Chemistry Flashcards
Give five functions of proteins:
Catalysts (enzymes) Structure of cells and organisms Regulation of info flow (receptors) Immune protection Storage and transport
At physiological pH, what form does an amino acid exist in?
Zwitterion
What type of configuration do amino acids most naturally occur?
L configuration
What four classes are the amino acid put into based on their R group?
Non-polar neutral amino acids have hydrophobic R groups.
Polar neutral amino acids have hydrophilic but neutral R groups.
Polar acidic amino acids have hydrophilic acid R groups, I.e. the R group contains a COOH.
Polar basic amino acids have R groups that contain a basic nitrogen group.
What is a peptide bond?
Amide formation between the –COOH of one amino acid and the amine group of another amino acid.
What shape are amino acids and why?
Planar, resonance delocalisation demands co polarity of p orbitals to be stable
What type of rotation is possible in a polypeptide?
Free rotation is possible around the sigma bonds to the a-carbon atoms
What are the secondary, tertiary and quaternary structures of proteins due to?
Interaction between the amino acid side chain residues (-R groups) and the backbone polypeptide chain.
What is responsible for the secondary structure of a protein?
Interactions between –CONH- groups of the peptide chain are responsible for a-helix conformation and b-pleated sheet conformations in peptides
What is the alpha helix secondary structure?
A right handed, coiled helical spring
Each peptide bond forms two H- bonds
What is the beta sheet secondary structure?
Represented by a thick arrow
Backbone forms a zig zag
The side chains are above and below the sheet
The B may be aligned parallel or anti- parallel to form the sheets
How are the 3º and 4º structure formed?
Maintained by interactions between side chains of amino acids
What are the four types of bonds in the 3º and 4º structure and are they covalent or not?
NON- COVALENT: - electrostatic interactions - hydrogen bonds - hydrophobic interactions COVALENT: - disulphide bonds
What can covalently crosslink polypeptide chains?
Cysteine thiols
Name five types of intermolecular interactions:
- Electrostatic /ionic bonds
- Hydrogen bonds
- Vander Waals interactions
- Hydrophobic
- Pi-pi stacking
Give five features of electrostatic/ ionic bonds:
Strongest of the intermolecular bonds (20-40 kJ mol-1)
Between groups of opposite charge
Strength of the ionic interaction is inversely proportional to the distance between the two charged groups
Stronger interactions occur in hydrophobic environments
The strength of interaction drops off less rapidly with distance than with other forms of intermolecular interactions
Give five features of hydrogen bonds:
- Weaker than electrostatic interactions but stronger than van der Waals interactions
- Takes place between an electron deficient hydrogen and an electron rich heteroatom (N or O)
- Electron deficient hydrogen usually attached to O or N
- Electron deficient hydrogen is called a hydrogen bond donor
- The electron rich heteroatom is called a hydrogen bond acceptor
Give five features of Van der Walls interactions:
Very weak interactions (2-4 kJmol-1)
Occur between hydrophobic regions of the drug and the
target
Due to transient areas of high and low electron densities leading to temporary dipoles
Interactions drop off rapidly with distance
Drug must be close to the binding region for interactions to occur
What are hydrophobic interactions and what is its purpose?
Water molecules interact with each other and form an ordered layer next to hydrophobic regions - negative entropy
Interactions between the hydrophobic interactions of a drug and its target ‘free up’ the ordered water molecules
Results in an increase in entropy
Beneficial to binding energy
What is pi- pi stacking?
Attractive, non covalent interactions between aromatic rings
Contain pi bonds
What is a lead compound?
A compound that interacts with the biological process under study
May not be the most active compound
May have severe side effects
What is the IC50 and what is the ideal unit range?
50% of Inhibitory, same as EC50 but for enzymes
Nm range
What are seven approaches to finding the lead compound?
- Natural Products
- Rational Design
- Library Screening
- Evolution of Existing Drugs
- Side Effects of Existing Drugs
- Metabolism of Existing Drugs
- Serendipity (Clinical Observation)- LUCK
How are lead compounds natural products found?
Screening
Medical Folklore
Give two advantages and two disadvantages of using natural products to get a lead compound:
- very complex structures
- novel arrangements of atoms
• difficult pharmaceutical properties
-degradable bonds low solubility
• difficult to synthesise and thus manufacture
Give examples of where a lead compound can be obtained from a natural product:
Plants and trees - Aspirin, morphine, taxol Bacteria, Viruses and Fungi - Amoxicillin Animal life - Venom
What is involved in the rational approach for exploiting natural ligands?
Modification of the natural agonist/ antagonist
Why are metabolism studies important when developing a drug?
Makes sure no toxic or active intermediates during metabolism
Give an example where serendipity has played a role in discovering a lead compound:
Sildenafil
In vitro – hampers blood clotting through inhibition of platelets
In vivo – specific effect on erectile dysfunction
What are the steps in identifying SAR / Pharmacophore from a lead compound?
Production of analogues
Allow identification of vital parts of molecule
Synthetic simplification
Enhanced activity through additional interactions
What is Lipinski’s rule of 5 to improve the pharmacokinetics of a lead compound?
- Molecular weight ≤ 500
- log P ≤5
- ≤10 H ‐ bond accepting groups
- ≤5 H‐ bond donating groups
What is LogP?
Measure of hydrophobicity of a whole molecule
Name 5 drug targets and state whether they are mammalian or non:
Mammalian Molecular Targets: - Receptors and ion channels - Enzymes - Nucleic acids Non‐ Mammalian Molecular Targets - Chemical - Bacteria, Fungi and Viruses
What is raw difference between agonists and antagonists which have the same functional group?
Antagonists feature the same functional groups as the agonist to interact with the receptor BUT are larger allowing additional interactions with the receptor
Is the 1º structure of an amino acid important for drug activity and why?
Yes, residues on side chains determine how well and how strongly a drug will bind
Is the 2º structure of an amino acid important for drug activity and why?
A little, H-bonds between peptide backbones leaving the residues outwith
Is the 3º structure of an amino acid important for drug activity and why?
Yes, VERY important
Achieved by additional interactions between side chain residue
It brings binding interactions from primary structure in close proximity to form a binding site
What is the strongest bond and describe its function in Drug‐Receptor Interactions:
Covalent bonds
• Rarely seen in pharmacodynamic receptors
• Lead to receptor block through irreversible bonding
• Important in Drug‐DNA interactions e.g. Alkyl halides
• Can be important in enzymes
Which amino acids can form covalent bonds?
Cysteine
Serine
Give the second most strongest bond and describe its function in Drug‐Receptor Interactions:
Ionic bonds
• Important in drug‐receptor interactions
• Allow the drug to bind but also to dissociate
• Mutual attraction between the receptor and drug based on opposing charges
Which amino acids form ionic bonds?
Glutamic acid Lysine Arginine Histidine Aspartic acid
Describe how Hydrogen bonds are used in drug-receptor interactions:
- Essential in drug –receptor interactions
- Dipole interactions
- Important to be additive – too weak alone
What are the three things interaction at a receptor depends on?
1) Types of functional groups
2) Number of functional groups
3) Relative arrangement of functional groups
Why can’t we make a drug from the lead?
Usually lead is not selective between different receptor subtypes with different biological activities, it doesn’t have good pharmacokinetic activity.
What’s the difference between pharmacokinetics and pharmacodynamics?
- Pharmacodynamics- what the drug does to the body (more specifically the study of how drugs interact with their targets).
- Pharmacokinetics – what the body does to the drug. This includes absorption, distribution, metabolism, elimination, ADME
What three things can be considered how the structure can be altered and the effect on activity?
- Simple substitution
- Altering 3D shape
- Chain Extension
What can happen in simple substitution to enhance the activity of a drug?
Remove the group
Change the group
Isosteres and Bioisosteres
What can happen in altering the 3D shape to enhance the activity of a drug?
Stereochemistry
Rigidification
For a 4º ammonium salt, what can you change to see if its ionic interactions are necessary and why?
Replace the N with a carbon as it still has the same shape (tetrahedral) but removes the charge
When changing the ionic properties of a 4º ammonium salt, how can you tell if it was necessary?
If the molecule no longer shows activity with the charge removed, it was needed
If the molecule still shows activity, then this can be removed and therefore simplified.
What can be changed on a 3º amine to see if its ionic interactions are necessary?
Change it to an amide as at physiological pH, it can’t be charged, if there’s still activity shows ionic interaction wasn’t necessary.
What would you change to a carboxylic acid to see if its ionic interactions are necessary?
Replace with
an aldehyde
an aliphatic alcohol
an ester- this is the worst option as Me group larger than H
How can you tell whether the H bond donor/ acceptor properties in an alcohol are necessary for drug interactions and why?
Can prepare an ether or an ester
Ether: Abolishes H bond donor May reduce H bond acceptor activity
Preferred as Me smaller
Ester: Abolishes H bond donor More likely to reduce H bond acceptor activity of alcohol oxygen
Bad as added carbonyl so more changes
How can you change the hydrogen acceptor properties on the carbonyl in an aldehyde/ ketone to see whether its important for drug interactions?
Can reduce to an alcohol
Still keeps H‐bonding potential BUT changes the shape of molecule
Carbonyl is planar and sp2
Alcohol is tetrahedral and sp3
Likely to weaken any H‐bonding interaction
What are the ways an amide can act as an H- bond acceptor and an H- bond donor?
Oxygen on carbonyl can be an acceptor
N in amide can act as a donor
Give four ways in how to change the amide acceptor/ donor properties and how would each of these way affect it?
- Methylated amide:
- Donor removed
- Rigid as amide - Amine
- Acceptor removed
- Not rigid - Alkene
- Donor and acceptor removed
- Rigid as amide - Ketone (best option)
- Donor removed
- Not rigid
What is an isostere?
Atoms or groups that have the same valency and similar chemical and physical properties
What is a bioisostere?
A chemical group used to replace another chemical group within the drug without affecting the important biological activity whilst improving the pharmaceutical properties
What is ∏–∏ stacking?
Aromatic and heteroaromatic rings
Planar and hydrophobic
Interact with flat hydrophobic areas in receptors
How could a drug molecule be changed to determine whether π–π stacking has a role in reactivity?
Replace with a non aromatic structure e.g. cyclohexane
Weakens binding interactions as less is in contact
May change shape sufficiently to change ‘fit’
What is inherent chirality?
One isomer is likely to be more active than the other due to optimised binding interactions
What is introduced chirality?
Can deliberately make a lead compound that is not chiral into a chiral one to exploit the shape of the receptor
With drugs that have enantiomers, what needs to happen to get it licensed?
Needs to prove other enantiomer isn’t doing any harm
Why is it important for a drug molecule to have rigidification?
Good binding and increased activity and limited off target effects
Why would it be important to add a ring to an aliphatic molecule?
Reduces rotation therefore making it less flexible
What type of groups can you add to an aliphatic chain to reduce conformations available and why?
Introduction of an amide, alkene or alkyne
All have double or higher bonds
Single bonds mean free rotation
What is conformational blocking and how is this important for rigidificaiton?
Introducing a steric clash so some conformations can’t be adopted
With smaller groups such as a H, there is free rotation allowed, larger groups such as Me groups are too large so rotation is blocked as e- clouds interact with each other
What is the difference between configuration and conformation?
Configuration: enantiomers
Conformation: shapes
How would you make a drug molecule better by chain extension?
Exploiting Hydrophobic pockets
Is the chain length the right size, there are gaps in hydrophobic pockets, increase the chain length to fill the space and maximise van Der Waals interactions
Where any, why would you add an additional functional group to improve a drug molecule?
To exploit new binding interactions and additional binding sites
In empty pockets, its a good fit for π–π stacking and ionic interactions
Often used for designing antagonists as its growing the molecule
Why would you use chain extension/ contraction to improve a drug molecule design?
A drug can be considered as a scaffold that presents binding interactions
The lead compound may not have the optimal scaffold, changing the length can see which is the optimum for binding correctly
What is a SAR?
Structure Activity Relationship
Qualitative SAR tells you what functional groups are necessary and for which bonding
What is a pharmacophore?
Defines the important functional groups that are required for binding and activity and their relative positions in space
Which three ways can a pharmacophore be represented?
2D – showing key groups required
3D – showing distances and angles
3D – detailing binding interactions
What effect do enzymes have on thermodynamic properties?
No effect on free energy, only affect the kinetic properties
What is the equation for an enzymatic reaction?
S + E ⇌ [ES] ⇌ E + P
Why, in the equation of an enzymatic reaction, is it reversible?
As they’re held by reversible bonds e.g. ionic/ H-bonds so can be broken
What is ∆G‡ and what does this determine?
The Free Energy of Activation and it will determine the rate of reaction
What is S‡ and what does it mean?
The free energy, the species with the highest free energy along the reaction pathway.
How does an enzyme (catalyst) work?
Lowers the Free Energy of Activation ∆G‡ for the reaction by stabilisation of the transition state S‡.
What are the factors that affect the binding of a substrate to an enzyme?
About the:
- size and shape of the molecule
- orientation and presence of bonds
What are Inorganic co-factors and give three examples:
Non- proteins usually permanently associated with the enzyme and at the active site
e.g. Zn, Cu, Fe
What are organic co-factors/ coenzymes and give two examples of each:
- Permanently associated with active site e.g. biotin in carboxylases
- Loosely and reversibly bound to the active site along with the substrate e.g.NAD+ and most vitamins
What is a haloenzyme?
Protein part of enzyme with co-factor bound
What is an apoenzyme?
Protein part of enzyme minus its cofactor
What is the difference between a co- enzyme and a prosthetic group?
Both co- factors
A co- enzyme is a dissociable co- factor
A prosthetic group is a non- dissociable co- factor
What is an induced fit in an enzyme and what happens after this?
Binding of substrate to enzyme produces change in the enzyme and/or the substrate to produce a better “induced” fit
After this, the amino acid side groups in the active site then interact with the substrate
How does the amino acids side chains on the enzyme interact with the substrate?
Distort or stress the target bond causing it to break
In reactions with more than one substrate, substrates bind in an orientation suitable for reaction
What is the Kcat in the Michelis Menton substrate kinetics and what is its unit?
The turnover number, how quickly it goes from reactants to products per unit time per single enzyme molecule.
s-1 , per second
What does a higher Kcat value mean?
The higher the Kcat, the faster the enzyme works so increased rate of reaction.
What is the Km in the Michelis Menton substrate kinetics?
Used to approximate binding affinity of enzyme for substrate
Concentration of substrate required for equilibrium to be a 50/50 distrubution
Is a higher or lower Km better and why?
A lower Km is better as it means higher affinity and more tighter binding.
What does enzyme efficiency depend on and what is the equation for this?
On both Kcat and Km
CATALYTIC EFFICIENCY = Kcat/Km
What is the main mechanism for enzyme function?
They facilitate the formation of the transition state by:
- stabilising the transition state
- destabilising the ground state
What is the correlation of Vmax and Km?
Km is half of the Vmax
How would you find the rate with the Kcat?
Rate= Kcat x [ES]
How would you increase the rate of a reaction by approximation and why?
Make it all part of the same molecule so there is less chance of an atom hitting an atom it doesn’t want to attack as its held in a position where it is ready to attack
How could the rate of reaction be increased by covalent catalysis and how?
Enhance the activity of the substrate
The enzyme uses the active site nucleophiles to form a covalent
enzyme-substrate intermediate
The covalent intermediate is more reactive than the substrate.
How could the rate of a reaction increase by electrostatic catalysis and how?
Stabilization of the transition state
This is by the enzyme using a partial ionic charge to interact with an opposite charge developing on the substrate at the transition state of the reaction
How does an enzyme use desolvation to enhance the rate of reaction?
The enzyme destabilizes the ground state of the substrate by removal of water molecules from charged groups, which exposes the substrate to a more hydrophobic environment
How does an enzyme use strain and distortion to enhance the rate of reaction?
The enzyme destabilizes the ground state of the substrate by inducing a strained/distorted high-energy conformation
How does temperature affect the active site of an enzyme?
Beyond the optimum temperature, the interactions in the proteins start breaking (H- bonds, ionic bonds) so the protein unfolds and therefore denatures
How does pH affect the enzyme activity, e.g. if a mechanism needs CO2- and is in acidic conditions?
If there are acidic conditions there will be more H+, the CO2- will become protonated into a carboxylic acid and therefore can’t work
What is an irreversible inhibitor?
Enzyme inhibitors that form a covalent bond with the enzyme
What is a reversible inhibitor?
Enzyme inhibitors that interact non-covalently with the enzyme
What are transition state analogues?
Enzyme inhibitors that mimic the structure of the substrate in the transition state (TS), playing on the particularly strong interactions between the enzyme and the transition state species
What are competitive inhibitors and how do they work?
Competes for the active site
Changes the Km
What are non- competitive inhibits and how do they work?
They bind elsewhere from the active site
Change Vmax
Describe an experimental procedure to test for enzyme inhibition:
- Have a fixed concentration assay- one assay per compound
- Find the IC50 and pick ones with the lower IC50
- Have 8-10 assays per compound and plot % enzyme activity against inhibition and pick again with lower IC50’s
- Have 20-30 assays per compound and screen for the mode of inhibition e.g competitive ect by plotting rate of enzyme reaction over conc of substrate
In the Lineweaver Burke curve for enzyme inhibition, where do the lines cross for competitive inhibition?
At the Y axis
In the Lineweaver Burke curve for enzyme inhibition, where do the lines cross for non-competitive inhibition?
At the X axis
What are the three main classes of proteases?
serine, threonine, cysteine proteases
metalloproteases
aspartyl proteases
What type of molecule goes with subsites of proteins and how would you make it bind more tightly?
Need a molecule that has similar properties as the subsite
Make a larger inhibitor that binds to more of the protein
What is a peptidomimetic?
A non- peptide drug to mimic the action of a peptide/ protein
Give four advantages of peptidomimetic instead of using proteins:
+ orally active so increased bioavailability
+ increased stability to digestive and metabolic enzymes
+ reduced antigenicity
+ reduced manufacturing costs
What are the three ways to convert a peptide into a peptidomimetic?
- Bioisosteric replacement of the peptide link
e. g changing into an alkene, ketone, amine - Replacement of a natural amino acid with a non-natural one
- Replacement of natural L-amino acids with their D-enantiomers
What is the difference between L and D enantiomers?
L= plain polarised left D= plain polarised right
What groups on each Serine-, Threonine, Cysteine-proteases are nucleophilic?
Serine, -OH
Threonine, -OH
Cysteine, -SH
What does the product vs time graph look like for reversible inhibitors and why?
Linear, with inhibitor less steep than without
As once inhibitor is added the [ES] drops and [EI] increases so the product decreases
What does the product vs time graph look like for irreversible inhibitors and why?
Curved, reaches a max, when more enzyme added the curve repeats again from the level off point.
This is because once all the enzyme has fully EI*, no product can be formed so the product levels off and stops as time goes on
Do calcium channel blockers directly block the channel?
No, they bind to a receptor which results in the channel becoming blocked
Give four classes ion calcium channel blockers and an example of each:
1,4- dihydropyridines e.g. nifedipine
Phenyalkyamines e.g verapamil
Benzothiazepenes e.g diltizem
Diaminopropaniethers e.g. bepridil
In which stage of movement do calcium channel blockers bind to the channel best?
When the channel is open/ inactivated rather than closed
What type of derivatisation can occur for 1,4- dihydropyridines?
Esters (R1)
Alkyl substituents
R2 substituent
Modification of the amine
Describe how the modification of the R2 substituent can enhance or decrease activity for calcium channel blockers:
Can enhance activity on the ortho or meta position
Can decrease activity on the para
Can be electron withdrawing or donating so not resonance effect
The substituents act as a steric lock which forces the two rings into a perpendicular conformation which confers activity
How can modification of the amine enhance or decrease activity for calcium channel blockers?
Introduction of substituents decrease activity
Changing the oxidation state of the ring removes activity
Oxidation by the P450 enzyme responsible for loss on metabolism, changes a N aromatic double double bond ring to a pyridine
How can modification of the ester enhance or decrease activity for calcium channel blockers?
Can alter to provide agonists which are calcium channel activators
By replacing one ester with a NO2 group, can increase vasoconstriction and force of cardiac contractility
Competitively antagonised by asymmetric esters introduce chirality
What is an ester called when the O double bond is on top of the alkyl chain and vice versa:
Top= synplannar Bottom= antiperiplannar
How do Thiazide diuretics work?
Act on Na+/Cl- symporter in distal convoluted tubule
Compete for chlorine binding site
Inhibit reabsorption of sodium leading to diuresis without changing the pH of the urine
What is common between all diuretics?
Sulfonamides
Name three types of diuretics:
Carbonic anyhdrade inhibitors
Thiazides
Loop diuretics
How were carbonic anhydrase inhibitors developed?
Sufonilamide was first developed as an antibiotic and a side effect was diuresis
How do carbonic anhydrase inhibitors work and what are they used for?
Normal acidification of urine achieved by secretion of H+ ions by tubular cells in the kidney
H+ ions provided by the action of carbonic anhydrase which catalyses the formation of carbonic acid by:
CO2 + H2O = H2CO3 = H+ + HCO3-
H+ are exchanged with Na+ in urine so inhibition leads to sodium loss through excretion
Now used for glaucoma as needs a high dose for hypertension
What are thiazide like diuretics and name two?
Contain saulfonamide moieties but don’t share the common ring structure
Chlorthalidone
Indapamide
How do loop diuretics work?
Work in the loop of Henle at Na+/K+/2Cl- symporter
Don’t work at Na+/Cl- sympoter
More effective diuretic
Name two loop diuretics:
Furosemide
Buthetanide
How important are the phenolic -OH groups on a catecholamine for adrenergic binding?
Very important, without the para OH, it significantly decreases Beta selectivity
Can change the meta OH group for a group that does H bonding
What substitution can be made to a catecholamine to increase a2 selectivity?
Add a methyl group to the chain
What evidence is shown that the B adrenoreceptor has a hydrophobic pocket whereas the a adrenoreceptor doesn’t?
The presence of a bulky N-alkyl group, such as isopropyl or butyl, is particularly good for β-adrenoceptor activity, shows there’s a pocket due to increase van Der walls, but when the same happened for a receptor, there was a loss in potency.
What is a modification to the B selectivity on the amine nitrogen?
Adding a polar functional group is placed at the end of the alkyl group, the situation changes. In particular, adding a phenol group to the end of a C2 alkyl chain results in a dramatic rise in activity
What three things do beta blockers do to work as anti hypertensives?
Reduce CO in the heart
Reduce renin production in the kidney
Act on the CNS to decrease activity in the sympathetic NS
Why can’t propanalol be used for asthmatics and what can be used instead?
It is a non selective B antagonist so works on B1 and B2, leading to contraction of bronchial smooth muscles, need only selective for B1 such as atenolol
