Ligand unbinding from the estrogen receptor: a computational study of pathways and ligand specificity

Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling

It is well-known that the potency of a drug is heavily associated with its kinetic and thermodynamic properties with the target. Nuclear receptors (NRs), as an important target family, play important roles in regulating a variety of physiological processes in vivo. However, it is hard to understand the drug-NR interaction process because of the closed structure of the ligand-binding domain (LBD) of the NR proteins, which apparently hinders the rational design of drugs with controllable kinetic properties. Therefore, understanding the underlying mechanism of the ligand-NR interaction process seems necessary to help NR drug design. However, it is usually difficult for experimental approaches to interpret the kinetic process of drug-target interactions. Therefore, in silico methods were utilized to explore the optimal binding/dissociation pathways of the NR ligands. Specifically, farnesoid X receptor (FXR) is considered here as the target system since it has been an important target for the treatment of bile acid metabolism-associated diseases, and a series of structures cocrystallized with diverse scaffold ligands were resolved. By using random acceleration molecular dynamics (RAMD) simulation and umbrella sampling (US), 5 main dissociation pathways (pathways I-V) were identified in 11 representative FXR ligands, with most of them (9/11) preferring to go through Pathway III and the remaining two favoring escaping from Pathway I and IV. Furthermore, key residues functioning in the three main dissociation pathways were revealed by the kinetic residue energy analysis (KREA) based on the US trajectories, which may serve as road-marker residues for rapid identification of the (un)binding pathways of FXR ligands. Moreover, the preferred pathways explored by RAMD simulations are in good agreement with the minimum free energy path identified by the US simulations with the Pearson R = 0.76 between the predicted binding affinity and the experimental data, suggesting that RAMD is suitable for applying in large-scale (un)binding-pathway exploration in the case of ligands with obscure binding tunnels to the target.

Structural mechanism of human oncochannel TRPV6 inhibition by the natural phytoestrogen genistein

Calcium-selective oncochannel TRPV6 is the major driver of cell proliferation in human cancers. While significant effort has been invested in the development of synthetic TRPV6 inhibitors, natural channel blockers have been largely neglected. Here we report the structure of human TRPV6 in complex with the plant-derived phytoestrogen genistein, extracted from Styphnolobium japonicum, that was shown to inhibit cell invasion and metastasis in cancer clinical trials. Despite the pharmacological value, the molecular mechanism of TRPV6 inhibition by genistein has remained enigmatic. We use cryo-EM combined with electrophysiology, calcium imaging, mutagenesis, and molecular dynamics simulations to show that genistein binds in the intracellular half of the TRPV6 pore and acts as an ion channel blocker and gating modifier. Genistein binding to the open channel causes pore closure and a two-fold symmetrical conformational rearrangement in the S4-S5 and S6-TRP helix regions. The unprecedented mechanism of TRPV6 inhibition by genistein uncovers new possibilities in structure-based drug design.

The prediction of protein-ligand unbinding for modern drug discovery

INTRODUCTION

Drug-target thermodynamic and kinetic information have perennially important roles in drug design. The prediction of protein-ligand unbinding, which can provide important kinetic information, in experiments continues to face great challenges. Uncovering protein-ligand unbinding through molecular dynamics simulations has become efficient and inexpensive with the progress and enhancement of computing power and sampling methods.

AREAS COVERED

In this review, various sampling methods for protein-ligand unbinding and their basic principles are firstly briefly introduced. Then, their applications in predicting aspects of protein-ligand unbinding, including unbinding pathways, dissociation rate constants, residence time and binding affinity, are discussed.

EXPERT OPINION

Although various sampling methods have been successfully applied in numerous systems, they still have shortcomings and deficiencies. Most enhanced sampling methods require researchers to possess a wealth of prior knowledge of collective variables or reaction coordinates. In addition, most systems studied at present are relatively simple, and the study of complex systems in real drug research remains greatly challenging. Through the combination of machine learning and enhanced sampling methods, prediction accuracy can be further improved, and some problems encountered in complex systems also may be solved.

Metadynamics-Based Approaches for Modeling the Hypoxia-Inducible Factor 2α Ligand Binding Process

Several methods based on enhanced-sampling molecular dynamics have been proposed for studying ligand binding processes. Here, we developed a protocol that combines the advantages of steered molecular dynamics (SMD) and metadynamics. While SMD is proposed for investigating possible unbinding pathways of the ligand and identifying the preferred one, metadynamics, with the path collective variable (PCV) formalism, is suggested to explore the binding processes along the pathway defined on the basis of SMD, by using only two CVs. We applied our approach to the study of binding of two known ligands to the hypoxia-inducible factor 2α, where the buried binding cavity makes simulation of the process a challenging task. Our approach allowed identification of the preferred entrance pathway for each ligand, highlighted the features of the bound and intermediate states in the free-energy surface, and provided a binding affinity scale in agreement with experimental data. Therefore, it seems to be a suitable tool for elucidating ligand binding processes of similar complex systems.

Ligand Pathways in Nuclear Receptors

Nuclear receptors (NRs) are ligand-inducible transcription factors that play an essential role in a multitude of physiological processes as well as diseases, rendering them attractive drug targets. Crystal structures revealed the binding site of NRs to be buried in the core of the protein, with no obvious route for ligands to access this cavity. The process of ligand binding is known to be an often-neglected contributor to the efficacy of drug candidates and is thought to influence the selectivity and specificity of NRs. While experimental methods generally fail to highlight the dynamic processes of ligand access or egress on the atomistic scale, computational methods have provided fundamental insight into the pathways connecting the buried binding pocket to the surrounding environment. Methods based on molecular dynamics (MD) and Monte Carlo simulations have been applied to identify pathways and quantify their capability to transport ligands. Here, we systematically review findings of more than 20 years of research in the field, including the applied methodology and controversies. Further, we establish a unified nomenclature to describe the pathways with respect to their location relative to protein secondary structure elements and summarize findings relevant to drug design. Lastly, we discuss the effect of NR interaction partners such as coactivators and corepressors, as well as mutations on the pathways.

Understanding the differences of the ligand binding/unbinding pathways between phosphorylated and non-phosphorylated ARH1 using molecular dynamics simulations

ADP-ribosylhydrolases (ARH1, ARH2 and ARH3) are a family of enzymes to catalyze ADP-ribosylation, a reversible and covalent post-translational modification (PTM). There are four phosphorylated sites (Tyr-4, Tyr-19, Tyr-20, and Tyr-205) in ARH1. To explore the structural changes and functional impact induced by phosphorylation, molecular dynamics (MD) simulations and steered molecular dynamics (SMD) simulations were performed for the phosphorylated and non-phosphorylated ARH1 with the ligands. MD simulations results indicate that: (1) Glu-25 is more frequently in the α helix group in the phosphorylated state with the adenosine-5-diphosphate-ribosylarginine (ADP-RA) complex (51.56%) than that of the non-phosphorylated state(2.12%); (2) Ser-124 and Ser-264 become less flexible in the phosphorylated state with ADP-RA complex, which helps two residues form hydrogen bonds with ADP-RA; and (3) Tyr-211 is also less flexible in the phosphorylated state with ADP-RA complex, which helps stabilize the cation-π interaction of Y211-R119. All these changes facilitate ADP-RA to bind ARH1. In addition, according to the crystal structure of adenosine-5-diphosphate-ribose (ADP-ribose) in complex with non-phosphorylated and phosphorylated ARH1, the possible unbinding pathways of ADP-ribose from non-phosphorylated and phosphorylated ARH1 were explored respectively using SMD simulations. Our results show that phosphorylated ARH1 has more ordered structures than the non-phosphorylated type.

Exploring the different ligand escape pathways in acylaminoacyl peptidase by random acceleration and steered molecular dynamics simulations

Acylaminoacyl peptidase (APH, EC 3.4.19.1) is a novel class of serine-type protease belonging to the prolyl oligopeptidase (POP) family.

The orientation and dynamics of estradiol and estradiol oleate in lipid membranes and HDL disc models

Estradiol (E2) and E2 oleate associate with high-density lipoproteins (HDLs). Their orientation in HDLs is unknown. We studied the orientation of E2 and E2 oleate in membranes and reconstituted HDLs, finding that E2 and E2 oleate are membrane-associated and highly mobile. Our combination of NMR measurements, molecular dynamics simulation, and analytic theory identifies three major conformations where the long axis of E2 assumes a parallel, perpendicular, or antiparallel orientation relative to the membrane's z-direction. The perpendicular orientation is preferred, and furthermore, in this orientation, E2 strongly favors a particular roll angle, facing the membrane with carbons 6, 7, 15, and 16, whereas carbons 1, 2, 11, and 12 point toward the aqueous phase. In contrast, the long axis of E2 oleate is almost exclusively oriented at an angle of ∼60° to the z-direction. In such an orientation, the oleoyl chain is firmly inserted into the membrane. Thus, both E2 and E2 oleate have a preference for interface localization in the membrane. These orientations were also found in HDL discs, suggesting that only lipid-E2 interactions determine the localization of the molecule. The structural mapping of E2 and E2 oleate may provide a design platform for specific E2-HDL-targeted pharmacological therapies.

Computational insights into inhibitory mechanism of azole compounds against human aromatase

We investigated the inhibitory mechanism of azole aromatase inhibitors. The results showed that letrozole and imazalil prefer different unbinding pathways.

Molecular modeling revealed that ligand dissociation from thyroid hormone receptors is affected by receptor heterodimerization

Numerous ligands bind tightly to thyroid hormone receptors (TRs), and exploring the binding and dissociation of these ligands from TRs will increase our understanding of their mechanisms of action. TRs form transcriptionally active heterodimers with retinoid X receptor (RXR); whether this heterodimerization affects ligand dissociation is poorly understood. To investigate the effects of heterodimerization, classical molecular dynamics (MD) simulations and random acceleration molecular dynamics (RAMD) simulations were performed to probe the dissociation of triiodothyronine (T3) from a TRα-RXR ligand binding domain (LBD) heterodimer and the TRα and TRβ LBDs at the atomic level. Seven (I-VII) dissociation pathways were identified for T3. Heterodimerization inhibited pathway I in the TRα-RXR LBD heterodimer, which may block the proper orientation of the helix 12 (H12), therefore affecting the biological functions of TRs. Upon TR heterodimerization, the second most dominant dissociation pathway switched from pathway IV for TRα LBD to pathway II for TRα-RXR LBD. No significant effects of TR heterodimerization were observed on the dominant dissociation pathway III that was located between H3, the H1-H2 loop and the β-sheet. Our study revealed that TR heterodimerization significantly affects T3 dissociation, which provides important information for the study of other TR ligands.

Unbinding pathways of GW4064 from human farnesoid X receptor as revealed by molecular dynamics simulations

Farnesoid X receptor (FXR, NR1H4) is a member of a nuclear receptor superfamily, which plays important roles in bile acid homeostasis, lipoprotein and glucose metabolism, and hepatic regeneration. GW4064 is a potent and selective FXR agonist and has become a tool compound to probe the physiological functions of FXR. Until now, the mechanism of GW4064 entering and leaving the FXR pocket is still poorly understood. Here, we report a computational study of GW4064 unbinding pathways from FXR by using several molecular dynamics (MD) simulation techniques. Based on the crystal structure of FXR in complex with GW4064, conventional MD was first used to refine the binding and check the stability of GW4064 in the FXR pocket. Random acceleration MD simulations were then performed to explore the possible unbinding pathways of GW4064 from FXR. Four main pathway clusters were found, among which three subpathways, namely Paths 2A, 2B, and 1B, were observed most frequently. Multiple steered MD simulations were further employed to estimate the maximum rupture force and the sum of the forces and to characterize the intermediate states of the ligand unbinding process. By comparing the average force profiles and structural changes, Paths 2A and 2B were identified to be the most favorable unbinding pathways. The former is located between the H1-H2 loop and the H5-H6 loop, and the latter is located in the cleft formed by the H5-H6 loop, H6, and H7. Moreover, the residues lining the pathways were analyzed for their roles in ligand unbinding. Based on our results, the possible structural modification strategies on GW4064 were also proposed.

In silico study of Aquaporin V: Effects and affinity of the central pore-occluding lipid

Because of its roles in human physiology, Aquaporin V (AQP5), a major intrinsic protein, has been a subject of many in vitro studies. In particular, a 2008 experiment produced its crystal structure at 2.0Å resolution, which is in a tetrameric conformation consisting of four protomers. Each protomer forms an amphipathic pore that is fit for water permeation. The tetramer has a pore along its quasi-symmetry axis formed by quadruplets of hydrophobic residues (every protomer contributes equally to the quadruplets). A lipid, phosphatidylserine (PS6), is bound to AQP5 in the central pore, totally occluding it. A 2009 experiment showed that AQP5 facilitates not only permeation of water but also permeation of hydrophobic gas molecules across the cell membrane. In this article, we present an in silico study of AQP5 to elucidate the effects of PS6's binding to and dissociating from AQP5's central pore. Computing the lipid's chemical-potential along its dissociation path, we find that PS6 inhibits the function of the central pore with an IC(50) in the micromolar range. Examining the central pore and the interstices between two adjacent protomers, we propose that nonpolar gas molecules (O(2)) permeate through AQP5's hydrophobic central pore when un-occluded.

Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units

Building on our recently introduced library-based Monte Carlo (LBMC) approach, we describe a flexible protocol for mixed coarse-grained (CG)/all-atom (AA) simulation of proteins and ligands. In the present implementation of LBMC, protein side chain configurations are pre-calculated and stored in libraries, while bonded interactions along the backbone are treated explicitly. Because the AA side chain coordinates are maintained at minimal run-time cost, arbitrary sites and interaction terms can be turned on to create mixed-resolution models. For example, an AA region of interest such as a binding site can be coupled to a CG model for the rest of the protein. We have additionally developed a hybrid implementation of the generalized Born/surface area (GBSA) implicit solvent model suitable for mixed-resolution models, which in turn was ported to a graphics processing unit (GPU) for faster calculation. The new software was applied to study two systems: (i) the behavior of spin labels on the B1 domain of protein G (GB1) and (ii) docking of randomly initialized estradiol configurations to the ligand binding domain of the estrogen receptor (ERα). The performance of the GPU version of the code was also benchmarked in a number of additional systems.

Putative binding sites, and pathways to them, for amidine and guanidine current inhibitors on acid-sensing ion channels (ASIC). A theoretical approach with hASIC1a homology model

Central inhibition of the acid-sensing hASIC1a channel, acting upstream of the opiate system, might serve to treat any type of pain, avoiding the unwanted addiction problems of the opioid drugs. To this end, inhibition of hASIC1a channel by PcTx1, a peptide from the Trinidad chevron tarantula, is under development. New inhibitors of the hASIC1a channel are also being sought, in the hope of further modulating the activity, from which antiplasmodial amidine and guanidine phenyl drugs have emerged as promising candidates. However, how such current inhibition takes place remains obscure from the molecular point of view, hindering any further progress in developing drugs. Therefore, the nature of the binding sites, and how they are reached by the amidine-guanidine drugs, was investigated here via automated docking and molecular dynamics with hASIC1a homology models. This study has revealed that this ion channel is rich in binding sites, and that flexible drugs, such as nafamostat, may penetrate it in a snake-like elongated conformation. Then, crawling like a snake through temporary holes in the protein, nafamostat either simply flips, or changes to a high-energy folded conformation to become adapted to the shape of the binding site.

Structure and elasticity of lipid membranes with genistein and daidzein bioflavinoids using X-ray scattering and MD simulations

This work reports the effects of the bioflavinoids genistein and daidzein on lipid bilayers as determined by volume measurements, X-ray scattering, and molecular dynamics simulations. The experimental and simulated total molecular volumes were found to be in outstanding agreement with each other before the addition of genistein and daidzein and also after their addition. Both bioflavinoids inserted into the hydrocarbon region of both DOPC and diphytanoylPC near the carbonyls of the lipids and both decreased the bilayer thicknesses. The long axes of both bioflavinoids were oriented nearly parallel to the plane of the bilayer with their carbonyl groups preferentially pointed toward the proximal surface. A difference is that daidzein had a solubility limit of ∼0.14 mol fraction in DOPC (∼0.12 mol fraction in diphytanoylPC), whereas genistein was soluble at least to 0.20 mol fraction in both lipid membranes. Measurements of bending modulus K(C) and simulation results for area compressibility modulus K(A) indicate that both bioflavinoids soften bilayers.

Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible?

Although the principle of microscopic reversibility has been studied for many decades, there remain ambiguities in its application to non-equilibrium processes of importance to chemistry, physics and biology. Examples include whether protein unfolding should follow the same pathways and in the same proportions as folding, and whether unbinding should likewise mirror binding. Using continuum-space calculations which extend previous kinetic analyses, we demonstrate formally that the precise symmetry of forward and reverse processes is expected only under certain special conditions. Approximate symmetry will be exhibited under a separate set of conditions. Exact, approximate, and broken symmetry scenarios are verified in several ways: using numerical calculations on toy and molecular systems; using exact calculations on kinetic models of induced fit in protein-ligand binding; and based on reported experimental results. The analysis highlights intrinsic challenges and ambiguities in the design and analysis of both experiments and simulations.

Structure of estradiol metal chelate and estrogen receptor complex: the basis for designing a new class of selective estrogen receptor modulators

Selective estrogen receptor modulators, such as 17β-estradiol derivatives bound to metal complexes, have been synthesized as targeted probes for the diagnosis and treatment of breast cancer. Here, we report the detailed 3D structure of estrogen receptor α ligand-binding domain (ERα-LBD) bound with a novel estradiol-derived metal complex, estradiol-pyridine tetra acetate europium(III), at 2.6 Å resolution. This structure provides important information pertinent to the design of novel functional ERα targeted probes for clinical applications.

Exploring the free-energy landscapes of biological systems with steered molecular dynamics

We perform steered molecular dynamics (SMD) simulations and use the Brownian dynamics fluctuation-dissipation-theorem (BD-FDT) to accurately compute the free-energy profiles for several biophysical processes of fundamental importance: hydration of methane and cations, binding of benzene to T4-lysozyme L99A mutant, and permeation of water through aquaglyceroporin. For each system, the center-of-mass of the small molecule (methane, ion, benzene, and water, respectively) is steered (pulled) at a given speed over a period of time, during which the system transitions from one macroscopic state/conformation (State A) to another one (State B). The mechanical work of pulling the system is measured during the process, sampling a forward pulling path. Then the reverse pulling is conducted to sample a reverse path from B back to A. Sampling a small number of forward and reverse paths, we are able to accurately compute the free-energy profiles for all the afore-listed systems that represent various important aspects of biological physics. The numerical results are in excellent agreement with the experimental data and/or other computational studies available in the literature.

Fatty acids derived from royal jelly are modulators of estrogen receptor functions

Royal jelly (RJ) excreted by honeybees and used as a nutritional and medicinal agent has estrogen-like effects, yet the compounds mediating these effects remain unidentified. The possible effects of three RJ fatty acids (FAs) (10-hydroxy-2-decenoic-10H2DA, 3,10-dihydroxydecanoic-3,10DDA, sebacic acid-SA) on estrogen signaling was investigated in various cellular systems. In MCF-7 cells, FAs, in absence of estradiol (E₂), modulated the estrogen receptor (ER) recruitment to the pS2 promoter and pS2 mRNA levels via only ERβ but not ERα, while in presence of E₂ FAs modulated both ERβ and ERα. Moreover, in presence of FAs, the E₂-induced recruitment of the EAB1 co-activator peptide to ERα is masked and the E₂-induced estrogen response element (ERE)-mediated transactivation is inhibited. In HeLa cells, in absence of E₂, FAs inhibited the ERE-mediated transactivation by ERβ but not ERα, while in presence of E₂, FAs inhibited ERE-activity by both ERβ and ERα. Molecular modeling revealed favorable binding of FAs to ERα at the co-activator-binding site, while binding assays showed that FAs did not bind to the ligand-binding pocket of ERα or ERβ. In KS483 osteoblasts, FAs, like E₂, induced mineralization via an ER-dependent way. Our data propose a possible molecular mechanism for the estrogenic activities of RJ's components which, although structurally entirely different from E₂, mediate estrogen signaling, at least in part, by modulating the recruitment of ERα, ERβ and co-activators to target genes.

In silico experiments of single-chain antibody fragment against drugs of abuse

Three sets of in silico experiments have been conducted to elucidate the binding mechanics of two drugs, (+)-methamphetamine (METH) and amphetamine (AMP) to the single-chain variable fragment (scFv) recently engineered from anti-METH monoclonal antibody mAb6H4 (IgG, κlight chain, K(d)=11nM). The first set of in silico experiments are long time equilibration runs of scFv:drug complexes and of drug-free scFv both in the solution. They demonstrate how the solution structures of scFv deviate from its crystallographic form with or without drug molecules bound to it. They lead to the prediction that the Arrhenius activation barrier is nearly zero for transitions from the dissociated state to the bound state. The second set of in silico experiments are nonequilibrium dynamics of pulling the drug molecules out of the binding pocket of scFv and the equilibration runs for drugs to fall back into the binding pocket. They demonstrate that extra water molecules (in addition to the two crystallographic waters) exist inside the binding pocket, underneath the drug molecules. These extra waters must have been evaporated from the binding pockets during the crystallization process of the in vitro experiments of structural determination. The third set of in silico experiments are nonequilibrium steered molecular dynamics simulations to determine the absolute binding free energies of METH and AMP to scFv. The center of mass of a drug molecule (METH or AMP) is steered (pulled) towards (forward) and away from (reverse) the binding site, sampling forward and reverse pulling paths. Mechanic work is measured along the pulling paths. The work measurements are averaged through the Brownian dynamics fluctuation dissipation theorem to produce the free-energy profiles of the scFv:drug complexes as a function of the drug-scFv separation. These experiments lead to the theoretical prediction of absolute binding energies of METH and AMP that are in agreement with the in vitro experimental results.

Protein dynamics and ligand migration interplay as studied by computer simulation

Since proteins are dynamic systems in living organisms, the employment of methodologies contemplating this crucial characteristic results fundamental to allow revealing several aspects of their function. In this work, we present results obtained using classical mechanical atomistic simulation tools applied to understand the connection between protein dynamics and ligand migration. Firstly, we will present a review of the different sampling schemes used in the last years to obtain both ligand migration pathways and the thermodynamic information associated with the process. Secondly, we will focus on representative examples in which the schemes previously presented are employed, concerning the following: i) ligand migration, tunnels, and cavities in myoglobin and neuroglobin; ii) ligand migration in truncated hemoglobin members; iii) NO escape and conformational changes in nitrophorins; iv) ligand selectivity in catalase and hydrogenase; and v) larger ligand migration: the P450 and haloalkane dehalogenase cases. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.