Revision Flashcards
(115 cards)
1
Q
Define chiral carbon
A
A carbon atom that is bonded to 4 different groups
2
Q
Define enantiomer
A
A pair of optical isomers
3
Q
Define racemic mixture
A
50:50 mixture of enantiomers
4
Q
Impact chirality has on how drug behaves
A
Enzymes are chiral. Different enzymes will exhibit different enatioselectivities toward a common racemic micxture. One enantiomer is a preferred substrate.
5
Q
Which amino acids are positively charged
A
lysine
arginine
histidine
6
Q
Which amino acids are negatively charged
A
aspartate glutamate
7
Q
Cation-pi interaction amino acids
A
tryptophan
tyrosine
phenylalanine
8
Q
Bioisostere
A
exchange of an atom or group of atoms with another, broadly similar atom or group of atoms
9
Q
Isostere
A
Atoms or groups of atoms which have the same number of valence electrons and which have chemical or physical similarities.
10
Q
Drugs that enter the CNS should have logP
A
> 2
11
Q
Substituents that are σ < 0
Substituents that are σ > 0
A
electron donating
electron withdrawing
12
Q
Which proteins are important in development
A
Transporters
Receptors
Enzymes
13
Q
Similarities between proteins
A
Protein-based
Interactions with LMW
14
Q
Differences between proteins
A
Enzymes - LMW chemically transformed
Receptors - LMW binds to receptor to pass message and leaves unchanged
Transporters - LMW compound binds to transporter and moved into cell unchanged
15
Q
Which amino acid is an imino acid
A
Proline has a secondary amino group
16
Q
Sulfur-containing AA
A
Cystine
Methionine
17
Q
Hydrophilic anino acids
A
Serine
Threonine
18
Q
Amide bond characteristics
A
Some double bond character
Rigidity
Planar
Resonance
19
Q
Which AA at protein surface
A
Polar amino acids
20
Q
Which AA interior
A
Non-polar and excludes water
Valine, alanine, isoleucine and leucine
21
Q
Know how a GPCR works
A
1) Agonist binds to receptor which induces change in receptor association
2) GDP is released and replaced with GTP
3) Alpha and beta gamma subunits dissociate
4) Alpha and beta gamma modulate the activity of intracellular
22
Q
What do full agonists of B1 also use outside of asparagine and aspartate
A
Two conserved serine
23
Q
Stoichiometry of NET
A
One Na+ and Cl- per noradrenaline
24
Q
What type of transporter is NET
A
Secondary active
25
Describe steps of mutagenesis
1. Design primer that introduce mutation
2. Amplify mutation-containing DNA using PCR
3. Remove methylated parental bacterial DNA
4. Confirm mutation using sequencing
5. Express protein using transfect cells or oocyte injections and check function
26
How does his-tag work
1. String of 8 histidine fused to end of protein
2. Tag forms coordination bond with Ni-NTA matrix within a column
3. Flush
4. Imidazole used to released his-tag bound proteins which competes for coordination sites
5. His-tag removed using thrombin digest
27
For crystals, a protein must be
Pure
Stable
Soluble
Large quantities
28
What is ITC
Measures thermodynamic parameters in solution with a ligand and protein
29
What binding assay is used
Fluorescence based assays using intrinsic e.g. tryptophan or introduced F
30
What is Gltph
Bacterial homologue to EAAT2
31
What can liposome reconstitution be used for?
Radiolabelled uptake and fluorescence assay (SPQ quenched)
32
What information is gained from crystallogaphy
Binding of substrate vs competitive inhibitor (TBOA)
| Proposed mechanism of transport
33
What did x-ray crystallography reveal about sialic acid
1. Sialic acid has an imperfect chair structure
2. Trigonal planar geometry at carboxylic acid
3. Carboxylic acid is crucial for interaction with arginine residue
34
What is the life cycle of the flu
1. Neuraminidase hydrolyses terminal sialic acid residues to allow virus access to the cell membrane
Haemagglutinin recognises sialic acid residues on cell surface
2. Virus is endocytosed into endosome.
3. Collapse causes release of (-)ssRNA and RNA polymerase
4. (-)viral ssRNA copied via polymerase to (+)RNA exits nucleus and acts as mRNA for translation of viral proteins. Copies of (-)ssRNA are also produced in the nucleus and exported into cytoplasm
5. Capsid proteins self-assemble to encapsulate (-)viral RNA
6. Budding takes place for exit
35
Balance of activity between NA and HA
If NA activity is too high, the recognition between HA and sialic acid-terminated cell surface receptors is decreased – virion entry is hindered.
If NA activity is too low, then the level of HA-sialic acid recognition is above the threshold that would allow for easy exit and the ready exit of the virion is compromised
36
What is the development pathway of neuraminidase inhibitors as antiviral agents
1. Create analogue of sialic acid
2. Sialic acid has imperfect chair structure
3. Carboxylic acid crucial to interaction with arginine residue
4. Transition state has trigonal planar geometry at carboxylic acid
37
What are important intermolecular interactions between sialic acid or zanamivir and neuraminidase
Carboxylic acid groups held by 2 invariant arginines
38
What is the nature of second generation antivirals
Ethyl ester used as prodrug instead of carboxylic acid which is not orally active
Change from 4-guanidino group to 4-amino group
Removal of ring oxygen for easier synthesis
Position of double bond changed which affected activity
39
Briefly describe the general structure of DNA
Polar backbone
| Hydrophobic interactions between heterocycles
40
What structural aspects of DNA make it a useful drug target
- Nucleobases: hydrophobicity, presence of heteroatoms, level of unsaturation, specificity of hydrogen bonding, pi-stacking
- Anionic phosphate backbone .- readily hydrolysable ester linkages
- Major minor groove
41
What features would you include in the design of a DNA intercalating compound
-Contain planar or heteroaromatic features that slip between the layers of base pairs. AROMATICS
Drugs held in place by VDW with base pairs above and below
- Charged groups which can interact with phosphate backbone
42
Name two drugs that target DNA
Proflavine
| Quinine - intercalator
43
Name a chain terminator and describe the mechanism of action
Aciclovir
Acts as false substrate by mimicking nucleotide triphosphates
Must be able to interact with template: guanine base to pair with cytosine
Added to chain
Chain is unable to extend as 3' hydroxy group is absent in ribose
44
How is cell uptake of cisplatin controlled
Differential in extracellular and intracellular [Cl-]
| High plasma [Cl-] mitigates against aquation
45
How does cisplatin bind to DNA
Aquation forms cationic metabolite to react with negatively charged polynucleotide.
Covalently to DNA via the Pt atom which lies in the major group
Binding to N7 atom of guanine
46
What is the most prevalent Pt-DNA lesion
Intrastrand adducts form mostly
| Causes significant distortion
47
What are high-mobility group proteins
Recognise Pt-DNA adducts and structure is further distorted and repair inhibited
48
What is heavy metal poisoning
Dimethylmercury
| Impairs CNS
49
How does chelation therapy work
Chelator competes with target binding sites for metal
50
What are some chelating agents in use
Dimercaprol for As, Hg, Pb
| EDTA for Ca
51
What are some endogenous chelators
Metallothionein
52
What does the ideal chelator have
```
Ligand groups specific to the metal
Polydentate
Forms stable metal-complexes
Easily excreted
Non-toxic
```
53
Name a soft donor
hard donor
soft acid
hard acid
Sulfur
Oxygen
Cu +
Fe 3+
54
What is a protein therapeutic vs protein biologic
> 5500 Da
Biologics include lipids and nucleic acids
Both are products produced by biologic expression system manipulated using genetic engineering
55
5 key advantages of protein therapeutics over SMD
1. SMD cannot mimic highly specialised functions
2. Well tolerated and unlikely to generate immune response
3. Avoids gene therapy
4. Faster approval
5. Easier patent protection
56
Classify protein therapeutics into categories and give an example
- Enzymatic/regulatory: Factor VIII
- Targeting: monoclonal antibodies rituximab
- Protein vaccines: HPV
- Protein diagnostics: TB
57
Challenges of delivery of protein therapeutics
Purity and potency across batches
Protein solubility and stability
Route of administration
Stability in circulation
58
Choice of production system for recombinant DNA depends on
Size
Properties
Modification
Humanisation
59
What are some production systems for recombinant DNA
```
Bacteria
Yeast
Mammalian cells
Transgenic animals
Transgenic plants
```
60
Describe an approach to protein modification that has been used to improve half-life
PEGylation or attachment of albumin
| Use an analogue i.e. GLP-1 analgoue
61
Advantages that recombinant production has over isolation and purification from animal source
- Exact product of human gene
- High specific activity
- Decreased chance of immunological rejection
- Efficient and inexpensive production
- Scalable
- Allows modification or gene variant with improved function
62
What system is likely best for production of a small cyclic peptide that is a novel treatment for chronic pain
Will E.coli allow for disulfide formation in cyclic peptide?
| More likely correctly folded and disulfide formed in yeast
63
How to improve therapeutic efficacy? Example
Improve uptake into cells by addition of sugar residues e.g. glucocerebrosidase to change glycosylation profile
64
What are key features of therapeutic proteins that must be monitored for bioequivalence
1. Post-translational modifications
2. Three-dimensional structures
3. Protein aggregation
65
What is drug specifcity
Only one effect within the biological system e.g. antimicrobial in humans where target protein is lacking
66
What is meant by drug selectivity
Preferential activity on one target e.g. selection of one isozyme over another similar enzyme
67
What is different between target identification and target validation
Target identification means protein X is identified as altered in disease state. Target validation is confirmation that protein X is central to the disease and modulation will treat the disease
68
What are advantages and disarvantages of natural compounds as leads
Adv: Unique structures not discovered and can be patented
Dis: Complex mixture of large macromolecules makes it difficult to identify and determine structure + subsequent chemical synthesis
69
What are four types of in vitro assay
Affinity – ligand’s binding to the enzyme or receptors
Activity – degree of enzyme inhibition
Efficacy – partial or full agonist
Functional – anti-inflammatory activity
70
What is the rule of 3 for fragment-based lead discovery
```
MW < 300
No more than 3 HBD or HBA
cLogP = 3
No more than 3 rotatable bonds
Polar SA = 3 X 20 A
```
71
What is Lipinski's Rule of 5
1. No more than 5 HBD
2. No more than 10 HBA
3. MW < 500
4. Calculated log P < 5
5. Exemptions: active transport
72
What are other important aspects of a lead compound
Free of toxic functional groups
Number of chiral centres
Ease of synthesis
Patent potential
73
Which residues to protein kinases phosphorylate in humans
(Ser, Thr) and Tyr
74
What is the main difference between Type I and Type II kinase inhibitors
Type 1 - bind active phosphorylated conformation of the kinase
Type 2 - recognise inactive unphosphorylated conformation
75
What are some kinase targets in cancer therapy
Kinases not controlled by normal regulation
Kinase where inhibition generates synthetic lethal prototype
Kinase expressed on tumour or surrounding tissue
76
Example of kinase inhibitor in cancer
EGFR signalling
Excessive kinase activity = uncontrolled cell proliferation
Gefitinib (Type I)
77
Example of kinase inhibitor in inflammation
Adalimumab
| JAK
78
What is the structural basis of kinase (4)
ATP binding in deep cleft between lobes
Adenine forms H-bonds with hinge between lobes
Ribose and P3 bind in hydrophilic channel
Conserved activation loop which can adopt multiple conformations
79
Advantages of polypharmacy
1. Targets several pathways
2. Less probability for drug resistance
3. Combination therapy with one drug
80
Give Lipinski's 5 again
xd
81
Disadvantages of Lipinski
Can restrict creativity
| Exceptions for MW, protein hijacking
82
Define prodrug
Compounds which themselves are inactive but are converted to an active drug in the body
83
Identify enzymes involved in prodrug transformations
Esterase
| N-demethylase
84
Example of prodrugs
Oseltamivir
Enalapril
Aspirin
85
Explain use of carboxylic acid protecting groups
Carboxylic acid is ionised at physiological pH and will not readily cross the gut wall cell membrane
86
Which drug uses a decarboxylase and Trojan Horse
Levodopa
| AA analogue which uses non-specific AA proteins
87
What is the difference between combinatorial synthesis and parallel synthesis
Combinatorial synthesis - mixtures of different compounds in a single vessel
Parallel synthesis - single product in each vessel
88
Why do we N-protect the amino acid
A protecting group knocks out the potential reactivity of the amine group. The single reactive group allows for clean chemistry. Deprotection with piperidine
89
Why are there different types of solid supports available
Different support for different linkages and couplings
90
What is enzyme-templated synthesis
The enzyme was used as the ‘beaker’ to provide a particular shape.
91
Disadvantages and advantages of combinatorial synthesis
Adv: not labour intensive, less reactions, reactions can be driven to completion with knowledge reagents can be washed off
Dis: can get false negatives due to intermolecular interactions with other compounds in mixture, have to separate molecules generated, combinatorial compounds cover narrow area in diversity
92
What does PET and SPECT stand for
Positron emission tomography
| Single photon emission computed tomography
93
How does PET and SPECT differ from other imaging modalities
PET and SPECT show function not just structure
94
How do we use PET to investigate pharmacokinetics
Drug needs to be radiolabelled. PET isotopes are useful
95
How do we use PET to investigate pharmacodynamics
Well-characterised radiotracer specifically targets potential active site of drug to allow study of drug interaction
96
What are the CNS requirements for radiotracers
- 2 < logP < 3
- High affinity to specific receptor (K1 < 1 nM)
- High subtype selectivity
- High specific activity (> 1000Ci/mmol)
- High ratio specfic to non-specific binding
- Metabolic stability during time of measurement
97
Describe fDG metabolism
FDG is an analog of glucose
It is transported from blood across the cell membrane by the glucose transporter
It becomes phosphorylated in the cytoplasm by the enzyme hexokinase to form FDG 6-P
Unlike glucose, FDG is not metabolised further and is effectively trapped in the cell
98
Advantageous impact of natural products on drug discovery
Plants have evolved to produce unusual compounds to prevent animals and insects from eating them. Drug design would not be able to hit on unusual motifs
99
Several examples of natural products in clinical use
Morphine
Paclitaxel
Penicillin
100
Define semisynthesis
A precursor that is available in larger yields can be converted chemically/enzymatically to the desired drug
101
Define precursor directed biosynthesis
Give bacteria an analogue of its normal substrate
102
Describe mutasynthesis
Knockout sequence in bacterium for precursor and use your own substrate
103
Design a separation strategy based on ion-exchange chromatography for a mixture of given compounds
Uses: ionic groups (-SO3- or -N(CH3)3+) covalently attached to the stationary solid phase, usually a resin. Solute ions are attracted to the stationary phase by electrostatic force
Depends on anion exchange or cation exchange
104
Negatives of natural compounds on drug design
- Periodic declines in natural products as lead compounds
- Difficult synthesis of complex structure
- Often difficult to obtain sufficient concentrations from natural sources
- Environmentally unsustainable in some cases
105
Which pathway do you get more diversity of natural compounds
Secondary metabolism - pathways for modifying metabolites of restricted occurence
106
Why are steric effects important parameters for drug design
They affect the SA andvolume
107
Why are electronic effects important parameters for drug design
They affect pKa, the charge and electrostatic potential
108
Why are lipophilic effects important parameters for drug design
They affect hydrophobicity and log P
109
Why are H-bonding effects important parameters for drug design
They affect number of HBD, HBA, logP and conformation
110
What is the DFG motif
Three AA at the beginning of the A-loop which type II inhibitors recognise in a DFG-out conformation
111
Each type I or type II kinase inhibitor has at least one H-bond to what region
Hinge region
112
How does PEGlyation or fusion with albumin/immunoglobin increase drug efficacy and tolerance
Masks protein surface = decreased immune recognition
Decreased proteolysis
Decreased GFR
113
Opium vs morphine
Morphine is main active alkanoid in opium
114
Main uses of opioids
Analgesia
Anti-diarrhoea
Sedative
115
What is a pharmacophore
Atoms and functional groups required for a specific pharmacological activity
