lecture I: drug-target interactions Flashcards
Affinity
The affinity of a drug for a receptor is a measure of how strongly (tightness) that drug binds to the receptor.
A compound with high affinity does not necessarily have high efficacy
→expressed as the equilibrium dissociation constant KD in M (mol/L)
Efficacy
Efficacy is a measure of the maximum biological effect that a drug can produce as a result of receptor binding.
A compound with high affinity does not necessarily have high efficacy
It is possible for a drug to be potent (i.e. active in small doses) but have a low efficacy
Potency
Potency of a drug refers to the amount of drug required to achieve a defined biological effect
→the smaller the dose required, the more potent the drug
It is possible for a drug to be potent (i.e. active in small doses) but have a low efficacy
Target
Any cellular macromolecule that a drug binds to initiate its effect.
EX: proteins (enzymes, receptors, transport proteins), DNA (nucleic acid)
Drug
A chemical substance that interacts with a receptor to produce a
physiologic effect.
→all drugs are chemicals but not all chemicals are drugs
Target + Drug
The ability of a drug to bind to a receptor is mediated by its chemical structure allowing interactions with the complementary surfaces on the receptor and eliciting intermolecular forces.
→shapes plays a role and facilitates IMFs
Pharmacodynamics
Pharmacodynamics is the study of how a drug binds to its target binding site and produces a pharmacological effect.
→”what the drug does to the body”
Pharmacokinetics
Pharmacokinetics is the study of how a drug is absorbed, distributed, metabolized, and excreted (ADME).
→”what the body does to the drug”
Binding
The interaction of a drug with a macromolecular target.
→dynamic, flexible, constant movement
→different modes of how a drug can interact with its target exist, some are better than others
Binding pocket
3D structure within the target, in which drugs fits and bind.
→usually a specific area of the macromolecule where binding takes place
Pharmacophore
The drug’s steric (shape and position) and electronic features (chemical functional groups) that are necessary to ensure the interactions with a specific biologic target and trigger (or block) a biologic response
Active site
Catalytic active site of an enzyme where reaction happens; amino acids involved in catalysis and substrate binding.
→not necessarily the binding pocket
Factors influencing binding
- IMFs (and thus affinity)
→the more IMFs, the tighter
→the more energy in the bond, the tighter
→you need to find the sweetspot because you don’t necessarily want it to bind too tight to allow for proper drug dosing - pH
→cellular location matters (different aa side chains are protonated differently at different pHs) - water shell
→has to be removed for proper interaction
Drug-target complex examples
- Valsartan & AT1R
- Gleevec & BCR-Abl kinase (at the DFG loop → if the loop is in or out, it will alter Gleevec’s ability to bind)
Models of drug-target binding
- Lock & key
- Induced fit
- Conformational selection / selected fit
Lock & key binding
To exercise an action a ligand must fit into a protein binding cavity like a key into a keyhole.
no longer very relevant, induced fit model makes more sense
Induced fit binding
The proximity of a drug to its target induces conformational changes that favour their interaction.
Conformational selection / Selected fit binding
Conformational changes occur prior to the binding of a ligand. Ligands “select” and stabilize certain sets of conformations, thus shifting equilibrium towards the “active conformation”.
→multiple conformations of a protein can exist where the drug can bind
Cryo-EM
Cryogenic electron microscopy
A cryomicroscopy technique applied on samples cooled to cryogenic temperatures.
Recent advances in detector technology and software algorithms have allowed for the determination of biomolecular structures at near-atomic resolution. This has attracted wide attention to the approach as an alternative to X-ray crystallography or NMR spectroscopy for macromolecular structure determination without the need for crystallization.
→allows us to determine the type of binding and fits!
IMFs
Intermolecular forces
“Tightness” (affinity) depends on the quality and number of intermolecular forces (and thus on how well complementary surfaces fit).
Biologically relevant IMFs
- Ionic interactions
- Dipole-dipole interactions (+ ion-dipole interactions)
- Hydrogen bonding
- Van der Waals interactions
- 𝜋-𝜋 stacking
- Repulsive forces
- Water shell
→Some drugs react with the binding site and become permanently attached via a covalent bond, but most interact through weaker IMFs
→None of these bonds is as strong as the covalent bonds that make up the skeleton of a molecule, and so they can be formed and then broken again. This means that an equilibrium takes place between the drug being bound and unbound to its target.
covalent bonds are NOT IMFs, but they are still relevant
Covalent bond
- basis of attraction: 2 atoms share a pair of electrons
- energy: 200 – 400 kJ/mol
→a lot used to break apart the 2 atoms - range: 1.0-1.54 Å
- technically not an IMF, since it becomes one entity once the electrons are shared
Ionic interactions
The strongest of the IM bonds and takes place between groups that have opposite charges.
- basis of attraction: cation–anion electrostatic attraction
- energy: 20 - 40 kJ/mol
- range: longer
→if an ionic interaction is possible, it is likely to be the most important initial interaction as the drug enters the binding site
Factors influencing ionic interactions
Dependent on the nature of the environment.
→stronger in hydrophobic environments than in polar environments
(the binding sites of macromolecules are more hydrophobic in nature than the surface and so this enhances the effect of an ionic interaction)
→pH
(causes drug/target to either be charged or not due to aa side chains)
Hydrogen-bonding
A hydrogen bond can vary substantially in strength and normally takes place between an electron-rich heteroatom and an electron-deficient hydrogen.
- basis of attraction: ability of proton (H+) to accept electron pair in part from donor
- energy: 16-60 kJ/mol
- range: 1.5-2.2 Å
Van der Waals
Van der Waals interactions between hydrophobic regions due to temporary dipoles.
- basis of attraction: hydrophobic interactions; slight distortions induced in electron clouds surrounding nucleus.
- energy: 2 – 4 kJ/mol
→low in E, but typically abundant
- range: very short
→the drug has to be close to the target binding site before the interactions become important.
Dipole-Dipole
If atoms in one molecule have different electronegativities, this molecule has a permanent dipole and can interact with a permanent dipole in the binding site.
- basis of attraction: molecules with permanent dipole; pi-interactions
- energy: 2 – 4 kJ/mol
- range: short
Water shell
Due to the body’s aqueous environment, the drug and the macromolecule are solvated with water molecules before they meet each other
→the water molecules surrounding the drug and the target binding site have to be stripped away before those interactions
- energy: 0.1-0.2 kJ/mol/Å^2
→if the energy required to desolvate both the drug and the binding site is greater than the stabilization energy gained by the binding interactions, then the drug may be ineffective.
Repulsive forces
- basis of attraction: charged groups
OTHER: If molecules come too close, their molecular orbitals start to overlap and this results in repulsion.
𝜋-𝜋 stacking
Amino acid side chains with an aromatic ring can interact with each other through the delocalized electrons.
- basis of attraction: aromatic rings
→the pi (π) systems present in alkynes and aromatic rings are regions of high electron density and can act as hydrogen bond acceptors
- energy: 6-10 kJ/mol
- range: 3.3 - 5.0 Å
EX: often occurs with steroids
HBA
Hydrogen bond acceptor
- provides the electron-rich atom to receive the hydrogen bond
- has a free electron pair
- the electron-rich heteroatom has to have a lone pair of electrons and is usually oxygen or nitrogen.
- any feature that affects the electron density of the hydrogen bond acceptor is likely to affect its ability to act as a hydrogen bond acceptor; the greater the electron density of the heteroatom, the greater its strength as a hydrogen bond acceptor.
EX: most are neutral functional groups, such as ethers, alcohols, phenols, amides, amines, and ketones. These groups will form moderately strong hydrogen bonds
HBD
Hydrogen bond donor
- provides the hydrogen for the hydrogen bond
- the electron-deficient hydrogen is usually linked by a covalent bond to an electronegative atom, such as oxygen or nitrogen. As the electronegative atom (X) has a greater attraction for electrons, the electron distribution in the covalent bond (X–H) is weighted towards the more electronegative atom and so the hydrogen gains its slight positive charge.
Electronegativity of key atoms
H: 2.2
C: 2.55
N: 3.04
O: 3.44
Electronegativity of key atoms
H: 2.2
C: 2.55
S: 2.58
N: 3.04
O: 3.44
Factors influencing H-bond strength
- depends on how strong the hydrogen bond acceptor and the hydrogen bond donor are
(ex: despite being electronegative, sulphur is a weak hydrogen bond acceptor because its lone pairs are in third-shell orbitals that are larger and more diffuse. This means that the orbitals concerned interact less efficiently with the small 1s orbitals of hydrogen atoms. (it’s not just electronegativity that mattes, but accessibility as well))
H-bond orientation
The optimum orientation is where the X–H bond points directly to the lone pair on Y such that the angle formed between X, H, and Y is 180°.
→short bond has more energy (where atoms are all aligned)
→kinked H-bond that is longer has less E
→angle can vary
Hydrogen bonds in Biomolecules
- protein & water shell
→between the hydroxyl group of an alcohol and water
→between the carbonyl group of a ketone and water - secondary protein structure
→between peptide groups in polypeptides - DNA double strand
→between complementary bases of DNA
Hydrogen bond flip-flop.
Some functional groups can act both as hydrogen bond donors and hydrogen bond acceptors (e.g. OH, NH2). When such a group is present in a binding site, it is possible that it might bind to one ligand as a hydrogen bond donor and to another as a hydrogen bond acceptor.
Dipole-dipole orientation
It is possible for the dipole moments of the drug and the binding site to interact as a drug approaches, aligning the drug such that the dipole moments are parallel and in opposite directions. If this positions the drug such that other intermolecular interactions can take place between it and the target, the alignment is beneficial to both binding and activity. If not, then binding and activity may be weakened.
Ion-dipole
A charged or ionic group in one molecule interacts with a dipole in a second molecule
→stronger than a dipole–dipole interaction
𝜋-𝜋 stacking orientation types
- face-to-face
- offset
- edge-to-face
Hydrophobic regions + water shell
It is not possible for water to solvate the non-polar or hydrophobic regions of a drug or its target binding site. Instead, the surrounding water molecules form stronger-than-usual interactions with each other, resulting in a more ordered layer of water next to the non-polar surface. This represents a negative entropy due to the increase in order. When the hydrophobic region of a drug interacts with a hydrophobic region of a binding site, these water molecules are freed and become less ordered. This leads to an increase in entropy and a gain in binding energy.
Factors influencing the length of time a drug remains at its target
- IMF’s relative strength
- number of IMFs
Factors influencing the number and types of IMFs
- structure of the drug
- functional groups present in the drug
Dissociation constant values
- good antibody: KD ≈1nM–10pM
- good drug: KD ≈ 100 microM - 100 nM
most drugs don’t go down to pM range
Dissociation constant equation
KD = Koff / Kon
KD = [R][L] / [RL]
*[R] + [L] ⇄ [RL]
→ : Kon
← : Koff
KD
Dissociation constant
- Concentration of the drugs required to bind to 50% of the receptors
- Small KD = High affinity
- Units: M (conc.)
- Curve shape: hyperbolic
Core amino acid structure
An amino acid is an organic molecule that is made up of:
- a Hydrogen
- a basic amino group (−NH2)
- an acidic carboxyl group (−COOH)
- an organic R group (or side chain) that is unique to each amino acid.
Amino acid chirality
Amino acids are chiral molecules – L- and D-configuration
→ L being the most common in the body
Zwitterion
A molecule or ion having separate positively and negatively charged groups.
→at neutral pH, amino group and carboxylic acid will be charged, thus the aa is zwitterionic (NH3+ & COO-)
Aliphatic / non-polar AAs
- glycine
- alanine
- proline
- valine
- leucine
- isoleucine
- methionine
Aromatic AAs
- phenylalanine
- tyrosine
- tryptophan
interesting for 𝜋-𝜋 interactions & light absorbance
tryptophan is often used as it is light sensitive
Polar, uncharged AAs
- serine
- threonine
- cysteine
- asparagine
- glutamine
→because of electronegative atoms in side chains
often involved in dipole-dipole interactions
Positively charged AAs
- lysine
- arginine
- histidine
often involved in ionic interactions
Negatively charged AAs
- aspartate
- glutamate
often involved in ionic interactions
AAs that can function as proton donors or acceptors
- glutamic acid
- aspartic acid
- lysine
- arginine
- cysteine
- histidine
- serine
- tyrorsine
→ general acid form: proton donor
→ general base form: proton acceptor
VdW & AAs
All non-polar AAs:
1. glycine
2. alanine
3. valine
4. cysteine
5. proline
6. leucine
7. isoleucine
8. methionine
9. tryptophan
10. phenylalanine
H-bonds & AAs
All polar AAs:
1. serine
2. threonine
3. tyrosine
4. asparagine
5. glutamine
→form peptide bonds
Ionic bonds & AAs
All charged AAs:
1. lysine
2. arginine
3. histdine
4. aspartic acid
5. glutamic acid
→form salt bridges
𝜋-𝜋 stacking & AAs
- tryptophan
- phenylalanine
- histidine
- tyrosine
Peptide bond
Formed between the α-nitrogen atom of one amino acid and the carbonyl carbon of a second.
→peptide bond is resonance stabilized/ partial double bond character
→planar (not flat or kinked)
→protein “backbone”
→HBD & HBA
→ribosomes contribute to condensation
→proteases contribute to hydrolysis
Protein structure levels
- Primary: sequence
- Secondary: alpha-helix & beta-sheet
- Tertiary: interactions between alpha-helices & beta-sheets
- Quaternary: oligomers
Folded protein examples
- Ferritin
→alpha-helices only - UDP N-acetylglucosamine acyltransferase
→beta-sheets only - Phosphofructokinase
→alpha/beta protein - GFP
→alpha + beta protein
What is needed for drug design
- affinity, drug-target interactions
- target validation
- complementary surfaces
- protein structures
Alphafold
AlphaFold is an artificial intelligence program which performs predictions of protein structure.
→trained with thousands of protein structures
→predicts the structures of all unsolved proteins
Molar mass
Mass of a given substance per mol.
-symbol: M or FW
-unit: g/mol
Molar concentration (M)
Measure of the concentration of a solute in a solution.
-symbol: c
-unit: mol/L (M)
