The classical mode of action of small molecule drugs is "occupancy-driven". Since the FDA approved the first oral small molecule targeted therapy for tumors-tamoxifen targeting the estrogen receptor (ER)-in 1977 for the treatment of breast cancer, small molecule drug development has typically focused on screening for high-affinity inhibitors. Small molecule inhibitors can bind to the active sites or allosteric sites of proteins to abolish their function, which is an “occupancy (of a specific site on the target protein) driven (loss of function of the protein)” mode of action.

Small molecule inhibitors face two major challenges: resistance mutations and difficult-to-drug targets. On the one hand, patients who respond to small molecule inhibitors eventually develop resistance, mainly due to resistant mutations. On the other hand, the “occupancy-driven” mode of action requires explicit pockets/grooves on the target protein that can be occupied by small molecules. However, some protein pockets/grooves are very shallow or even lack catalytic regions, resulting in less than ideal effects of small molecule inhibitors. These target proteins are often referred to as difficult-to-drug targets.

Protein targets that act in the form of protein complexes

Inhibiting one subunit of a protein complex is difficult to completely deactivate the complex. Additionally, protein-protein interactions are difficult to block with small molecules. Therefore, protein complexes have traditionally been considered difficult-to-drug targets, such as the PRC protein complex involved in epigenetic regulation and the BAF chromatin remodeling complex.

Protein targets with scaffold functions

Some proteins do not depend on or lack enzymatic catalytic sites themselves but indirectly exert their function by binding/recruiting other proteins. Binding of small molecule drugs to such proteins is difficult to completely abolish the function of the target protein, with representative proteins such as focal adhesion kinase (FAK). Recently, BTK has also been found to have scaffold functions.

Protein targets with numerous homologous genes

Some proteins have multiple homologous genes, and these homologous proteins have highly similar structures and sequences (especially in kinase active regions) but different functions. Selectivity of small molecule inhibitors for specific target proteins may be relatively limited, leading to significant side effects, with representative proteins such as the CDK family.

Due to limitations of small molecule inhibitors, two-thirds of potential targets have not been drugged. There are approximately 20,000 protein-coding genes in the human body, and current research indicates that about 10% of these proteins are associated with disease, accounting for approximately 2,000 potential targets. However, according to a 2017 review by NRDD, at that time, the FDA had approved only 667 target proteins out of 1,578 drugs, with small molecule drugs targeting 549 and large molecule drugs targeting 146, accounting for only one-third of potential targets. A large number of potential targets are limited by the limitations of small molecule drugs in drug development.