Evolving Experimental Techniques for Structure-Based Drug Design

Abstract

Structure-based drug design (SBDD) is a prominent method in rational drug development and has traditionally benefitted from the atomic models of protein targets obtained using X-ray crystallography at cryogenic temperatures. In this perspective, we highlight recent advances in the development of structural techniques that are capable of probing dynamic information about protein targets. First, we discuss advances in the field of X-ray crystallography including serial room-temperature crystallography as a method for obtaining high-resolution conformational dynamics of protein-inhibitor complexes. Next, we look at cryogenic electron microscopy (cryoEM), another high-resolution technique that has recently been used to study proteins and protein complexes that are too difficult to crystallize. Finally, we present small-angle X-ray scattering (SAXS) as a potential high-throughput screening tool to identify inhibitors that target protein complexes and protein oligomerization.

Figure 1.

Comparing the serial room temperature and cryo-cooled X-ray crystal structures of BPTES bound to GAC. A) The serial room temperature crystal structure of BPTES bound to GAC (light yellow) adopts an extended, semi-linear conformation. B) The cryo-cooled crystal structure of BPTES (PDB ID 4JKT) bound to GAC (light cyan) forms a “cup-like” orientation. BPTES is color coded by B-factor. B-factors represented by blue to green colors suggest regions of little movement, while red and orange colors suggest regions of greater movement. The distance between the terminal rings of BPTES are measured in Å and are indicated in the figure.

Figure 2.

Panel A: Examples of high-resolution structures of protein-inhibitor complexes obtained using cryoEM. From left to right, the GLP-1R:Gs PF inhibitor complex, the Serotonin receptor bound to granisetron (2.9 Å, PDB ID: 6NP0), and the pancreatic beta-cell KATP channel bound to glibenclamide (3.63 Å, PDB ID: 6BAA). Panel B: Atomic model from a 3.2 Å cryoEM structure of the glucagon-like peptide-1 receptor (GLP-1R):Gs complex bound to a small molecule inhibitor (PF 06882961), obtained with a 200 kV electron microscope (PDB ID: 7LCI, EMDB: 23274). The cryoEM map is shown within 2.5 Å of key residues and the inhibitor.

Figure 3.

Theoretical SAXS profiles of two potential protein targets, determined using the Fast X-ray Scattering (FoXS) web server. Panel A shows a Lin-Lin plot for the scattering of the EGFR monomer and dimer (green and dark green, respectively. PDB ID: 5WB7). Panel B shows a Kratky plot of the X-ray scattering of tissue transglutaminase (tTG) in the open (Red, PDB ID: 2Q3Z) and closed (Blue, PDB ID: 1KV3) conformational states.