Three-dimensional pharmacophore modeling of liver-X receptor agonists

High cholesterol levels contribute to hyperlipidemia. Liver X receptors (LXRs) are the drug targets. LXRs regulate the cholesterol absorption, biosynthesis, transportation, and metabolism. Novel agonists of LXR, especially LXRβ, are attractive solutions for treating hyperlipidemia. In order to discover novel LXRβ agonists, a three-dimensional pharmacophore model was built based upon known LXRβ agonists. The model was validated with a test set, a virtual screening experiment, and the FlexX docking approach. Results show that the model is capable of predicting a LXRβ agonist activity. Ligand-based virtual screening results can be refined by cross-linking by structure-based approaches. This is because two ligands that are mapped in the same way to the same pharmacophore model may have significantly different binding behaviors in the receptor's binding pocket. This paper reports our approach to identify reliable pharmacophore models through combining both ligand- and structure-based approaches.     

Antagonist binding in the rat muscarinic receptor A study by docking and X-ray crystallography

A series of agonists to the rat muscarinic receptor have been docked computationally to the active site of a homology model of rat M1 muscarinic receptor. The agonists were modelled on the X-ray crystal structure of atropine, which is reported here and the docking studies are shown to reproduce correctly the order of experimental binding affinities for the agonists as well as indicate where there appear to be inconsistencies in the experimental data. The crystal and molecular structure of atropine (tropine tropate; -[hydroxymethyl]benzeneacetic acid 8-methyl[3.2.1]oct-3-yl ester C₁₇H₂₃NO₃) has been determined by X-ray crystallography using an automated Patterson search method, and refined by full-matrix least-squares to a final R of 0.0452 for 2701 independent observed reflections and 192 parameters using Mo K radiation, λ = 0.71073 Å at 150 K. The compound crystallises in space group Fdd2 with Z = 16 molecules per unit cell.     

Structural Insights into Ligand—Receptor Interactions Involved in Biased Agonism of G-Protein Coupled Receptors

G protein-coupled receptors (GPCRs) are versatile signaling proteins that mediate complex cellular responses to hormones and neurotransmitters. Ligand directed signaling is observed when agonists, upon binding to the same receptor, trigger significantly different configuration of intracellular events. The current work reviews the structurally defined ligand – receptor interactions that can be related to specific molecular mechanisms of ligand directed signaling across different receptors belonging to class A of GPCRs. Recent advances in GPCR structural biology allow for mapping receptors’ binding sites with residues particularly important in recognition of ligands’ structural features that are responsible for biased signaling. Various studies show particular role of specific residues lining the extended ligand binding domains, biased agonists may alternatively affect their interhelical interactions and flexibility what can be translated into intracellular loop rearrangements. Studies on opioid and angiotensin receptors indicate importance of residues located deeper within the binding cavity and direct interactions with receptor residues linking the ortosteric ligand binding site with the intracellular transducer binding domain. Collection of results across different receptors may suggest elements of common molecular mechanisms which are responsible for passing alternative signals from biased agonists.     

距离比较法构建M1受体激动剂药效团模型

在M1受体三维结构未知的情况下,利用距离比较法（DISCO）对24个具有M1受体激动活性的化合物进行了研究,构建了M1受体激动剂可能的药效团模型,为设计新M1受体激动剂提供了参考,并以此为提问结构在ACD数据库和中草药数据系统（TCMDB）中进行搜索,得到一系列结构新颖并可能具有M1激动活性的化合物.     

Modeling and molecular dynamics simulation of the human gonadotropin-releasing hormone receptor in a lipid bilayer

In the present study, a model for the human gonadotropin-releasing hormone receptor embedded in an explicit lipid bilayer was developed. The final conformation was obtained by extensive molecular dynamics simulations of a homology model based on the bovine rhodopsin crystal structure. The analysis of the receptor structure allowed us to detect a number of specific contacts between different amino acid residues, as well as water- and lipid-mediated interactions. These interactions were stable in six additional independent 35 ns long simulations at 310 and 323 K, which used the refined model as the starting structure. All loops, particularly the extracellular loop 2 and the intracellular loop 3, exhibited high fluctuations, whereas the transmembrane helices were more static. Although other models of this receptor have been previously developed, none of them have been subjected to extensive molecular dynamics simulations, and no other three-dimensional structure is publicly available. Our results suggest that the presence of ions as well as explicit solvent and lipid molecules are critical for the structure of membrane protein models, and that molecular dynamics simulations are certainly useful for their refinement.     

Exploring the molecular basis of selectivity in A1 adenosine receptors agonists: a case study

Adenosine is a naturally occurring purine nucleoside that has a wide variety of well-documented regulatory functions and physiological roles. Selective activation of the adenosine A₁ receptor has drawn attention in drug discovery for the therapeutic effects on neural and cardiovascular disorders. We have developed a model of the human A₁ adenosine receptor using bovine rhodopsin as a template. A flexible docking approach has been subsequently carried out for evaluating the molecular interactions of twenty-one selective A₁ agonists with the receptor model. The results of these studies are consistent with mutational and biochemical data. In particular, they highlight a wide hydrogen-bonding network between the nucleoside portion of the ligands and the A₁ receptor as well as key amino acids for hydrophobic interactions with the different N⁶-groups of the agonists. The models presented here provide a detailed molecular map for the selective stimulation of the adenosine A₁ receptor subtype and a steady basis for the rational design of new A₁ selective ligands.     

Three-dimensional models of glutamate receptors

Structural models of glutamate receptors have been produced as part of a multidisciplinary study of neuronal function--both ligand/receptor interactions and ion transport--at the atomic level. The models have concentrated on the agonist binding and transmembrane domains of ionotropic (i.e. ligand-gated) glutamate receptors (iGluRs), and have aided our understanding of the molecular determinants of (1) ligand binding and (2) channel activity. The model building process involved a combination of homology modelling, distance geometry, molecular mechanics, protein-ligand and protein-protein docking, electrostatic calculations and manual adjustment, in conjunction with restraints from site-directed mutagenesis, ligand binding and electrophysiological studies. The initial models were used to produce hypotheses which were tested experimentally; these models have been subsequently refined as part of an extremely effective multidisciplinary study using an iterative molecular modelling/experimental verification cycle in which restraints derived from experimental studies are used at all stages, and the findings from one round of modelling are used as restraints in the next. By studying a variety of agonists and antagonists, details have been built up of (1) those residues involved in ligand binding and (2) the role of agonist binding (i.e. agonist-induced conformational change) in channel gating. The models also aid our understanding of the conductance properties of the channels.     

距离比较法构建M1受体激动剂药效团模型

在M1受体三维结构未知的情况下,利用距离比较法(DISCO)对24个具有Mi受体激动活性的化合物进行了研究,构建了Mi受体激动剂可能的药效团模型,为设计新M1受体激动剂提供了参考,并以此为提问结构在ACD数据库和中草药数据系统(TCMDB)中进行搜索,得到一系列结构新颖并可能具有Mi激动活性的化合物.     

表皮生长因子受体和抑制剂之间分子对接的研究

研究了表皮生长因子受体(EGFR)和4-苯胺喹唑啉类抑制剂之间的相互作用模式，表皮生长因子受体的三维结构通过同源蛋白模建的方法得到，而抑制剂和靶酶结合复合物结构则通过分子力学和分子动力学结合的方法计算得到。从模拟结果得到的抑制剂和靶酶之间的相互作用模式表明范德华相互作用、疏水相互作用以及氢键相互作用对抑制剂的活性都有重要的影响，抑制剂的苯胺部分位于活性口袋的底部，能够与受体残基的非极性侧链产生很强的范德华和疏水相互作用，抑制剂双环上的取代基团也能和活性口袋外部的部分残基形成一定的范德华和疏水性相互作用，而抑制剂喹唑啉环上的氮原子能和周围的残基形成较强的氢键相互作用，对抑制剂的活性有较大的影响，计算得到抑制剂和靶酶之间的非键相互作用能以及抑制剂和靶酶之间的相互作用信息能够很好地解释抑制剂活性和结构的关系，为全新抑制剂的设计提供了重要的结构信息。     

A model of the human M2 muscarinic acetylcholine receptor

The M₂ muscarinic acetylcholine receptor belongs to the family of rhodopsin like G-Protein Coupled Receptors. This subtype of muscarinic receptors is of special interest because it bears, aside from an orthosteric binding site, also an allosteric binding site. Based on the X-ray structure of bovine rhodopsin a complete homology model of the human M₂ receptor was developed. For the orthosteric binding site point mutations and binding studies with different agonists and antagonists are available. This knowledge was utilized for an initial verification of the M₂ model. Allosteric modulation of activity is mediated by structurally different ligands such as gallamine, caracurine V salts or W84 (a hexamethonium-derivative). Caracurine V derivatives with different affinities to M₂ were docked using GRID-fields. Subsequent molecular dynamics simulations yielded different binding energies based on diverse electrostatic and lipophilic interactions. The calculated affinities are in good agreement to experimentally determined affinities.     

Modelling of ORL1 receptor-ligand interactions

An opioid receptor like (ORL1) receptor is one of a family of G-protein-coupled receptors (GPCR); it represents a new pharmaceutical target with extensive therapeutic potential for the regulation of important biological functions such as nociception, mood disorders, drug abuse, learning or cardiovascular control. Although the crystal structure of the inactive form of the ORL1 receptor has been determined, little is known about its activation. By using X-ray structures of the β2-adrenegic receptor in its inactive (2RH1) and active (3P0G) states as templates, inactive and active homology models of the ORL1 receptor were constructed. Structurally diverse sets of strongly binding antagonists and agonists were docked with both ORL1 receptor forms. The major receptor-ligand interactions responsible for antagonist and agonist binding were identified. Although both sets of ligands, agonists and antagonists, bind to the same region of the receptor, they occupy partially different binding pockets. Agonists bind to the inactive receptor in a slightly different manner than antagonists. This difference is more pronounced in binding to the active ORL1 receptor model and points to the amino acids at the extracellular end of TM6, suggesting that this region is important for receptor-activation.     

Unbinding of nicotine from the acetylcholine binding protein: steered molecular dynamics simulations

The ligand binding/unbinding process is critical to our understanding of the pharmacology of both the nicotinic acetylcholine receptor (nAChR) and the acetylcholine binding protein (AChBP). Steered molecular dynamics simulations were performed to learn about the unbinding process of the full agonist nicotine. Three different pulling models were designed to investigate the possible binding/unbinding pathways: radial and tangent models, and also a mixed model. Of the three, the tangent pulling model finally failed to dissociate nicotine from the ligand binding pocket. The efficiency of the pulling force profiles was superior, and the opening of the C-loop was smaller in the mixed pulling model than that in the radial model. The most favorable pathway for the cholinergic agonist nicotine to enter or leave the binding pocket is through the principal binding side, following a curvilinear track. Noticeably, it has been seen that the unbinding of the nicotine is concomitant with a global rotation of the protein-ligand complex which could be caused by the interactions of the ligand with protein at the tangent direction.     

Toward deciphering the code to aminergic G protein-coupled receptor drug design

The trace amine-associated receptor 1 (TAAR(1)) is a biogenic amine G protein-coupled receptor (GPCR) that is potently activated by 3-iodothyronamine (1, T(1)AM) in vitro. Compound 1 is an endogenous derivative of the thyroid hormone thyroxine which rapidly induces hypothermia, anergia, and bradycardia when administered to mice. To explore the role of TAAR(1) in mediating the effects of 1, we rationally designed and synthesized rat TAAR(1) superagonists and lead antagonists using the rotamer toggle switch model of aminergic GPCR activation. The functional activity of a ligand is proposed to be correlated to its probable interactions with the rotamer switch residues; agonists allow the rotamer switch residues to toggle to their active conformation, whereas antagonists interfere with this conformational transition. These agonist and antagonist design principles provide a conceptual model for understanding the relationship between the molecular structure of a drug and its pharmacological properties.     

基于结构和药效团特征的人类腺苷受体拮抗剂选择性比较

腺苷受体是重要的治疗靶标,选择性腺苷受体拮抗剂具有广泛的临床应用前景.本文通过同源模建构建了腺苷A₁、A_2B和A₃受体的结构,采用LigandScout 3.12软件分别构建了腺苷受体四种亚型的拮抗剂药效团模型.然后利用Schrödinger程序中的Induced Fit Docking模块完成受体-拮抗剂结合模式的预测,并与药效团结果进行比对.结果发现,由于结合口袋部位的残基在家族间高度保守,模建得到的各个亚型受体的初始结构活性口袋部位极为相似,无法用于亚型选择性拮抗剂的识别.而腺苷受体四种亚型拮抗剂药效团的药效特征与空间排布都不同,并与以前突变实验信息相吻合.研究结果说明,结合口袋部位的优化是模建中的关键步骤,基于配体的药效团模型所包含的一系列药效特征元素如氢键受体、氢键供体、疏水基团、芳环中心,可以很好地表征受体结合部位氢键、疏水空腔的位置及其方向.本文研究结果可以为进一步的优化同源模建结果,寻找新型的人类腺苷受体选择性拮抗剂提供理论依据.     

A computational model of the 5-HT3 receptor extracellular domain: search for ligand binding sites

A three-dimensional model of the 5-HT₃ receptor extarcellular domain has been derived on the basis of the nicotinic acetylcholine receptor model recently published by Tsigelny et al. Maximum complementarity between the position and characteristics of mutated residues putatively involved in ligand interaction and the pharmacophoric elements derived by the indirect approach applied on several series of 5-HT₃ ligands have been exploited to gain insights into the ligand binding modalities and to speculate on the mechanistic role of the structural components. The analysis of the three-dimensional model allows one to distinguish among amino acids that exert key roles in ligand interactions, subunit architecture, receptor assembly and receptor dynamics. For some of these, alternative roles with respect to the ones hypothesized by experimentalists are assigned. Different binding modalities for agonists and antagonists are highlighted, and residues which probably play a role in the transduction of binding into a change in conformational state of the receptor are suggested. Received: 27 July 2000 / Accepted: 15 September 2000 / Published online: 21 December 2000     

Structure of the virus capsid protein VP1 of enterovirus 71 predicted by some homology modeling and molecular docking studies

The homology modeling technique has been used to construct the structure of enterovirus 71 (EV 71) capsid protein VP1. The protein is consisted of 297 amino acid residues and treated as the target. The amino acid sequence identity between the target protein and sequences of template proteins 1EAH, 1PIV, and 1D4M searched from NCBI protein BLAST and WorkBench protein tools were 38, 37, and 36%, respectively. Based on these template structures, the protein model was constructed by using the InsightII/Homology program. The protein model was briefly refined by energy minimization and molecular dynamics (MD) simulation steps. The protein model was validated using some web available servers such as ERRAT, PROCHECK, PROVE, and PROSA2003. However, an inconsistency between the docking scores and the measured activity was observed for a series of EV 71 VP1 inhibitors synthesized by Shia et al. (J Med Chem 2002, 45, 1644) and docked into the binding pocket of the protein model using the DOCK 4.0.2 program. The protein model with an EV 71 VP1 inhibitor docked and engulfed was then refined further by some MD simulation steps in the presence of water molecules. The docking scores obtained for these inhibitors after such a MD refinement were well correlated with the activities. The structure-activity relationships for the ligand-protein model system was also analyzed using the GRID-VOLSURF programs and the corresponding noncrossvalidated and crossvalidated (by leave-one-out) r2 and q2 were 0.99 and 0.61, respectively. The hydrophobic nature of the binding pocket of the protein model was also examined using the GRID21 program. The possibility of improving the potency of the current series of EV 71 VP1 inhibitors was discussed based on all the studies presented.     

Identifying conformational changes of the β2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators

The new β₂ Adrenoceptor (β₂AR) crystal structures provide a high-resolution snapshot of receptor interactions with two particular partial inverse agonists, (−)-carazolol and timolol. However, both experimental and computational studies of GPCR structure are significantly complicated by the existence of multiple conformational states coupled to ligand type and receptor activity. Agonists and antagonists induce or stabilize distinct changes in receptor structure that mediate a range of pharmacological activities. In this work, we (1) established that the existing β₂AR crystallographic conformers can be extended to describe ligand/receptor interactions for additional antagonist types, (2) generated agonist-bound receptor conformations, and (3) validated these models for agonist and antagonist virtual ligand screening (VLS). Using a ligand directed refinement protocol, we derived a single agonist-bound receptor conformation that selectively retrieved a diverse set of full and partial β₂AR agonists in VLS trials. Additionally, the impact of extracellular loop two conformation on VLS was assessed by docking studies with rhodopsin-based β₂AR homology models, and loop-deleted receptor models. A general strategy for constructing and selecting agonist-bound receptor pocket conformations is presented, which may prove broadly useful in creating agonist and antagonist bound models for other GPCRs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Sequence-selective recognition of peptides within the single binding pocket of a self-assembled coordination cage

The single binding pocket of a self-assembled Pd6L4 coordination cage recognizes oligopeptides in a highly sequence-selective fashion. In particular, the Trp-Trp-Ala sequence is strongly bound by the cavity (Ka >/=106 M-1). Tripeptides possessing the same residues but in different sequences (i.e., Trp-Ala-Trp and Ala-Trp-Trp) show much poorer affinity. Even singly mutated tripeptides with aromatic-aromatic-aliphatic sequences of the residues (e.g., Trp-Trp-Gly and Trp-Tyr-Ala) are not recognized efficiently. X-ray analysis and NMR reveal that all residues of the Trp-Trp-Ala sequence cooperatively interact with the cage via CH-pi and pi-pi interactions.     

A two model receptor system of the alpha1D adrenergic receptor to describe interactions with epinephrine and BMY7378

In this study, we have developed a two receptor model system to describe the R and R states of G-protein coupled receptors, specifically the alpha(1D) adrenergic receptor. The two models interact with agonist (epinephrine) and antagonist (BMY7378) differently. The active model has increased interactions with epinephrine. The inactive model has increased interactions with BMY7378. We also explored the protonation state of the ligands. When the most basic amine was protonated, we found increased hydrogen bonding and increased aromatic interactions. Protonated epinephrine hydrogen bonds with Asp176 and has aromatic residues Trp172, Trp235, Trp361, and Phe388 within 3 Angstroms. Protonated BMY7378 hydrogen bonds with Trp172 and Lys236 and has aromatic residues Trp172, Trp254, Phe364, Phe384, and Phe388 within 3 Angstroms. We conclude that the two model system is required to represent the two states of the receptor and that protonation of the ligand is also critical.     

Binding of agonists and antagonists to muscarinic receptors.

The binding of one irreversible and two reversible radioactive antagonists to muscarinic receptors in synaptosome preparations of rat cerebral cortex has been studied. The ligands all bind to the same receptor pool and directly and competitively yield self-consistent binding constants closely similar to those obtained by pharmacological methods on intact smooth muscle. The binding process for antagonists seems to be a simple mass action-determined process with a Hill slope of 1.0. The quantitative correlations strongly support the view that the receptor studied by ligand binding corresponds to the receptor studied by pharmacological methods. Inhibition of antagonist binding by most agonists shows a reduced Hill slope which also applies to direct binding studies of [3H] acetylcholine. Mechansims that might account for the behavior of agonists are discussed but do not conclusively point to any single mechanism.