Drug Design_L4 Flashcards
What are the three methods of SBDD?
(1) Structure and known inhibitor/ligand design
Known inhibitor or co-factor is modified to improve binding affinity or selectivity/potent
(2) Virtual High Throughput Screening (vHTS)
Docking of small molecules into the crystal structure which are scored and ranked
(3) De novo design
A molecule is designed from scratch to bind in the active site. Fragments are docked then joined to create full molecules. These molecules are then scored and ranked.
What two key parameters are required to be known in SBDD?
the position of binding site and the ligand binding pose
What can be done if the protein crystal structure is unclear?
The homologous alignment can be a replacement.
What are the basic principles of SBDD?
(1) Solve the X-ray structure of the target at high resolution, cryo-EM structure is also useful
(2) Solve the structure in the presence of the substrate if possible, the critical residues in combination with the substrate and the interactions(i.e. hydrogen bonds formed between the side chains and the water molecules) at the active site are identified, as well as the binding cleft.
(3) Use this structure as a template for screening of small molecules, the structure can be programmed to mimic or dock the binding mode
(4) Redesign the molecules to fit and/or bind better, the potent is increased and the toxicity is reduced.
explain the virtual high throughput screening
(1) Docking
(2) In vitro high-throughput screening or from known substrates/inhibitors to identify leads, the high-throughput is expensive and not easily to be accessed.
(3) Identify the chemical groups of the ligands that are important for binding and specificity
(4) Avoid toxic side-effects my modifications, the toxicity may be resulted from the by-product in the side reactions.
(5) Test activity (enzymatic and pharmacokinetics)
(6) Solve crystal structures to verify binding mode
What are the challenges of the SBDD in compared with the LBDD?
(1) Although the SBDD is more commonly applied than LBDD, the energetics of protein-ligand interactions can be complicated
(2) Both proteins and ligands can be quite flexible, for example, the rotatable bonds and chiral centres.
(3) Many target-binding ligands are not good drug candidates, some of them may be too hydrophobic and stuck in the membrane.
(4) The structures of many important drug targets are difficult to determine, consider the design of how to approach the target based on SBDD.
What molecular properties/structures are rendered as important parameters?
(1) 1D-descriptors: chemical composition & physicochemical properties
MW, chemical composition ,hydrophobicity
(2) 2D-descriptors: chemical topology, hoe the groups are connected to each other
Connectivity indices, degree of branching, degree of flexibility, chiral centre
(3) 3D-descriptors: shape, volume, functionality, surface area, need a good docking
Pharmacophore – the spatial arrangement of chemical groups that determines its activity
What does structre activity relationship(SAR) inform the programming of?
(1) Correlations that are constructed between the features of chemical structure in a set of candidate compounds and parameters of biological activity, such as potency, selectivity and toxicity.
- > Identify important groups of the lead compound that are important to biological activity
(2) X-ray crystallography can be used to identify important interactions between drug and protein
(3) Test for biological activity and comparing them with the original compound in cell-based assay. If an modification shows a significant lower activity, then the group that has been modified must be important. If the activity remain similar, then the group is not essential.
What is the expression of Lipinski’s rule of Fives and what conditions should be reached?
(1) MW < 500, the molecular size should not be large, otherwise, it cannot easily penetrate the membrane
(2) Fewer than five H-bond donating functions
(3) Fewer than 10 H-bond accepting functions
(4) Calculated logP (ClogP) between –1 and +5
P is the ratio of the molecular concentrration in the lipid over that in the water, logP is derived from P
what is virtual screening?
(1) In silico to identify potential lead compounds from a database score, rank and filter a set of chemical structures, in addition to the pose prediction which gives information about how the molecule potentially binds.
(2) Requires to have a high resolution structure
(3) Identify key residues in the binding site: identify the water molecules and interacting residues.
(4) Dock compound by selecting proper streochemistry
What is contained in the search algorithms?
Rigid docking:
1. The ligand is treated as a rigid structure and only the translational and rotational degrees of freedom are considered (translational freedom: the dynamic freedom of movement; rotational freedom: molecular rotation flexibility around the centre, the rotation around the bond is not considered)
- Different ligand conformations:
each conformation is docked separately, however, their flexibility is not taken into account - Protein is considered rigid:
no flexibility in the substrate
many residue-joining catalysis due to the flexibility is disregarded - Orient ligand in the active site using simple geometry descriptors, like spheres or triangles (sphere centres, the protein and ligand are translated into triangles): the sphere represents the atomic volume anf the triangle gives the rough estimation about the conformation and position
- Plausible conformations (prior to docking)- match binding site shape
- Plausible orientations and position geometrical descriptors; usually combined with chemical and electrostatic descriptors to guide ligand placement.
- Satisfy stereochemistry, no clashes, if the electrocomplementarity is not satisfied, the drug is not a good candidate.
What is the scoring and in which way it proceeds?
(1) Many different poses of the same ligand need to be ranked for accuracy. Different poses of different ligands need to be ranked based on their receptor affinity
(2) first principle scoring: Molecular Mechanics
force field. Force fields typically contain
intra-molecular terms: bond lengths, bond angles and dihedral terms, as well as inter-molecular terms: Van der Waals contacts (non-polar), electrostatic interactions (polar) and hydrogen bonds between the side chains and the hydroxyl groups on the substrate. First principle scoring is applied when the higher affinity is more favoured. The equation measures the affinity is: Ebind=Eintra+Enonpolar+Epolar.
(3) Empirical scoring: Scores ligands very rapidly
ΔGbind= ΔG0 + ΔGpolar · Σ f(Complex) + ΔGnon-polar · Σ f(Complex) + ΔGrot · Nrotatable-bonds
ΔG0, ΔGpolar, ΔGnon-polar, and ΔGrot are
empirically parameterised weights.
f(Complex) is a penalty function aimed
at penalising any unfavourable interactions.
What is flexible docking?
(1) Ligand flexibility along torsion angles
Flexibility/conformations during the docking process
the flexibility allowed in the ligand matches better at the active site
(2) Different binding models
(3) Protein is considered “rigid”- small flexibility is allowed
(4) Large protein conformational changes challenging for docking. Small conformational changes can be accommodated.
Considerations before docking
(1) Requires high resolution structure:
1. Water molecules might be disordered or “not resolved”: water molecules may be involved in the catalysis and should not be ignored.
2. Electron density for flexible side chains might be weak (“wrong” asignment), rigid docking produces the less likely fitting results with false positives
3. Hydrogen bonds are absent (problem with charged residues) with glutamate/lysine/asparate
4. pKa of the active site side chains– influence from crystallisation buffer, in crystals, the pH may not be physiological
5. The protonation state and tautomeric form of the ligand (test all pausible combinations): the two states are not distinguishishable if the intermediate has been identified, for example, the conversion between the keto(rely on the hydrophobic interaction) and enol forms(form hydrogen bonds with the side chains)
(2) Torsion angles provide flexibility to the ligand
(3) Rotatable bonds can be a problem: there can be way too many rotatable bonds
(4) Ring conformations (chair or boat)
(5) Potency: the amount of drug required for its specific effect to occur; inverse of the EC50
(6) Efficacy: the maximum strength of the effect itself, at saturating drug concentrations.
(7) Pharmacokinetics: determining the fate of xenobiotics: extend and rate of adsorption, distribution, metabolism, and excretion (ADME).
(8) Pharmacodynamics: determining the biochemical and physiological effects of drugs, the mechanism of drug action, and the relationship between drug concentration and effect.
define the structue-based fragment screening(de novo screening)
(1) modify the ligand progressively until the reactive residues fit at the active site, the active site is treated as the lattice structure
(2) the fitted fragments are covalently connected to obtain the desired drug
(3) Searching space of possible poses & conformations (search algorithm):
Orientation of molecule in binding site
(4) Predicting energetics of protein-ligand binding (scoring function)
Binding affinity
Thermodynamics
(5) For example, if the binding site comprising three binding pockets, crystallographic screening locates molecular fragments that bind to one, two or all three pockets. A lead compound is designed by organising all three fragments around a core template to grow out of a single fragment
