes to cross
- blood-brain barrier
- blood-testes barrier
- blood-thymus barrier
- blood-ocular barriers
67
To pass blood-brain barrier...
need little branching
few rotatable bonds
few H-bond acceptors
more aromaticity
more H-bond donors
mor liphophilic
68
Fatty Acid Chain Branching
alters activity and binding
69
Conformational Restraints
- increase potency
- decrease rotation
- increase bioavailability
70
Bioisosteres
substituents or functional groups with chemical/physical similarities that produce similar biological effects (LOOK AT SLIDES)
71
Isostere Replacement Effects
- structural
- receptor interactions
- pharmacokinetics
- metabolism
72
Notable Isosteres
- Fluorine replacing Hydrogen
- Bicyclo[1.1.1]pentane in place of phenyl
- oxetane in place of carbonyl
73
Peptidomimetics
compounds that mimic peptides without undesirable pharmacokinetic characteristics
74
Psuedopeptides
type of peptidomimetic where peptide backbone is changed but R groups are maintained
75
Drug Discovery/Development Cycle
- identify lead via bioassays
- make modifications/ predictions for new structures
- synthesize new compounds
- bioassay
- make modifications/predictions
- repeat
76
Drug Resistance
when a formerly effective drug dose is no longer effective
77
Drug Tolerance
adaptation by the body to the drug dose, which requires higher doses to achieve same effect
78
How does resistance occur?
1. Natural Selection
2. Genetic Transfer
79
Natural Selection
- random mutation in populations
- treatment with drugs selects for resistant individuals to proliferate
80
Genetic Transfer
- plasmid encoded resistance elements
- mostly in ineffective agents
81
Nosocomial Infections
resistant infections commonly in hospitals form overuse of antibiotics
82
Methods of Gene Transfer (3)
1. transduction
2. transformation
3. conjugation
83
Transduction
phage transfers genetic DNA
84
Transformation
Take up of environmental DNA after other cell dies
85
Conjugation
DNA transfer between 2 microbes
86
Mechanisms of Drug Resistance (8)
1. Altered Target Enzyme
2. Overproduction of Target Enzyme or Receptor
3. Overproduction of Substrate or Ligand of Target
4. Increased Drug-destroying Mechanisms
5. Decreased Drug-Activating Mechanism (Prodrugs)
6. Upregulation of Alternative Pathways
7. Reversal of Drug Action
8. Altered Drug Distribution to Site of Action
87
Altered Target
- altered gene sequencing in target in later generations causing inability of drug to bind
overcome by:
- closely mimic ligand to avoid point mutation resistance
- treat with multiple drugs
88
Overproduction of Target
- producing more of the target than the treatment can bind to
overcome this by:
- increasing dosage but careful of toxicity
89
Overproduction of Substrate/Ligand
- more natural ligand to bind with target so drug cannot bind and unable to work
90
Increased Drug-Destroying Mechanisms
- increase mechanisms that inactivate the drug or metabolize drugs
91
Decreased Drug-Activating Mechanism
- if drug is prodrug it needs to be metabolized specifically to work
- resistance can occur by decreasing the production of that enzyme therefore the drug is never activated
92
Upregulation of Alternative Pathways
- Drug blocks one pathway so other pathways for product production are increased
93
Reversal of Drug Action
the drug will bind but the repair enzymes will remove it and reverse the effects of the drug
94
Altered Distribution to Site of Action
- modifications to cell membrane to prevent passive diffusion of the drug
- reorganize charges
- or pumped out of the cell after it enters
95
Drug Synergism and Overcoming Resistance (5)
1. Inhibiting Drug-Destroying Enzymes
2. Sequential Blocking (blocking the pathway that produces drug blocking product)
3. Inhibition of Targets in Different Pathways
4. Efflux Pump Inhibitors
5. Using Multiple Drugs for the Same Target
96
Area Under the Curve (AUC)
total drug exposure, integration for area under the curve
97
Cmax
highest concentration of drug in blood, must be below toxicity threshold
98
T1/2
half-life; time it takes for drug to lose half its maximum concentration
- depends on metabolism
99
Cmin
lowest concentration of drug in blood
- point where drug can be readministered
100
How can drugs be administered?
- oral - stays in system longer, slower to circulate, less concentrated
- injection (subcutaneous, intramuscular, or intravenous) - more of drug in system, quickly metabolized
- inhalation
- rectal - low concentration, slowly absorbed
- topical
101
First Pass Effect
does not get to go through a round of circulation before it starts getting metabolized by the liver
- prodrugs usually protect from liver enzymes
102
Food alters Absorption
high fats = slower emptying of stomach and longer exposure
high fiber = less water in stomach and increase bacteria in guts
- can increase or decrease effects
103
Distribution
the parameter that deals with how drugs move through circulation and arrive at their active site
- either free in plasma or bound to carrier proteins
104
If the drug is more _____, it is free in the plasma during distribution and excreted via urine.
hydrophilic
105
If the drug is more _____, it is bound to proteins during distribution and excreted via feces.
hydrophobic
106
Drug Distribution was monitored via
- isotope labeling and tracking
- animal models
- stable isotope labeling (more common now)
107
Modeling Drug Distribution
1. One-compartment model
2. Two-compartment model
108
One-compartment model
- drug is absorbed and immediately reaches systemic distribution
- useful for intravenous
109
Two-compartment model
- drug is absorbed and distributed to certain organs first, before reaching systemic distribution
- circulation = one compartment
- tissues = second compartment
110
How to Direct Drugs to Targets
monoclonal antibody drug conjugates
111
Metabolism of Drugs occurs...
- by enzymes
- primarily In the liver
112
Excretion of drugs...
through liver and feces (more hydrophilic)
through kidneys and urine (more hydrophobic)
113
Phase 1 of Metabolism
Mask/Unmask Functional Group
- oxidation, reduction, hydrolysis
- makes more polar
- handle for phase 2
- changes functional group --> can inactivate
114
Phase 2 of Metabolism
Increases hydrophilicity through conjugation reactions
- makes drug more polar and charged
- bulky conjugates to make inactive
- hydrophilic
115
Phase 1 Oxidative Enzyme
Cytochrome P450s (heme containing)
Flavin Monooxygenases (FAD)
Alcohol/Aldehyde Dehydrogenase (metabolize alcohols)
116
Phase 1 Metabolism Oxidation Reactions (7)
increasing the oxidation state or adding oxygen
1. aromatic oxidation
2. alken epoxidation
3. alpha carbon oxidation
4. aliphatic oxidation
5. carbon-nitrogen oxidation
6. carbon-oxygen oxidation
7. alcohol/aldehyde oxidation
117
Phase 1 Metabolism Reduction Reactions
decreasing the oxidation stare or removing oxygens/double bonds
1. carbonyl reduction
2. azo reduction
118
Aromatic Hydroxylation
- done by CYP450s
- OH added to aromatic rings
119
Alkene Epoxidation
- done by CYP450s
- remove double bond in rings to add alcohols
120
Alpha Carbon oxidation
Carbon immediately adjacent to sp2 hybridized carbon
- done by CYP450s
- OH added to alpha carbon
121
omega oxidation
oxidation of the terminal carbon in an aliphatic chain
122
omega-1 oxidation
oxidation of penultimate carbon in aliphatic chains
123
Aliphatic Oxidations
- done by CYP450s
- terminal carbons become alcohol become aldehyde become carboxylic acids
124
primary amine oxidation
If N is oxidized, Nitro group is formed
If C is oxidized the deamination occurs
125
secondary amine oxidation
If N is oxidized, N-oxide is formed
If C is oxidized, N-dealkylation occurs
126
tertiary amine oxidation
If N is oxidized, then N-oxide is formed
If C is oxidized then N-dealkylation occurs
127
carbon-oxygen oxidation
esterases remove ester and add alcohol
128
alcohol/aldehyde oxidation
alcohol/aldehyde dehydrogenases or CYP450s
- forms aldehyde (from alcohol) or carboxylic acid (from aldehyde)
129
Carbonyl Reduction
aldo-keto reductases
makes C=O to alcohols
130
azo reduction
azoreductases
- N=N becomes split with 2 primary amines
131
Carboxylation Reactions
- adding carboxylic acid from dissolved CO2 to amines
132
Hydrolytic Reactions
esterases and amidases
- esters to alcohols `
133
Drug-Drug Interactions (bad)
- due to metabolizing enzymes
- increases or inhibiting metabolizing enzymes alter circulation time like grapefruit juice
134
Phase 2 Modifications
- glucuronic acide
- sulfate
- amino acid
- glutathione
135
glucuronic acid conjugation
- add glucuronic acid to drug
136
Phase 2 Conjugations
add polar, bulky groups to deactivate by making more hydrophilic
137
sulfate conjugation
- add sulfate to drug
138
amino acid conjugation
- add amino acid to drug
- usually glycine and glutamine
139
glutathione conjugation
- add glutathione
- adds to epoxides, esters, quinones, sulfoxides
140
prodrugs
a pharmacologically inactive compound that is converted to the active drug by a metabolic transformation
- usually activated by cleaving an ester
141
Absorption and Distribution of a Prodrug
modify drug to make it easier to absorb or move through circulation
- can help pass specialized barriers
142
Prodrugs are good because they ...
- decrease toxicity
- increase selectivity
- taste better for oral administration
- ex: acyclovir
143
Co-drugs
two synergistic drugs that are physically linked to be delivered together
- helps to bind them together to reach target at the same time
144
Macromolecular Delivery systems
- reach desired target
- sugars (syrups)
- fats (liposomes)
- proteins (antibodies)
- other polymers - vinyl alcohol, amino acids, etc.
145
Antibody drug conjugates
bind to drug and direct drugs to particular target by binding to specific antibody target
146
Nanoparticle Delivery
- organic (liposomes) or inorganic (metals)
147
dendrimers
branched and functionalized polymeric structures that provide scaffolding for drug molecules
148
Pros of Macromolecular Delivery
- directly deliver large numbers of the drugs at a time (inc. potency)
- absorption/distribution depends of macromolecular carrier, can attain better targeting
- direct drugs to particular tissues (selectivity)
149
Cons of Macromolecular Delivery
- macromolecular absorption is lower and more complicated than small molecule absorption
- more difficult to design oral administration of macromolecules
- macromolecules may have immunogenicity problems
