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