2. Binding Affinity 2.1 What is binding affinity? Binding affinity is the strength of the binding interaction between a single biomolecule (e.g. protein or DNA) to its ligand/binding partner (e.g. drug or inhibitor).
Binding affinity is typically measured and reported by the equilibrium inhibition constant (Ki), which is used to evaluate and rank order strengths of biomolecular interactions. The smaller the Ki value, the greater the binding affinity of the ligand for its target. The larger the Ki value, the more weakly the target molecule and ligand are attracted to and bind to one another.
Binding affinity is influenced by non-covalent intermolecular interactions such as hydrogen bonding, electrostatic interactions, hydrophobic and Van der Waals forces between the two molecules. In addition, the binding affinity between a ligand and its target molecule may be affected by the presence of other molecules. 2.2 Why is it important?
Whenever you are characterizing proteins, nucleic acids, and any biomolecule, understanding the binding affinity to substrates, inhibitors, and cofactors is key to the appreciation of the intermolecular interactions driving biological processes, structural biology, and structure-function relationships. In drug discovery, binding affinity is used to rank hits binding to the target and design drugs that bind their targets selectively.
"Selectively" means the drug must have a high affinity to the selected target and the lowest possible affinities to other targets to avoid off-target binding and caused side effects. 2.3 How to measure it?
There are many experimental ways to measure binding affinity and inhibition constants, such as ELISAs, gel-shift assays, pull-down assays, equilibrium dialysis, analytical ultracentrifugation, surface plasmon resonance, and spectroscopic assays.
Experimental methods are expensive in terms of required human efforts, time, and resources. Due to the tremendous number of chemical compounds, experimental bioactivity screening
efforts require the aid of computational approaches. A set of such approaches is called virtual screening