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Year 3 > Molecules Med Chem Exam > Flashcards

Molecules Med Chem Exam Flashcards

1
Q

Molecules with molecular weights of less than 900Da (prefer 500Da)

A

Small molecules

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2
Q

Generally macromolecules such as proteins, antibodies, and vaccines

A

Biologics

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3
Q

% of drugs that are biologics

A

27%

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4
Q

How many drugs are approved each year?

A

Approx 32

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5
Q

% of drugs that are small molecules

A

80-90%

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6
Q

3 things that define that shape of a molecule

A
  1. Bonding/hybridization
  2. Stereochemistry
  3. Conformation
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7
Q

If __________ isn’t the same on two molecules even if the shape is, they will probably not have the same effect on a target

A

Aromaticity

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8
Q

Alkyl side chains
Isolated heteroatoms
Tetrahedral

A

Sp3

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9
Q

Double bonds
Carbonyls
Heteroatoms NEXT to the double bonds are this hybridization
Planar

A

Sp2

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10
Q

Triple bonds
Linear

A

Sp

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11
Q

Do smaller or larger rings have more strain?

A

Smaller

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12
Q

Bonds form via sharing electrons (most common)

A

Covalent interaction

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13
Q

Don’t actually form a bond i.e. Van der Waals, H-bonds, Ionic interactions

A

Noncovalent Interactions

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14
Q

Covalent bond where the electrons are NOT shared equally

A

Polar covalent bonding

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15
Q

An atoms ability to pull electron density toward itself

A

Electronegativity

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16
Q

Carbonyl-like groups
Halogens
Alcohols
Amines
Withdrawing or donating?

A

Withdrawing

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17
Q

By resonance
Oxygen, sulfur, or nitrogen atom next to a double bond/aromatic system due to resonance
Must be Sp2!
Withdrawing or donating?

A

Donating

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18
Q

Accept electrons

A

Electrophile

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19
Q

Donates electrons

A

Nucleophile

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20
Q

Why is fluorine NOT and electrophile? (doesn’t accept electrons)

A

It’s present in many drug molecules. Has significantly stronger bonding with carbon than other halogens

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21
Q

Why are halogens, NOT fluorine, not good drug molecules?

A

Them accepting electrons from the nucleophile displaces good leaving groups to form new bonds. Easy reaction?

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22
Q

Sulfates and phosphates increase _________

A

Water solubility

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23
Q

Why are nitrogen atoms more electron donating to the carbonyl than oxygen atoms?

A

Because nitrogen atoms are less electronegative

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24
Q

Movement of electrons through multiple bonds of a molecule

A

Resonance

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25
Q

If one of the lone pairs is able to line up with the pi system of the double bond, it will ____________ resonance stability

A

Increase

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26
Q

Fat-loving
Non-polar (alkanes)

A

Lipophilic

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27
Q

Water-loving
Polar groups i.e. OH, COOH, and amines

A

Hydrophilic

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28
Q

The tendency of non-polar substances to aggregate in solution OR bind to a protein

A

Hydrophobic effect

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29
Q

Interaction between 2 non-polar groups (drug and receptor)
Forces out water molecules and breaks up H-bonding

A

Hydrophobic interaction

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30
Q

Aromatic ring on top of another one

A

Pi stacking

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31
Q

Pi stacking with different electron densities

A

Charge transfer interaction

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32
Q

Non-identical mirror images

A

Enantiomers

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33
Q

R direction

A

Clockwise

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34
Q

S direction

A

Counterclockwise

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35
Q

A measured property for each individual molecule
Doesn’t matter how many stereogenic centers are present of if they are R/S
ONLY matters how the molecule rotates plane polarized light

A

+/- (physical measurement)

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36
Q

Dextrorotatory

A

+

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37
Q

Levorotatory

A

-

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38
Q

For a molecule that has 3 points of contact with a target molecule, its enantiomer will have at most, only 2

A

Easson-Stedman Model

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39
Q

Is a single enantiomer always better?

A

No. One confirmation may go to the other and produce bad effects i.e. thalidamide

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40
Q

1.3kcal/mol ratio

A

10:1

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41
Q

2.6kcal/mol ratio

A

100:1

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42
Q

The _______ the energy, the more a molecule will exist in that conformation. (Does not always mean it is the most biologically active)

A

Lower

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43
Q

They do not have a role in the primary metabolism of the producing organism. No nutritional/structural function
Defensive
Possess desired chirality to exhibit biological activity

A

Secondary Metabolites

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44
Q

Natural products are meant to interact with _________ of growth/survival in organisms

A

Enzymes

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45
Q

The physical, chemical, biochemical, and biological properties of drugs, drug substances, or potential drugs and drug substances of natural origin, as well as the search for new drugs from natural sources

A

Pharmacognosy

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46
Q

% of drugs associated with natural products

A

50%

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47
Q

% of natural product cancer drugs

A

80%

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48
Q

% of natural product vaccines

A

21%

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49
Q

% of drugs that are synthetic

A

30%

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50
Q

Conversions of pure drug morphine

A

Codeine
Heroin
Methadone
Meperidine
Oxycodone

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51
Q

Conversions of pure drug Quinine (malaria)

A

Chloroquine
Mefloquine

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52
Q

Conversions of pure drug Taxol (cancer)

A

Taxotere

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53
Q

Conversions of pure drug lovastatin

A

Lipitor
Crestor
Pravastatin
Fluvastatin
Zocor

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54
Q

Natural products occupy a _____________ region of chemical space with synthetic compounds

A

Complementary

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55
Q

The relationship between man and his ambient vegetation. Medicinal uses of plants.

A

Ethnobotany

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56
Q

Increased biodiversity = Increased ___________

A

Chemical diversity

57
Q

Regions containing a high percentage of endemic plant species that are threatened with destruction due to primary loss of vegetation

A

Biodiversity Hotspots

58
Q

Profiling and screening of plant extracts for bioactive compounds with potential sources of new bio-based drugs

A

Bioassay guided fractionation

59
Q

End up with multiple fractions containing compounds separated by polarity

A

Partition scheme

60
Q

Newer technique to use versus partition scheme

A

Gene editing

61
Q

4 types of biologics

A

Antibody-based
Vaccines
RNAi
Gene Therapy

62
Q

Therapeutic genes packaged in a “delivery vehicle”
Viruses modified to carry human DNA
Cell makes new protein using new gene

A

Vector

63
Q

Stem cell and bone marrow transplants are examples of _________

A

Cell therapies

64
Q

Virus that permanently alters gene

A

Retrovirus

65
Q

Virus where DNA is never integrated, retains epigenetic signature

A

Adenovirus

66
Q

Immunity that is highly specific to a particular pathogen

A

Adaptive Immunity

67
Q

Immunity that is just recognition of foreign particles

A

Innate Immunity

68
Q

Natural passive immunity

A

Maternal

69
Q

Natural active immunity

A

Infection

70
Q

Artificial passive immunity

A

Antibody transfer

71
Q

Artificial active immunity

A

Immunization

72
Q

Antigen-presenting cells that digest most of the pathogen except antigens
Display antigens on their surface

A

Macrophages

73
Q

White blood cells in the immune system

A

Lymphocytes

74
Q

Cells that produce 100 million antibody proteins to combat foreign entities

A

B Cells

75
Q

Cells that are cytotoxic, meaning they can kill infected cells
Stimulate and direct activity of B cells

A

T cells

76
Q

Goal of vaccines is to…

A

Produce immunity effect (Lymphocytes, B cells, and T cells)

77
Q

A live or inactivated substance capable of producing an immune response OR anything that can be bound by an antibody

A

Antigen

78
Q

mRNA encoding for spike protein

A

mRNA/COVID-19 Vaccine

79
Q

Glycoproteins that are produced by antibody-secreting B cells
Designed to recognize specific antigens through production from only one type of B cell

A

Antibodies

80
Q

Antigen binding site

A

Paratope

81
Q

Produced through hybridoma tech
2 different cell lines fused together
The immortalized cells provide survivability and ability to be reproduced in culture
Provide increased SPECIFICITY for antigen recognition over polyclonal varients

A

Monoclonal Antibodies

82
Q

Monoclonal antibodies attached to biologically active drugs by chemical linkers with liable bonds
Facilitates the use of more toxic compounds

A

Antibody drug conjugates (ADCs)

83
Q

Benefit of ADCs

A

Discriminated between healthy and diseased tissues, can eliminate diseased cells without harming the healthy cells

84
Q

Substance that inserts itself into a cell and binds to its DNA

A

Intercalator

85
Q

Calicheamicin

A

An intercalator where antibodies are not recognized/metabolized in the same way that drugs are based on size
Trojan horse for the drug to get into the cells undetected

86
Q

3 Parts of PROTAC

A
  1. Target-binding ligand
  2. E3 ligase ligand
  3. Linker
87
Q

Advantages to traditional inhibitors

A

Catalytic activity
Complete removal of protein

88
Q

Role of E3 ligase in PROTAC

A

To ubiquinate (alter) another protein via post translational modification
Can mark for degradation

89
Q

What activates degradation in PROTAC?

A

Proteasome

90
Q

How much drug reaches the blood supply and becomes available to target tissue

A

Bioavailability

91
Q

What does a drug need to be able to do to get to the site of action?

A

Cross cell membranes and pass through blood supply

92
Q

Challenges in the GI tract

A

pH changes
Encounters enzymes designed to hydrolyze large molecules

93
Q

Does passive or active transport have structural specificity?

A

Active

94
Q

Taking in molecules via surrounding by the membrane and formation of a vacuole

A

Endocytosis

95
Q

Sending molecules out of cells

A

Efflux

96
Q

Passing between cells

A

Paracellular

97
Q

Physiochemical properties are dependent on a molecules’ _____________

A

Functional groups

98
Q

What compounds are much easier to purify and handle?

A

Crystalline

99
Q

MP and crystalline relationship

A

The more crystalline (ordered), the higher the MP

100
Q

Qualities of an ordered compound

A

High aromaticity
High planar
Low alkyl chains
Pi stacking
High IMF

101
Q

3 ways to manipulate MPs

A
  1. Salt formatin
  2. Introduction of symmetry
  3. Making derivatives with something that tends to crystallize i.e. phosphate derivative
102
Q

Lipinski’s Rule of 5

A

Solubility is key
Mol weight of < 500
LopP < 5
No more than 5 H bond donors
No more than 10 H bond acceptors

103
Q

Lipinski’s rule only works on which type of molecules?

A

Synthetic

104
Q

Rule of 3

A

Scaled back Lipinski’s rule
Mol weight < 300
Up to 3 H bond donors
Up to 3 H bond acceptors
LopP less than or equal to 3

105
Q

Any single, non-ring bond attached to a non-terminal, non-hydrogen atom

A

Rotatable bond

106
Q

What bond has high barrier to rotation?

A

C-N nitrile bond

107
Q

A more rigid molecule will have _________ polar surface area and will not be as susceptible to promiscuous binding to metabolic enzymes or transporters

A

Lower

108
Q

The __________ the # of rotatable bonds, the better oral bioavailability

A

Lower

109
Q

Rigidity in relation to bioavailability

A

More rigid, higher bioavailability

110
Q

If a compound is too ________ it may bind too strongly to plasma protein and free blood [ ] will be too low to produce good effect. Why?

A

Lipophilic; It will be distributed into the lipid bilayers and be unable to reach the inside of the cell

111
Q

Lipophilicity in relation to excretion and metabolism

A

High lipophilicity = High metabolism and excretion

112
Q

Measure of solubility; estimates how well a drug will pass through a biological system by stimulating membrane and blood

A

Partition coefficient

113
Q

LogP in relation to water solubility

A

The smaller the LogP, the more water soluble the molecule is

114
Q

Why do we want high lipophilicity?

A

High lipophilicity means that it will activate P450, which increases metabolism. Increased metabolism means increased clearance. This overall decreases the lipophilicity, which is good

115
Q

Why do we want more heteroatoms for water solubility?

A

More heteroatoms means more opportunities to H bond, which increases polarity and water solubilty

116
Q

LogP only works for __________ molecules

A

Neutral

117
Q

Drugs are absorbed ___________ when they are un-ionized due to lipophilic membrane

A

Passively

118
Q

The effective lipophilicity of a compound at a given pH, and is a function of both the lipophilicity of the un-ionized compound and the degree of ionization

A

LogD

119
Q

If a compound can ionized, then the observed partitioning between water and octane will be _____ dependent

A

pH

120
Q

Do salts have high or low water solubility?

A

High

121
Q

A measure of stability of the deprotonated species

A

pKa

122
Q

Only need to use if pKa is within 2 units of pH; otherwise can assume that it exists in only one of them

A

Henderson Hasselbauch Eqn

123
Q

What kind of groups would increase drug solubility?

A

Groups that can be ionized (acids and amines) and introducing more heteroatoms capable of H bonding

124
Q

Why are the ester and amide significantly LESS withdrawing than the aldehyde and ketone?

A

Because the heteroatoms in esters and amides donate electron density back into the carbonyl making it less withdrawing

125
Q

Active site consists of hydrophobic substrate binding domain containing a heme prosthetic group
Radical mediated process with Fe intermediate
Binds O2 and substrate

A

CYP450

126
Q

Most of the oxidations we cover in class are ________________

A

Hydroxylations

127
Q

Drugs and other compounds that come from the outside (exogenous) that an organism encounters. Metabolism will eliminate the harmful/useless ones

A

Xenobiotics

128
Q

Primary site of metabolism in the body

A

Liver

129
Q

Denotes the site of radioactive label in a molecule, typically a weak B emitter
Radioactive atoms can be introduced through chemical synthesis or through feeding experiements for some NPs

A

Radiolabeling

130
Q

2 tools to ID Metabolites

A

NMR
Mass spec

131
Q

Involved in the metabolism of approx 50% of drugs
It’s rate of transcription is increased by certain drugs
Mediated by PXR
Ability to accommodate a wide variety of substrates in active site

A

CYP3A4

132
Q

What is CYP3A4 made of?

A

Erythromycin and ketoconazole

133
Q

Resonance relationship to resistance

A

Higher resonance = stronger resistance to nucleophilic attack because it doesn’t want to give up lone pairs

134
Q

Omega P450 binding and benefit

A

Binds to terminal carbon and is less sterically hindered

135
Q

Omega-1 P450 binding and benefit

A

Binds to least sterically hindered, non-terminal carbon, is more stable/less energetic

136
Q

Why do N, O, and S dealkylation fall apart after hydroxylation?

A

It is unstable and can easily break apart

137
Q

Do amides or esters hydrolyze slower and why?

A

Amides hydrolyze slower because they are resonance stabilized, meaning they want to hold on to their electrons more, making the process take longer

138
Q

The linking of highly polar groups to a drug in order to facilitate excretion

A

Conjugation

139
Q

Why is glucuronidation so prevalent?

A

UGT’s are located along the ER of the liver and epithelial cells of the intestine. As such, it is situated near many CYP450s so more metabolism of them

Year 3 (7 decks)

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