Pharmacological Chaperones and Protein Conformational Diseases: Approaches of Computational Structural Biology

Abstract

Whenever a protein fails to fold into its native structure, a profound detrimental effect is likely to occur, and a disease is often developed. Protein conformational disorders arise when proteins adopt abnormal conformations due to a pathological gene variant that turns into gain/loss of function or improper localization/degradation. Pharmacological chaperones are small molecules restoring the correct folding of a protein suitable for treating conformational diseases. Small molecules like these bind poorly folded proteins similarly to physiological chaperones, bridging non-covalent interactions (hydrogen bonds, electrostatic interactions, and van der Waals contacts) loosened or lost due to mutations. Pharmacological chaperone development involves, among other things, structural biology investigation of the target protein and its misfolding and refolding. Such research can take advantage of computational methods at many stages. Here, we present an up-to-date review of the computational structural biology tools and approaches regarding protein stability evaluation, binding pocket discovery and druggability, drug repurposing, and virtual ligand screening. The tools are presented as organized in an ideal workflow oriented at pharmacological chaperones' rational design, also with the treatment of rare diseases in mind.

Keywords: computational structural biology; drug repurposing; molecular docking; pharmacological chaperones; pocket druggability; protein conformational diseases; protein stability; transient pockets; virtual screening.

Figure 1

Native state protein has high activity and stability (green sphere). Misfolded proteins have lower stability, activity (orange spheres), or both (red). Pharmacological chaperones, binding with misfolded protein, increase its stability and activity. After binding with chaperones, proteins with high residual activity (upper left square) assume stability and activity similar to the wild-type. Proteins with lower residual activity (lower left square) assume high stability after binding with pharmacological chaperones, increasing the availability of protein in the cell.

Figure 2

Three-dimensional structure of tafamidis-bound transthyretin (TTR). (A) The TTR homotetramer, arranged as a dimer of dimers (colored in yellow/orange and cyan/blue), is represented as ribbons; subunits assemble around a central channel that accommodates two drug molecules at the weak interacting surface of the dimers. (B) Close view of a tafamidis molecule filling the gap between surfaces of two dimers. Representations are made with PyMol using a structure from Protein Data Bank (PDB ID 3TCT, accessed on 10 January 2023).

Figure 3

Example of unfolding MDs for wild-type HGD protomer from H. sapiens (Bernini A., unpublished data). The protein hydrated in a water box has been simulated at room temperature (300 K) and in increasing unfolding conditions (500 K and 700 K) for 1 ms with GROMACS and the amber force field. For each trajectory, the secondary structure content along the protein sequence (ordinate) has been evaluated as a function of time (abscissa) and plotted in different colors (see legend). A different rate of unfolding for the β-sheets is apparent by comparing the pictures.

Figure 4

(A–D) Snapshots from an MD simulation showing the gradual opening/closing of a transient pocket on the surface region (blue) surrounding the Y220C mutation of the protein p53 (white). The red circle spots the transient pocket in the maximum depth conformation. (E) The transient pocket identified in the MD superposed to that occupied by the pyrrolic moiety of PhiKan7099 small molecule ligand (in pink) [132] in the experimental structure from PDB ID 5AOK (accessed on 10 January 2023).

Figure 5

A general workflow for the application of computational structural biology to the development of pharmacological chaperones.