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Pharmacy > Chemistry of Drugs Week 9 > Flashcards

Chemistry of Drugs Week 9 Flashcards

1
Q

What are the first few letters of the greek alphabet?

A

alpha, beta, gamma, delta, epsilon, zeta

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2
Q

What is the carbon next to a carboxylic acid called?

A

alpha carbon

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3
Q

What is the carbon 2 carbons away from a carboxylic acid called?

A

beta carbon

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4
Q

What is the difference between a L-amino acid and a D-amino acid?

A

L has the NH2 group on the left, D has NH2 group on the right

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5
Q

What are the 2 most relevant side chain interactions?

A

salt bridges and hydrogen bonds

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6
Q

When will an amino acid be protonated?

A

when pH is lower than pKa

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7
Q

When will an amino acid be deprotonated?

A

when the pH is above the pKa

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8
Q

What is a hydrogen bond donor?

A

the molecule that provides a hydrogen atom in a hydrogen bond

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9
Q

What is a hydrogen bond acceptor?

A

a species that accepts a hydrogen atom in a hydrogen bond

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10
Q

Which amino acid side chains are hydrogen bond donors?

A

arginine, lysine, tyrosine (remember mesomeric effect)

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11
Q

Which amino acid side chains are hydrogen bond acceptors?

A

aspartic acid, glutamic acid

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12
Q

Which amino acid side chains are hydrogen bond donors OR acceptors?

A

aspargine, glutamine, histidine, serine, threonine

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13
Q

Which amino acid side chains undergo pi stacking?

A

phenylalanine, tyrosine, tryptophan, histidine

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14
Q

Which properties stabilise the internal structure of a protein and therefore stabilise drug-protein binding?

A

hydrogen bonds, salt bridges, pi stacking

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15
Q

What are the 4 amino acids that act as nucleophiles in chemical reactions at or near physiological pH?

A

cysteine, glutamic acid, aspartic acid, serine

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16
Q

When may amino acid sidechains be modified?

A

at the post-translational level by enzymes

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17
Q

How may amino acid sidechains be modified?

A

phosphorylation, methylation, acylation

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18
Q

What is monomethylation, dimethylation and trimethylation?

A

adding 1,2,3 methyl groups to NH2-R group

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19
Q

What are the 7 amino acids with aliphatic side chains?

A

alanine, glycine, isoleucine, leucine, methionine, proline, valine (a giant iguana likes many perfect vegetables)

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20
Q

What are the 3 amino acids with aromatic side chains?

A

phenylalanine, tyrosine, tryptophan

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21
Q

What are the 3 amino acids with acidic side chains?

A

aspartic acid, glutamic acid, cysteine

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22
Q

What are the 3 amino acids with basic sidechains?

A

arginine, histidine, lysine

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23
Q

What are the 4 amino acids with neutral but polar sidechains?

A

serine, threonine, aspargine, glutamine

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24
Q

What 3 factors does specificity rely on in biology?

A
  1. molecular shape
  2. chemical complementarity (interactions)
  3. spatiotemporal overlap
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25
Q

What can specific interactions involving protein be with?

A

small molecules (substrates or neurotransmitters) or large molecules (other proteins)

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26
Q

Where does specific protein-protein interaction occur?

A

on the protein surface

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27
Q

Where does specific protein-substrate interaction occur?

A

in the active site

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28
Q

What is an example of interactions in an active site?

A

class A beta-lactamases in antimicrobial resistance

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29
Q

What are b-lactam antibiotics?

A

most prescribed antibiotic class, includes penicillin

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30
Q

What do b-lactam antibiotics do?

A

target enzymes called pencillin-binding proteins (PBPs)

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31
Q

What do pencillin-binding protein do?

A

they are involved in the biosynthesis of the cell wall in gram-negative bacteria and are irreversibly inhibited by b-lactam antibiotics

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32
Q

What are b-lactamases?

A

a class of enzymes found in some gram-negative bacteria that hydrolyse the amide bond of the 4-membered b-lactam ring in antibiotics

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33
Q

define drug design

A

the identification of an API and its optimisation

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34
Q

What are the 3 main sources of drug molecules?

A
  1. natural sources
  2. semi-synthetic
  3. synthetic
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35
Q

define semi-synthetic drugs

A

drugs that was a natural source and has been modified a little in the lab

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36
Q

define synthetic drug

A

a drug made entirely in the lab

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37
Q

What are the advantages of semi-synthesis?

A
  1. parts of molecule may be too complex to make in the lab
  2. finite resources
  3. modification can result in better specificity
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38
Q

What are the advantages of synthetic drugs?

A
  1. reliable, NOT from finite source
  2. cost effective as from small abundant molecules
  3. quality control
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39
Q

What are the disadvantages of synthetic drugs?

A
  1. limited chemical space –> limited reactions we can do
  2. limited number of steps we can use
  3. identity of the target is unknown
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40
Q

define rational drug design

A

the process of rationally discovering the identity of an API using many techniques and methods

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41
Q

What are the 8 main steps in the drug development process?

A
  1. identify the disease
  2. isolate the protein involved in the disease
  3. preclinical testing
  4. find effective drug
  5. formulation
  6. scale up
  7. human clinical trials
  8. FDA approval
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42
Q

What are the 3 main ‘druggable’ targets?

A

enzymes, receptors, ion channels

43
Q

What makes a compound a drug molecule instead of an organic molecule?

A

it has properties that give a biological response

44
Q

What are 4 main properties of drug-like molecules?

A
  1. low molecular weight
  2. not too lipophilic
  3. not too hydrophilic
  4. presence of functional groups
45
Q

What are the 3 main properties of druggable targets?

A
  1. usually a protein
  2. leads to a biological response
  3. does not cause toxicity
46
Q

Which rule quantifies drug-like properties?

A

Lipinski’s rule of 5 -> a drug should have these properties

47
Q

define bioisosteres

A

structurally distinct molecular fragments (functional groups)

48
Q

What is the main reason some drugs fail to make it to market?

A

their chemistry means their efficacy is not high enough and simply do not have a biological effect

49
Q

How are genomics used in modern drug design?

A
  1. identify differences in mRNA in disease state
  2. can identify changes in the proteins
50
Q

What is high throughput screening?

A

a technique where large numbers of chemical compounds are rapidly tested for ‘activity’ against a chosen drug target

51
Q

What is virtual screening?

A

a process that uses computational methods to predict:
1. how a compound will bind to a target
2. what compounds might bind to a target (protein)
3.how strongly

52
Q

What is protein crystallography?

A

a technique that can reveal the 3D structure of a protein and its bound compounds through crystallisation

53
Q

What is combinatorial chemistry?

A

a set of techniques for producing large numbers of compounds in a short period of time, using defined reaction routes and a large number of start materials and reagents

54
Q

What is molecular modelling?

A

taking a molecule and putting it into a crystal structure of a drug and trying to minimise the energy to look for favourable and unfavourable interactions

55
Q

What are ADME techniques?

A

techniques that help model how a drug will likely act in the body (ADME)

56
Q

What are in vitro techniques?

A

using compounds on real tissue samples

57
Q

What are in silico ADME models?

A

computational methods that can predict compound properties that are important to ADME, such as LogP, solubility, permeability and cytochrome P450 metabolism

58
Q

define biological

A

a medicinal products which is produced by, or derived from, a living system or extracted from a biological source

59
Q

How are proteins different to small molecule drugs?

A
  1. much BIGGER
  2. synthesis by biochemical reactions within cells
  3. usually very hydrophilic
  4. not membrane permeable
60
Q

How do proteins active receptor signalling?

A

they bind to a ligand to cause a physiological response

61
Q

How are monoclonal antibodies produced?

A
  1. population of B cells (clones) are derived from a single ancestral B cell
  2. the antibodies are produced by plasma B cells in the blood in response to foreign substances
62
Q

How do proteins inhibit receptor signalling?

A

if binding of a ligand causes a harmful physiological effect, proteins may inhibit a receptor

63
Q

How do monoclonal antibodies prevent harmful physiological responses?

A

they bind to a receptor to stop another ligand binding to that receptor, so block a harmful reponse

64
Q

What is an example of a monoclonal antibody preventing a harmful response?

A
  1. Human Epidermal growth Factor Receptor (HER) monomers 1,2,3, and 4 are inactive
  2. HER2 is the preferred binding partner of the other three and is overexpressed in some cancers
  3. a ligand binding to HER2 forms a HER dimer and activates it causing cell growth
  4. Herceptin is a monoclonal antibody which binds to HER2 and stops it dimerising with another HER molecule
65
Q

What are the steps of production of therapeutic monoclonal antibodies? (hybridomas)

A
  1. immunisation
  2. separation
  3. fusion
  4. selection
  5. expansion
66
Q

immunisation

A

BALC/c mice are immunised with an antigen to stimulate antibody production

67
Q

separation

A

the antibody producing B cells are isolated

68
Q

fusion

A

B cells are fused with myelomas (cancer cells) to generate hybridomas and grow rapidly and produce antibodies

69
Q

selection

A

hybridomas producing many antibodies are selected

70
Q

expansion

A

expansion of the selected hybridomas to produce monoclonal antibodies

71
Q

Which two ways is therapeutic protein production scaled up?

A

bacteria and yeast, mammalian cells

72
Q

Which two methods are proteins irreversibly inactivated?

A

conformational changes and chemical changes

73
Q

How do proteins undergo irreversible conformational changes?

A

formation of the incorrect structure, which inactivates the protein, may also be by aggregation

74
Q

define aggregation

A

multiple protein molecules aggregating together into a large mass

75
Q

How may proteins be chemically changed and inactivated?

A

hydrolysis, oxidation, deamidation etc and peptide backbone may break and residues are modified

76
Q

What are operations that may denature or aggregate proteins?

A

pH, salt, freezing and thawing, contact with silicone oil

77
Q

How does silicone aggregate proteins?

A

the silicone is hydrophobic and the hydrophobic parts of the protein may be exposed to it

78
Q

What else can cause protein aggregation?

A

interfaces e.g. air-water, oil-water, hydrophobic surfaces

79
Q

define gene therapy

A

replacing a faulty gene with a functional one to cure a disease

80
Q

How does DNA mutation lead to disease?

A

leads to a faulty protein OR increased levels of a particular protein

81
Q

define RNA interference

A

when small pieces of RNA can stop protein translation by binding to the mRNA that codes for those proteins, decreasing expression of that protein

82
Q

What is small interfering RNA (siRNA)?

A

a short, double-stranded RNA molecule that can be used to target and degrade specific messenger RNA (mRNA) sequences

83
Q

How does siRNA act on mRNA?

A
  1. double stranded RNA is cleaved into a shorter segment
  2. helicase unwinds it into ssRNA
  3. ssRNA binds to complementary single strand of mRNA
  4. mRNA is cleaved and can no longer produce the proteins
84
Q

What is micro RNA (miRNA)?

A

a 22 nucleotide single stranded RNA (ssRNA) -> they are important in regulating gene expression

85
Q

What does miRNA do?

A

it does NOT cause mRNA destruction, but represses or destabilises target mRNA

86
Q

How can miRNAs be used to treat disease?

A

overexpressed miRNAs can be inhibited by anti-miRNAs, which are complementary nucleotides that bind to the miRNAs causing the issue

87
Q

How do RNA vaccines work?

A
  1. by introducing a piece of mRNA that corresponds to a viral protein, usually a small piece of a protein found on the virus’s outer membrane
  2. the body raises antibodies against them
88
Q

What is cell therapy?

A

a therapy that involves delivering cells to a patient to correct disease or damage

89
Q

What is CAR T cell therapy?

A

T cells are taken from the patient and engineering to have a special antigen receptor that can recognise an antigen on cancer cells and attack them

90
Q

What are the steps of CAR T cell therapy?

A
  1. remove blood from the patient to collect their T cells
  2. make CAR T cells in the lab
  3. grow millions of these cells
  4. infuse CAR T cells into patient
  5. the CART T cells bind to cancer cells and kill them
91
Q

What is gene editing?

A

permanently editing the genome to correct a defect or prevent expression of a specific gene, or activate a gene

92
Q

What are the 3 methods of gene editing?

A

gene disruption, gene correction, gene insertion

93
Q

What is tissue engineering?

A

replacing diseased or damaged living tissue with living tissues made for the needs of an individual

94
Q

What are the steps of tissue engineering?

A
  1. isolate cells
  2. expand cell number
  3. seed the cells on a suitable scaffold
  4. culture the cells under suitable conditions to generate a mature tissue
  5. implant the tissue into the patient
95
Q

What is 3D bioprinting?

A

printing tissues or organs to replace those damaged or diseased in a patient

96
Q

What is controlled drug delivery?

A

long-term release of a drug over a very long period of time

97
Q

How is controlled drug delivery done?

A

entrap the drug in a polymer matrix, and either:
1. the polymer slowly degrades and releases the drug
2. the polymer does NOT degrade, and the drug slowly diffuses

98
Q

What are 4 methods of targeted drug delivery?

A

antibody-drug conjugates, oncolytic viruses, enhanced permeability and retention effect, use of bacteria to fight cancer

99
Q

How does targeted drug delivery by antibody-drug conjugates work?

A

the monoclonal antibody binds to an antigen on the target cells and delivers a drug to that cell

100
Q

How does targeted drug delivery by oncolytic viruses work?

A

viruses selectively kill tumour cells

101
Q

How does targeted drug delivery by the enhanced permeability and retention effect?

A

blood vessels in tumours are leaky, but poorly drained, so macromolecule and nanoparticle drugs can accumulate in tumours, enhancing targeted drug delivery

102
Q

How does targeted drug delivery by the use of bacteria to fight cancer?

A
  1. oxygen-deficient (hypoxic) areas of tumours tend to be resistant to chemotherapy and radiotherapy
  2. obligate anaerobe bacteria can colonise in hypoxic areas of tumours
103
Q
A

Pharmacy (16 decks)

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