Principles Of Molecular Recognition PDF

2024‐01‐17 Principles of Molecular Recognition  The function of every biological system is based on molecular recognition (e.g., neurotransmitter/receptor, enzyme/substrate)  Molecular recognition is driven by thermodynamics (Gibbs free energy differences)  In biochemistry, there are two prominen...

2024‐01‐17 Principles of Molecular Recognition  The function of every biological system is based on molecular recognition (e.g., neurotransmitter/receptor, enzyme/substrate)  Molecular recognition is driven by thermodynamics (Gibbs free energy differences)  In biochemistry, there are two prominent proposals for molecular recognition:  Emil Fischer’s Lock‐and‐key principle (a)  Daniel Koshland’s Induced‐fit hypothesis (b) → generally accepted today 1 Equilibrium determining receptor‐ligand interactions The interaction between receptor and ligand may involve conformational changes in the ligand (red) or receptor (blue) or both (induced‐fit model), desolvation and solvent reorganization. All these contribute to the overall Gibbs free energy changes. R = gas constant (8.315 J/K/mol) T = temperature (Kelvin) K = equilibrium constant (for the formation of a receptor‐ligand complex) KI = inhibition constant 𝐾 G G 𝑅𝑇 ln 𝐾 𝑅𝑇 ln 𝐾 because 𝐾 The inhibition constant is often used in Medicinal Chemistry to express the affinity of a ligand for a molecular target (enzyme, receptor, …) 2 1 2024‐01‐17  As mentioned on the previous slide, medicinal chemists often use KI to express the affinity of a ligand for a receptor  Alternatively, IC50 values are frequently used to express affinities  The IC50 denotes the concentration of an inhibitor that causes the dissociation of 50% of a receptor‐bound radioactively labeled ligand in a radioligand displacement assay (note: in enzyme assays, it represents the inhibitor concentration at which the enzyme displays 50% activity)  It is possible to determine the KI value from the IC50 value using the Cheng‐Prusoff equation 𝐾 IC50 half‐inhibitory concentration [L] concentration of the radioligand dissociation constant (of the ligand) Kd 3  A higher affinity (more negative G) corresponds to a smaller value of KI (nM, M)  Based on G 𝑅𝑇 ln 𝐾 : a 10‐fold loss in affinity corresponds to an increase in G by 5.6 kJ/mol at room temperature (293 K)  The example below shows that even slight structural changes (e.g., from a perpendicular to a coplanar CH3 group in ethylbenzene) can cause a similar increase in G  This means that slight structural changes can significantly alter binding affinities (needs to taken into account when designing new ligands or drug candidates) 4 2 2024‐01‐17 The forces that drive molecular recognition and their contribution to G G ∆𝐺 ∆𝐺 ∆𝐺 ∆𝐺 ∆𝐺 5 G ∆𝑮𝒕𝒓𝒂𝒏𝒔𝒍 ∆𝐺 ∆𝐺 ∆𝐺 ∆𝐺 ∆𝐺 𝒓𝒐𝒕  Receptor‐ligand binding involves the loss of translational and rotational degrees of freedom, and therefore the loss of entropy, S (even smart ligand/drug design cannot get around this)  The loss of entropy increases G (since G = H – TS)  Estimates for ∆𝐺 range from +12 kJ/mol to +45 kJ/mol ∆𝑮𝒄𝒐𝒏𝒇  This contribution originates from internal motion (e.g., bond or side chain rotation) which may be impaired in a receptor‐ligand complex (loss of internal degrees of freedom and entropy)  Estimates for ∆𝐺 for one restricted internal motion range from +1 kJ/mol to +6 kJ/mol  It is possible to reduce this energy penalty by constraining the ligand (e.g., introduction of rings or double bonds) 6 3 2024‐01‐17 ∆𝑮𝒄𝒐𝒏𝒇  Another consequence is that binding can induce conformational changes (by rotation around single bonds) along with an energy penalty Example 1: Binding of palmitic acid to adipocyte lipid‐binding protein  Binding of palmitic acid to the protein changes its conformation (penalty of 10.5 kJ/mol – corresponds to a 100‐ fold lower affinity; see slide 4)  This energy penalty must be compensated for by favourable interactions (so that Gtotal < 0)  These aspects should be taken into account during ligand/drug design 7 Example 2: Binding to acetylcholine binding protein (AChBP)*  Conformational changes can also occur in proteins (not just in the ligand)  Some domains in proteins can be quite mobile in the unbound state, but become conformationally restrained when a ligand binds Purple: AChBP in complex with a nAChR antagonist (R stands for receptor) Cyan: AChBP in complex with a nAChR agonist Panel b shows both AChBP proteins super‐ imposed, highlighting the mobility/flexibility of loop C Note: Protein flexibility is a major challenge in structure‐based drug design * AChBP was originally isolated from snail glial cells. It is a soluble protein and much easier to study than the actual membrane‐bound ACh receptors. 8 4 2024‐01‐17 G ∆𝐺 ∆𝐺 ∆𝐺 ∆𝐺 ∆𝐺 ∆𝑮𝒑𝒐𝒍𝒂𝒓  This contribution is due to the electrostatic interactions between polar groups in the ligand and protein (side chains, back‐bone amides) – sometimes interactions with solvent molecules also play a role  Electrostatic interactions are often divided into (listed in descending order of strength)  Ion‐ion interactions (salt bridges) – not orientation‐dependent  Ion‐dipole interactions – orientation‐dependent  Dipole‐dipole interaction – orientation‐dependent acetylcholine 9 ∆𝑮𝒑𝒐𝒍𝒂𝒓 – H‐bonds  H‐bonds can be regarded as a dipole‐dipole interaction between a hydrogen atom bound to an electronegative atom and an additional electronegative H‐bond acceptor atom  Typical H‐bond distance between the donor and acceptor atoms: 2.5‐3.0 Å  H‐bonds are orientation‐dependent (optimal angle is 180 deg) Energy contribution per H‐bond in a binding cavity (kJ/mol) 2 – 6.5 10 – 20* 10 – 20* * Equivalent to 50 – 500‐fold increase in affinity! 10 5 2024‐01‐17 ∆𝑮𝒑𝒐𝒍𝒂𝒓 – Aromatic ring systems  ‐stacking) and cation‐ interactions are electrostatic interactions  Such interactions can occur with protein side chains (Phe, Tyr, Trp as aromatics or Lys, Arg as cations)  Cation‐ interactions can be quite strong (8 – 17 kJ/mol) Acetylcholine in the binding pocket of AChBP. Cation‐ interactions are shown as gray dashed lines. 11 G ∆𝐺 ∆𝐺 ∆𝐺 ∆𝐺 ∆𝐺 ∆𝑮𝒉𝒚𝒅𝒓𝒐𝒑𝒉𝒐𝒃  The hydrophobic effect describes the propensity of non‐polar compounds to transfer to an organic phase or to interact with each other  Such interaction is not due to an attractive force between non‐polar compounds, but rather due to an entropically favoured rearrangement of water/solvent molecules  Energy contribution: 0.1 – 0.24 kJ/mol Å2 (e.g., CH3 group: 25 Å2 → 2.5 – 6 kJ/mol)* When two non‐polar groups approach each other, the water molecules around one group become disordered in order to associate with the water molecules of the other group. * The magnitude of the hydrophobic effect is related to the surface area of the non‐polar groups. Leads to increases in entropy, and therefore decreases in G. 12 6 2024‐01‐17  Ligand/drug design mainly focuses on electrostatic interactions (especially H‐bonding) because of the larger contributions to G  However, strong H‐bonds can sometimes be replaced by hydrophobic interactions  Example: Compound 2.1 is a fairly potent inhibitor of influenza neuraminidase (IC50 = 150 nM)  2.1 interacts favourably with the enzyme via strong H‐bonds involving the side chain of Glu and the glycerol moiety of 2.1  Elimination of the glycerol moiety by hydrophobic alkyl groups (compound 2.2) forces the Glu residue into a different position, thereby opening up a new hydrophobic pocket.  This increases the affinity to 2.2 dramatically (IC50 = 1 nM) 13 G ∆𝐺 ∆𝐺 ∆𝐺 ∆𝐺 ∆𝐺 ∆𝑮𝒗𝒅𝑾  vdW interactions are electrostatic in nature  The weak (0.2 kJ/mol) attractive force at intermediate distances (about 3 Å) is due to dispersion forces (temporary/induced dipoles) 𝐸𝑣𝑑𝑊 𝐴 𝑟 𝐵 𝑟 r = interatomic distance A and B are atom‐specific coefficients  Hydrophobic and vdW interactions can be used to map out a receptor cavity or an enzyme active site (if there are no crystal structures available) 14 7 2024‐01‐17 Example of using CH3 groups to scan or map a receptor‐ligand binding site  Here: The binding of a variety of methyl‐substituted flavones to the GABAA* receptor was explored  Through the measurement of inhibition constants it is possible to estimate the dimensions of the binding site  When favoured regions are found, it is worth exploring other, bulkier substituents *GABA = ‐aminobutyric acid 15 8