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Medicinal Chemistry > Unit 2 > Flashcards

Unit 2 Flashcards

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1
Q

What are Natural Products?

A

Compounds produced by organisms that provide them with an evolutionary advantage (protect them from attacks, predators, etc.)

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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
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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
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4
Q

Natural Product Discovery (4)

A

Extraction
Fraction
Bioassay screening
Bioactive Natural Products

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5
Q

Requirements for Field Collection

A
  • Easily collected
  • Get them back
  • Easily stored
  • Can be grown in lab
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6
Q

Biopiracy

A

The stealing of biodiversity or indigenous knowledge (take back to your own country and make money from it)

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7
Q

Difficulties Obtaining Natural Products

A
  • Need a lot
  • Lots of wasted solvents and chromatography
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8
Q

Chromatography/Isolation

A
  • stationary phase (solid, can be liquid)
  • mobile phase - solvents or buffers (liquid, can be gas)
  • scale
    -dry
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9
Q

Testing for bioactivity

A
  • must be easily tested
  • specific targets
  • phenotype
  • scale
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10
Q

Structure Elucidation

A
  • solve structure by NMR or X-ray crystallization
  • can use mass spectrometry, UV, IR
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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

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12
Q

Infrared Spectroscopy measures

A

functional groups and bond flexibility

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13
Q

Mass Spectrometry measures

A

molecular weight and molecular formula

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14
Q

Ultraviolet Spectroscopy measures

A

bond conjugation and aromaticity

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15
Q

Genomics

A

DNA sequencing and bioinformatics have allowed the mapping and annotation of organism genomes and BGCs

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16
Q

Metabolomics

A

use of large LC-MS/MS data sets gas allowed comparative analyses of produced compounds across organisms

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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

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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”)

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19
Q

Discovering Antibiotics from Genomes

A

Bacteria BGCs are studied in silico on the computer - bioinformatics

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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
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21
Q

Bioinformatics to Predict Structures

A

BGCs are used to predict function and using bioinformatics online in databases, the structure can be predicted

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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
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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
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24
Q

Organic molecules used to build natural products (6)

A
  • acetates
  • sugars
  • amino acids
  • isoprene
  • shikimate
  • lipid
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25
Q

Ribosomally Encoded and Post-Translationally Modified Peptides (RiPPs)

A
  • peptide natural products
  • sequence found in genome
  • found in plants and fungi
  • proteases free the sequence from a larger one
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26
Q

Non-ribosomal Peptides

A
  • production encoded by non-ribosomal peptide synthetases (NRPS)
  • often contain non-proteinogenic amino acids
  • can hybridize with polyketide natural products
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27
Q

Polyketides

A
  • 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
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28
Q

Terpenes

A
  • composed of isoprene units (5 carbon structure)
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29
Q

alkaloids

A
  • basic nitrogen containing compound (nitrogens)
  • bitter
  • bioactive
  • many known toxins are alkaloids
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30
Q

Lead Compound

A

a compound that has the desired effect on a drug target and is the starting point for designing a new drug

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31
Q

Chemical Synthesis of Drugs

A
  • use molecule with know drug target
  • modify to increase potency, efficacy, and bioavailability
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32
Q

Arylomycin

A
  • natural product originally isolated from an actinobacteria off the coast of Nigeria
  • inhibits signal peptidase in gram + bacteria and not gram -
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33
Q

Drug Leads

A
  • natural products
  • natural ligands
  • enzyme substrates (kinases)
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34
Q

Biological Screening

A

Testing tens of thousands of drugs to determine what can bind to desired target using natural product libraries and synthetic chemical libraries

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35
Q

Natural Product Libraries

A

can use purified compounds or natural product extracts - usually more diverse library

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36
Q

Synthetic Chemical Libraries

A

Many Pharma companies have the same massive synthetic libraries that they screen for drug leads

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37
Q

High Throughput Screening

A
  • usually done robotically
  • used to test on a target and see what hits
  • does not tell pharmacokinetics
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38
Q

What do we want out of our drugs?

A
  • Interact with target (potency, efficacy, and selectivity)
  • Reach target (selectivity and bioavailability)
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39
Q

Bioavailability

A

proportion of the drug that enters circulation and can therefore have an effect on the target

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40
Q

Importance of hydrophobicity and hydrophilicity…

A
  • 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)
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41
Q

Lipinski’s Rule of 5

A

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)

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42
Q

Why use a smaller compound?

A

if too big, it is less likely to passively diffuse across membranes
- bigger usually means less soluble
- bigger = harder to synthesize

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43
Q

LogP

A

how hydrophobic is the compound
>1 hydrophobic
<1 hydrophilic

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44
Q

Exceptions to Lipinski’s rule of 5

A

~mostly just guidelines~
many natural products break these rules but in general these rules assume passive diffusion and determine bioavailability

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45
Q

Privileged Structures

A
  • can break Lipinski’s rules
  • can be capable of binding to many targets
  • often aromatic rings with side chains
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46
Q

Toxicophoric Groups

A
  • groups that cause toxicity
  • include overly electrophilic groups, metal chelating groups, metabolized into electrophilic groups
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47
Q

False Positive in Screening

A
  • compounds that aggregate on drug targets without binding specifically (no specificity)
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48
Q

PAINS compound

A

Pan-Assay Interference Compounds
- quinones, catechols, enones, curcumin

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49
Q

Fragment Based Screening - De Novo Synthesis

A
  • looks for several small molecules that bind and then links them
  • use NMR or X-ray Crystallography to identify fragments that bind to target
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50
Q

Virtual Screening

A

Use computers, interactions between targets and digital libraries can be modeled
- complex computational tools

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51
Q

Targets Computed

A
  • Protein Data Bank
  • crystallized structures
  • computed structures using software
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52
Q

Digital Compounds

A
  • line structure can be produced by digital libraries
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53
Q

Computational High Throughput Screening

A

Software used to match 3D compound shapes into protein active sites

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54
Q

Pharmacophore

A
  • Active Center of a Drug
  • most important interactions between drug and target
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55
Q

Modify and Optimize the compound

A
  • add functional groups
  • remove functional groups
  • open rings
  • close rings
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56
Q

If modifications result in lower potency…

A
  • most of the molecule is the pharmacophore (important)
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57
Q

Add groups to…

A

optimize pharmacokinetics and stabilization of pharmacophore

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58
Q

Why modify?

A
  • change potency
  • change selectivity
  • change activity
  • can make it easier to make
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59
Q

Structure-Activity Relationships (SAR)

A

structure is directly related to activity

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60
Q

Homologation

A
  • increases lipophilicity by adding CH2
  • better passage through membranes
  • more flexibility
61
Q

Ring Formation

A
  • increase lipophilicity and constrain flexibility
  • better bioavailability (more soluble)
  • constrain pharmacophoric groups into optimal positions
62
Q

Bioisosterism

A
  • swap functional groups but maintain or amplify biological activity/interactions
  • alleviate toxicity/off target effects
  • decrease susceptibility to metabolism
  • potentially simplify synthesis
63
Q

Lipophilicity Effects on PK and PD

A
  • high lipophilicity = poor oral absorption and easy metabolism
  • low lipophilicity = no passive diffusion
64
Q

Drug Action Depends on:

A
  1. drug has to reach site of action (PK)
  2. drug has to interact with the site of action (PD)
65
Q

Blood-brain barrier

A

surrounds capillaries of circulatory system in brain
- protects CNS from undesirable polar molecules in blood
- difficult to pass

66
Q

Special Membranes to cross

A
  • blood-brain barrier
  • blood-testes barrier
  • blood-thymus barrier
  • blood-ocular barriers
67
Q

To pass blood-brain barrier…

A

need little branching
few rotatable bonds
few H-bond acceptors
more aromaticity
more H-bond donors
mor liphophilic

68
Q

Fatty Acid Chain Branching

A

alters activity and binding

69
Q

Conformational Restraints

A
  • increase potency
  • decrease rotation
  • increase bioavailability
70
Q

Bioisosteres

A

substituents or functional groups with chemical/physical similarities that produce similar biological effects (LOOK AT SLIDES)

71
Q

Isostere Replacement Effects

A
  • structural
  • receptor interactions
  • pharmacokinetics
  • metabolism
72
Q

Notable Isosteres

A
  • Fluorine replacing Hydrogen
  • Bicyclo[1.1.1]pentane in place of phenyl
  • oxetane in place of carbonyl
73
Q

Peptidomimetics

A

compounds that mimic peptides without undesirable pharmacokinetic characteristics

74
Q

Psuedopeptides

A

type of peptidomimetic where peptide backbone is changed but R groups are maintained

75
Q

Drug Discovery/Development Cycle

A
  • identify lead via bioassays
  • make modifications/ predictions for new structures
  • synthesize new compounds
  • bioassay
  • make modifications/predictions
  • repeat
76
Q

Drug Resistance

A

when a formerly effective drug dose is no longer effective

77
Q

Drug Tolerance

A

adaptation by the body to the drug dose, which requires higher doses to achieve same effect

78
Q

How does resistance occur?

A
  1. Natural Selection
  2. Genetic Transfer
79
Q

Natural Selection

A
  • random mutation in populations
  • treatment with drugs selects for resistant individuals to proliferate
80
Q

Genetic Transfer

A
  • plasmid encoded resistance elements
  • mostly in ineffective agents
81
Q

Nosocomial Infections

A

resistant infections commonly in hospitals form overuse of antibiotics

82
Q

Methods of Gene Transfer (3)

A
  1. transduction
  2. transformation
  3. conjugation
83
Q

Transduction

A

phage transfers genetic DNA

84
Q

Transformation

A

Take up of environmental DNA after other cell dies

85
Q

Conjugation

A

DNA transfer between 2 microbes

86
Q

Mechanisms of Drug Resistance (8)

A
  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
Q

Altered Target

A
  • 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
Q

Overproduction of Target

A
  • producing more of the target than the treatment can bind to
    overcome this by:
  • increasing dosage but careful of toxicity
89
Q

Overproduction of Substrate/Ligand

A
  • more natural ligand to bind with target so drug cannot bind and unable to work
90
Q

Increased Drug-Destroying Mechanisms

A
  • increase mechanisms that inactivate the drug or metabolize drugs
91
Q

Decreased Drug-Activating Mechanism

A
  • 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
Q

Upregulation of Alternative Pathways

A
  • Drug blocks one pathway so other pathways for product production are increased
93
Q

Reversal of Drug Action

A

the drug will bind but the repair enzymes will remove it and reverse the effects of the drug

94
Q

Altered Distribution to Site of Action

A
  • modifications to cell membrane to prevent passive diffusion of the drug
  • reorganize charges
  • or pumped out of the cell after it enters
95
Q

Drug Synergism and Overcoming Resistance (5)

A
  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
Q

Area Under the Curve (AUC)

A

total drug exposure, integration for area under the curve

97
Q

Cmax

A

highest concentration of drug in blood, must be below toxicity threshold

98
Q

T1/2

A

half-life; time it takes for drug to lose half its maximum concentration
- depends on metabolism

99
Q

Cmin

A

lowest concentration of drug in blood
- point where drug can be readministered

100
Q

How can drugs be administered?

A
  • 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
Q

First Pass Effect

A

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
Q

Food alters Absorption

A

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
Q

Distribution

A

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
Q

If the drug is more _____, it is free in the plasma during distribution and excreted via urine.

A

hydrophilic

105
Q

If the drug is more _____, it is bound to proteins during distribution and excreted via feces.

A

hydrophobic

106
Q

Drug Distribution was monitored via

A
  • isotope labeling and tracking
  • animal models
  • stable isotope labeling (more common now)
107
Q

Modeling Drug Distribution

A
  1. One-compartment model
  2. Two-compartment model
108
Q

One-compartment model

A
  • drug is absorbed and immediately reaches systemic distribution
  • useful for intravenous
109
Q

Two-compartment model

A
  • drug is absorbed and distributed to certain organs first, before reaching systemic distribution
  • circulation = one compartment
  • tissues = second compartment
110
Q

How to Direct Drugs to Targets

A

monoclonal antibody drug conjugates

111
Q

Metabolism of Drugs occurs…

A
  • by enzymes
  • primarily In the liver
112
Q

Excretion of drugs…

A

through liver and feces (more hydrophilic)
through kidneys and urine (more hydrophobic)

113
Q

Phase 1 of Metabolism

A

Mask/Unmask Functional Group
- oxidation, reduction, hydrolysis
- makes more polar
- handle for phase 2
- changes functional group –> can inactivate

114
Q

Phase 2 of Metabolism

A

Increases hydrophilicity through conjugation reactions
- makes drug more polar and charged
- bulky conjugates to make inactive
- hydrophilic

115
Q

Phase 1 Oxidative Enzyme

A

Cytochrome P450s (heme containing)
Flavin Monooxygenases (FAD)
Alcohol/Aldehyde Dehydrogenase (metabolize alcohols)

116
Q

Phase 1 Metabolism Oxidation Reactions (7)

A

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
Q

Phase 1 Metabolism Reduction Reactions

A

decreasing the oxidation stare or removing oxygens/double bonds
1. carbonyl reduction
2. azo reduction

118
Q

Aromatic Hydroxylation

A
  • done by CYP450s
  • OH added to aromatic rings
119
Q

Alkene Epoxidation

A
  • done by CYP450s
  • remove double bond in rings to add alcohols
120
Q

Alpha Carbon oxidation

A

Carbon immediately adjacent to sp2 hybridized carbon
- done by CYP450s
- OH added to alpha carbon

121
Q

omega oxidation

A

oxidation of the terminal carbon in an aliphatic chain

122
Q

omega-1 oxidation

A

oxidation of penultimate carbon in aliphatic chains

123
Q

Aliphatic Oxidations

A
  • done by CYP450s
  • terminal carbons become alcohol become aldehyde become carboxylic acids
124
Q

primary amine oxidation

A

If N is oxidized, Nitro group is formed
If C is oxidized the deamination occurs

125
Q

secondary amine oxidation

A

If N is oxidized, N-oxide is formed
If C is oxidized, N-dealkylation occurs

126
Q

tertiary amine oxidation

A

If N is oxidized, then N-oxide is formed
If C is oxidized then N-dealkylation occurs

127
Q

carbon-oxygen oxidation

A

esterases remove ester and add alcohol

128
Q

alcohol/aldehyde oxidation

A

alcohol/aldehyde dehydrogenases or CYP450s
- forms aldehyde (from alcohol) or carboxylic acid (from aldehyde)

129
Q

Carbonyl Reduction

A

aldo-keto reductases
makes C=O to alcohols

130
Q

azo reduction

A

azoreductases
- N=N becomes split with 2 primary amines

131
Q

Carboxylation Reactions

A
  • adding carboxylic acid from dissolved CO2 to amines
132
Q

Hydrolytic Reactions

A

esterases and amidases
- esters to alcohols `

133
Q

Drug-Drug Interactions (bad)

A
  • due to metabolizing enzymes
  • increases or inhibiting metabolizing enzymes alter circulation time like grapefruit juice
134
Q

Phase 2 Modifications

A
  • glucuronic acide
  • sulfate
  • amino acid
  • glutathione
135
Q

glucuronic acid conjugation

A
  • add glucuronic acid to drug
136
Q

Phase 2 Conjugations

A

add polar, bulky groups to deactivate by making more hydrophilic

137
Q

sulfate conjugation

A
  • add sulfate to drug
138
Q

amino acid conjugation

A
  • add amino acid to drug
  • usually glycine and glutamine
139
Q

glutathione conjugation

A
  • add glutathione
  • adds to epoxides, esters, quinones, sulfoxides
140
Q

prodrugs

A

a pharmacologically inactive compound that is converted to the active drug by a metabolic transformation
- usually activated by cleaving an ester

141
Q

Absorption and Distribution of a Prodrug

A

modify drug to make it easier to absorb or move through circulation
- can help pass specialized barriers

142
Q

Prodrugs are good because they …

A
  • decrease toxicity
  • increase selectivity
  • taste better for oral administration
  • ex: acyclovir
143
Q

Co-drugs

A

two synergistic drugs that are physically linked to be delivered together
- helps to bind them together to reach target at the same time

144
Q

Macromolecular Delivery systems

A
  • reach desired target
  • sugars (syrups)
  • fats (liposomes)
  • proteins (antibodies)
  • other polymers - vinyl alcohol, amino acids, etc.
145
Q

Antibody drug conjugates

A

bind to drug and direct drugs to particular target by binding to specific antibody target

146
Q

Nanoparticle Delivery

A
  • organic (liposomes) or inorganic (metals)
147
Q

dendrimers

A

branched and functionalized polymeric structures that provide scaffolding for drug molecules

148
Q

Pros of Macromolecular Delivery

A
  • 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
Q

Cons of Macromolecular Delivery

A
  • macromolecular absorption is lower and more complicated than small molecule absorption
  • more difficult to design oral administration of macromolecules
  • macromolecules may have immunogenicity problems

Medicinal Chemistry (2 decks)

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