Discovery of Novel GR Ligands toward Druggable GR Antagonist Conformations Identified by MD Simulations and Markov State Model Analysis

Abstract

Binding of different ligands to glucocorticoid receptor (GR) may induce different conformational changes and even trigger completely opposite biological functions. To understand the allosteric communication within the GR ligand binding domain, the folding pathway of helix 12 (H12) induced by the binding of the agonist dexamethasone (DEX), antagonist RU486, and modulator AZD9567 are explored by molecular dynamics simulations and Markov state model analysis. The ligands can regulate the volume of the activation function‐2 through the residues Phe737 and Gln738. Without ligand or with agonist binding, H12 swings from inward to outward to visit different folding positions. However, the binding of RU486 or AZD9567 perturbs the structural state, and the passive antagonist state appears more stable. Structure‐based virtual screening and in vitro bioassays are used to discover novel GR ligands that bias the conformation equilibria toward the passive antagonist state. HP‐19 exhibits the best anti‐inflammatory activity (IC50 = 0.041 ± 0.011 µm) in nuclear factor‐kappa B signaling pathway, which is comparable to that of DEX. HP‐19 also does not induce adverse effect‐related transactivation functions of GR. The novel ligands discovered here may serve as promising starting points for the development of GR modulators.

Understanding the P-Loop Conformation in the Determination of Inhibitor Selectivity Toward the Hepatocellular Carcinoma-Associated Dark Kinase STK17B

“…For each system, MD simulations were performed in explicit water environment, collecting multiple μs-length trajectories (i.e., 3 replicates of 3 μs each) and yielding a total of sampling of 27 μs. Such a multiple and independent μs-length MD trajectory has been proved efficient for investigating the interdependent conformational plasticity of the kinase domains (i.e., P-loop and A-loop) and their interactions with the ADP or the ligand ( Lu et al, 2019b ; Zhang et al, 2019 ; Lu et al, 2021a ; Lu et al, 2021b ; Maloney et al, 2021 ; Ni et al, 2021 ; Hu et al, 2022 ).…”

Uncovering the Mechanism of Drug Resistance Caused by the T790M Mutation in EGFR Kinase From Absolute Binding Free Energy Calculations

“…In this section, we investigated the relationship between the structural changes of these key elements and binding affinity. We characterized the conformational changes of these key elements of EGFR by measuring the distance between these critical elements and ligand ( Hu et al, 2022 ). As shown in Figure 4A , the location of AMP relative to A-loop, αC-helix and P-loop have a shorter distance in the L858R/T790M mutant, contributing to the favorable interactions that existed in the complex.…”

Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning

“…Although it is possible to design drugs targeting other binding sites of an NR with more accessible molecular property, for example, design of antagonists targeting the activation function 2 (AF2) , or the binding function 3 (BF3) , sites of the LBD and the surface of protein–DNA interaction of DBD , in androgen receptor (AR), currently most drugs are still designed to target the LBP of NRs, which may suffer from the basic question that whether the designed compound is an agonist or an antagonist because both types of the ligands bind to the same position of the LBP, whereas exhibiting different downstream physiological effects. To answer this question, numerous studies have been conducted to investigate the binding mechanisms of agonists and antagonists to the LBP of NRs, explaining that the difference of binding preference of the agonists and antagonists may help to stabilize different conformation of the H12 helix of an NR. ,− However, developing experimental methods for determining the category of the NR ligands is usually complicated and the proposed method may only work in certain systems, and it is also very time-consuming to determine the category of an NR ligand through investigating the conformational change of the H12 helix derived from theoretical approaches such as long-time MD simulation. − As a result, more efficient strategies should be devised for distinguishing between agonists and antagonists.…”