Three Binding Conformations of BIO124 in the Pocket of the PICK1 PDZ Domain

Abstract

The PDZ family has drawn attention as possible drug targets because of the domains' wide ranges of function and highly conserved binding pockets. The PICK1 PDZ domain has been proposed as a possible drug target because the interactions between the PICK1 PDZ domain and the GluA2 subunit of the AMPA receptor have been shown to progress neurodegenerative diseases. BIO124 has been identified as a sub µM inhibitor of the PICK1-GluA2 interaction. Here, we use all-atom molecular dynamics simulations to reveal the atomic-level interaction pattern between the PICK1 PDZ domain and BIO124. Our simulations reveal three unique binding conformations of BIO124 in the PICK1 PDZ binding pocket, referred to here as state 0, state 1, and state 2. Each conformation is defined by a unique hydrogen bonding network and a unique pattern of hydrophobic interactions between BIO124 and the PICK1 PDZ domain. Interestingly, each conformation of BIO124 results in different dynamic changes to the PICK1 PDZ domain. Unlike states 1 and 2, state 0 induces dynamic coupling between BIO124 and the αA helix. Notably, this dynamic coupling with the αA helix is similar to what has been observed in other PDZ-ligand complexes. Our analysis indicates that the interactions formed between BIO124 and I35 may be the key to inducing dynamic coupling with the αA helix. Lastly, we suspect that the conformational shifts observed in our simulations may affect the stability and thus the overall effectiveness of BIO124. We propose that a physically larger inhibitor may be necessary to ensure sufficient interactions that permit stable binding between a drug and the PICK1 PDZ domain.

Keywords: BIO124; PDZ domain; PICK1; dynamic allosterism.

Figure 1

The PICK1 PDZ domain. (a) PICK1 PDZ domain with labeled secondary structures (PDB ID: 6BJO). (b) PICK1 PDZ-BIO124 complex with BIO124 shown in blue (PDB ID: 6BJO). Note that (b) is the starting structure of the all-atom MD simulations.

Figure 2

Hydrogen bonding network between BIO124 and the PICK PDZ domain. (a) Hydrogen bonds identified in both experimental work and our MD simulations include I33-carboxyl (cyan), G34-carboxyl (orange), and I35-carboxyl (green). Hydrogen bonds identified only in our MD simulations include I37-carboxyl (red) and I37-ketone (purple). (b) Distance distribution between each hydrogen bonding pair in the complex. Note that each hydrogen bonding pair produces distinct distance peaks.

Figure 3

The three binding conformations of BIO124. (a) Hydrogen bonding pairs between BIO124 and the PICK1 PDZ domain. (b) Atom-atom distance analysis of the hydrogen bonding pairs in the PICK1 PDZ-BIO124 complex by trajectory. Distance analysis suggests unique binding conformations of BIO124. (c) State 0 of BIO124 (trajectory 4). Hydrogen bonding network (left) and cluster analysis (right) are in good agreement. State 0 resembles the conformation of the ligand in the crystalized structure. (d) State 1 of BIO124 (trajectories 1 and 3). Hydrogen bonding network (left) and cluster analysis (right) are in good agreement. State 1 is new stable conformations taken by the ligand during our simulations. (e) State 2 of BIO124 (trajectory 2). Hydrogen bonding network (left) and cluster analysis (right) are in good agreement. State 2 is new stable conformations taken by the ligand during our simulations.

Figure 4

Hydrophobic interactions between BIO124 and the PICK1 PDZ domain across the three states of BIO124. (a) Most probable contacts between BIO124 and the PICK PDZ domain. (b) Visual representation of hydrophobic interactions between BIO124 and the PICK PDZ domain.

Figure 5

Protein network analysis across the three states of BIO124. (a) In State 0, the major motions of BIO124 couple with the βB strand, βC strand, and αA helix of the PICK1 PDZ domain. (b) In State 1, the major motions of BIO124 couple with the αB helix of the PICK1 PDZ domain. (c) In State 2, the major motions of BIO124 couple with the αB helix of the PICK1 PDZ domain.

Figure 6

The role of I35 in inducing dynamic allosterism at the αA helix of the PICK PDZ domain. (a) Distance distribution between I35 of the PICK1 PDZ domain and BIO124 in each state. (b) Punctual stress on I35 of the PICK1 PDZ domain induced by BIO124 in each state.