Differences in Binding Sites of Two Melatonin Receptors Help to Explain Their Selectivity to Some Melatonin Analogs: A Molecular Modeling Study

Synthesis of New 2,3-Dihydroindole Derivatives and Evaluation of Their Melatonin Receptor Binding Affinity

2,3-Dihydroindoles are promising agents for the synthesis of new compounds with neuroprotective and antioxidant properties. Usually, these compounds are obtained by direct reduction of the corresponding indoles containing acceptor groups in the indole ring for its activation. In this work, we propose a synthetic strategy to obtain new 2,3-dihydroindole derivatives from the corresponding polyfunctional 2-oxindoles. Three methods were proposed for reduction of functional groups in the 2-oxindole and 2-chloroindole molecules using various boron hydrides. The possibility of chemoselective reduction of the nitrile group in the presence of an amide was shown. The proposed synthetic strategy can be used, for example, for the synthesis of new analogs of the endogenous hormone melatonin and other compounds with neuroprotective properties.

Ultra-broadband terahertz fingerprint spectrum of melatonin with vibrational mode analysis

Melatonin (MLT), as a neurotransmitter and an endogenous neurohormone, plays an important role in physiological functions through interactions with specific receptors. The conformations of MLT are closely related to its biological activities and functions. However, the internal relationship between the structure and interaction of MLT and its allosteric transition remains unclear. In this work, we obtain the broadband fingerprint terahertz (THz) spectrum of MLT in the range of 0.5-18 THz using the air-plasma terahertz time-domain spectroscopy (THz-TDS) system. DFT calculations are employed to analyze the vibration characteristics of MLT. The result shows that the low-frequency vibrations mainly come from the strong coupling between inter- and intramolecular vibrations, and the contribution of intramolecular vibrations gradually dominates with increasing frequency. Meanwhile, the local vibrations of the different functional groups distribute widely in the THz low-frequency band, relating to the diversity of conformational changes in the molecule. The intermolecular hydrogen bonds (HBs) have distinct resonant responses and play critical roles in the THz low-frequency vibrations. The study reveals the complex characteristics of the resonant coupling of MLT with THz electromagnetic waves. The results will help to understand the conformational preferences of MLT in neural signal transmission processes.

Molecular basis defining the selectivity of substituted isoquinolinones for the melatonin MT2 receptor

Melatonin MT₁ and MT₂ receptors represent attractive drug targets for the treatment of various disorders. However, the high conservation of the melatonin binding pocket has hindered the development of subtype-selective compounds. By leveraging on the recently resolved crystal structures of MT₁ and MT₂ receptors, this study aims to elucidate the structural basis of MT₂-selectivity of a panel of isoquinolinone derivatives. Molecular modelling and ligand docking approaches were employed to predict residues involved in forming interactions with the MT₂-selective isoquinolinones. Seven conserved residues (Asn¹⁷⁵, His²⁰⁸, Trp²⁶⁴, Asn²⁶⁸, Gly²⁷¹, Tyr²⁹⁴ and Tyr²⁹⁸) were selected as targets for site-directed mutagenesis. Ca²⁺ mobilization, cAMP inhibition, phosphorylation of extracellular signal-regulated kinase, and ligand binding assays were performed to functionally characterize the receptor mutants in transfected CHO cells. Unlike melatonin, isoquinolinones bearing a 3-methoxybenzyloxyl substituent were unaffected by alanine substitution at His²⁰⁸ of MT₂. Although alanine substitutions at Tyr²⁹⁴ or Tyr²⁹⁸ reduced the potency of melatonin and some isoquinolinones on MT₂, similar mutations on MT₁ allowed five hitherto ineffective isoquinolinones to act as agonists. An isoquinolinone antagonist bearing a 4-methoxybenzyloxyl moiety turned into an agonist at MT₂ mutants with alanine substitutions at His²⁰⁸, Tyr²⁹⁴ or Tyr²⁹⁸. A subset of residues is apparently involved in forming a hydrophobic binding cavity to confer selectivity upon the aromatic substituent of isoquinolinone compounds. Two conserved tyrosine residues on transmembrane helix 7 may confer ligand selectivity at MT₁ and MT₂ receptors, while a conserved histidine on transmembrane helix 5 is apparently involved in receptor activation.

Going beyond base-pairs: topology-based characterization of base-multiplets in RNA

Identification and characterization of base-multiplets, which are essentially mediated by base-pairing interactions, can provide insights into the diversity in the structure and dynamics of complex functional RNAs, and thus facilitate hypothesis driven biological research. The necessary nomenclature scheme, an extension of the geometric classification scheme for base-pairs by Leontis and Westhof, is however available only for base-triplets. In the absence of information on topology, this scheme is not applicable to quartets and higher order multiplets. Here we propose a topology-based classification scheme which, in conjunction with a graph-based algorithm, can be used for the automated identification and characterization of higher order base-multiplets in RNA structures. Here, the RNA structure is represented as a graph, where nodes represent nucleotides and edges represent base-pairing connectivity. Sets of connected components (of n nodes) within these graphs constitute subgraphs representing multiplets of "n" nucleotides. The different topological variants of the RNA multiplets thus correspond to different nonisomorphic forms of these subgraphs. To annotate RNA base-multiplets unambiguously, we propose a set of topology-based nomenclature rules for quartets, which are extendable to higher multiplets. We also demonstrate the utility of our approach toward the identification and annotation of higher order RNA multiplets, by investigating the occurrence contexts of selected examples in order to gain insights regarding their probable functional roles.

Docking studies for melatonin receptors

INTRODUCTION

Melatonin is a neurohormone that controls many relevant physiological processes beyond the control of circadian rhythms. Melatonin's actions are carried out by two main types of melatonin receptors; MT₁ and MT₂. These receptors are important, and not just because of the biological actions of its natural agonist; but also, because melatonin analogues can improve or antagonize their biological effect. Area covered: The following article describes the importance of melatonin as a biologically relevant molecule. It also defines the receptors for this substance, as well as the second messengers coupled to these receptors. Lastly, the article describes the amino acid residues involved in the docking process in both MT₁ and MT₂ melatonin receptors. Expert opinion: The biological actions of melatonin and their interpretations are becoming more relevant and therefore require the development of new pharmacological tools. Understanding the second messenger mechanisms involved in melatonin actions, as well as the characteristics of the docking of this molecule to MT₁ and MT₂ melatonin receptors, will permit the development of more selective agonists and antagonists which will help us to better understand this molecule as well to develop new therapeutic compounds.

Update on melatonin receptors: IUPHAR Review 20

Melatonin receptors are seven transmembrane-spanning proteins belonging to the GPCR superfamily. In mammals, two melatonin receptor subtypes exist - MT1 and MT2 - encoded by the MTNR1A and MTNR1B genes respectively. The current review provides an update on melatonin receptors by the corresponding subcommittee of the International Union of Basic and Clinical Pharmacology. We will highlight recent developments of melatonin receptor ligands, including radioligands, and give an update on the latest phenotyping results of melatonin receptor knockout mice. The current status and perspectives of the structure of melatonin receptor will be summarized. The physiological importance of melatonin receptor dimers and biologically important and type 2 diabetes-associated genetic variants of melatonin receptors will be discussed. The role of melatonin receptors in physiology and disease will be further exemplified by their functions in the immune system and the CNS. Finally, antioxidant and free radical scavenger properties of melatonin and its relation to melatonin receptors will be critically addressed.

Why does substitution of thymine by 6-ethynylpyridone increase the thermostability of DNA double helices?

Efficiency of 6-ethynylpyridone (E), a potential thymine (T) analogue, which forms high-fidelity base pairs with adenine (A) and gives rise to stabler DNA duplexes, with stability comparable to those containing canonical cytosine(C):guanine(G) base pairs, has been reported recently. Estimates of the interaction energies, involving geometry optimization at the DFT level (including middle range dispersion interactions) followed by single point energy calculation at MP2 level, in excellent correlation with the experimentally observed trends, show that E binds more strongly and more discriminately with A than T does. Detailed analysis reveals that the increase in base-base interaction arises out of conjugation of acetylenic π electrons with the ring π system of E, which results in not only an extra stabilizing C-H···π interaction in the EA pair, but also a strengthening of the conventional hydrogen bonds. However, the computed base-base interaction energy for the EA pair was found to be much less than that of the canonical CG pair, implying that the difference in the TA versus EA base pairing interaction alone cannot explain the large experimentally observed increase in the thermostability of DNA duplexes, where a TA pair is replaced with an EA pair. Our computations show that the conjugation of acetylenic π electrons with the ring π system also possibly plays a role in increasing the stacking potential of the EA pair, which in turn can explain its marked influence in the enhancement of duplex stability.

Homology models of melatonin receptors: challenges and recent advances

Melatonin exerts many of its actions through the activation of two G protein-coupled receptors (GPCRs), named MT1 and MT2. So far, a number of different MT1 and MT2 receptor homology models, built either from the prototypic structure of rhodopsin or from recently solved X-ray structures of druggable GPCRs, have been proposed. These receptor models differ in the binding modes hypothesized for melatonin and melatonergic ligands, with distinct patterns of ligand-receptor interactions and putative bioactive conformations of ligands. The receptor models will be described, and they will be discussed in light of the available information from mutagenesis experiments and ligand-based pharmacophore models. The ability of these ligand-receptor complexes to rationalize structure-activity relationships of known series of melatonergic compounds will be commented upon.

Structure-based virtual screening of MT2 melatonin receptor: influence of template choice and structural refinement

Developing GPCR homology models for structure-based virtual screening requires the choice of a suitable template and refinement of binding site residues. We explored this systematically for the MT2 melatonin receptor, with the aim to build a receptor homology model that is optimized for the enrichment of active melatoninergic ligands. A set of 12 MT2 melatonin receptor models was built using different GPCR X-ray structural templates and submitted to a virtual screening campaign on a set of compounds composed of 29 known melatonin receptor ligands and 2560 drug-like decoys. To evaluate the effect of including a priori information in receptor models, 12 representative melatonin receptor ligands were placed into the MT2 receptor models in poses consistent with known mutagenesis data and with assessed pharmacophore models. The receptor structures were then adapted to the ligands by induced-fit docking. Most of the 144 ligand-adapted MT2 receptor models showed significant improvements in screening enrichments compared to the unrefined homology models, with some template/refinement combinations giving excellent enrichment factors. The discriminating ability of the models was further tested on the 29 active ligands plus a set of 21 inactive or low-affinity compounds from the same chemical classes. Rotameric states of side chains for some residues, presumed to be involved in the binding process, were correlated with screening effectiveness, suggesting the existence of specific receptor conformations able to recognize active compounds. The top MT2 receptor model was able to identify 24 of 29 active ligands among the first 2% of the screened database. This work provides insights into the use of refined GPCR homology models for virtual screening.

Melatonin signaling and cell protection function

Besides its well-known regulatory role on circadian rhythm, the pineal gland hormone melatonin has other biological functions and a distinct metabolism in various cell types and peripheral tissues. In different tissues and organs, melatonin has been described to act as a paracrine and also as an intracrine and autocrine agent with overall homeostatic functions and pleiotropic effects that include cell protection and prosurvival factor. These latter effects, documented in a number of in vitro and in vivo studies, are sustained through both receptor-dependent and -independent mechanisms that control detoxification and stress response genes, thus conferring protection against a number of xenobiotics and endobiotics produced by acute and chronic noxious stimuli. Redox-sensitive components are included in the cell protection signaling of melatonin and in the resulting transcriptional response that involves the control of NF-κB, AP-1, and Nrf2. By these pathways, melatonin stimulates the expression of antioxidant and detoxification genes, acting in turn as a glutathione system enhancer. A further and converging mechanism of cell protection by this indoleamine described in different models seems to lie in the control of damage and signaling function of mitochondria that involves decreased production of reactive oxygen species and activation of the antiapoptotic and redox-sensitive element Bcl2. Recent evidence suggests that upstream components in this mitochondrial route include the calmodulin pathway with its central role in melatonin signaling and the survival-promoting component of MAPKs, ERK1/2. In this review article, we will discuss these and other molecular aspects of melatonin signaling relevant to cell protection and survival mechanisms.

[Prediction of the spatial structure of proteins: emphasis on membrane targets]

Knowledge of the spatial structure of proteins is a prerequisite for both awareness of their functional mechanisms and the framework for rational drug discovery and design. Meanwhile, direct structural determination is often hampered or impractical due to the complexity, expensiveness, and limited capabilities of experimental techniques. These issues are especially pronounced for integral membrane proteins. On numerous occasions, the theoretical prediction of protein structures may facilitate the process by exploiting physical or empirical principles. This paper surveys modern techniques for the prediction of the spatial structure of proteins using computer algorithms, and the main emphasis is placed on the most "complex" targets - membrane proteins (MPs). The first part of the review describes de novo methods based on empirical physical principles; in the second part, a comparative modeling philosophy, which accounts for the structure of related proteins, is described. Special focus is made regarding pharmacologically relevant classes of G-coupled receptors, receptor tyrosine ki-nases, and other MPs. Algorithms for the assessment of the models quality and potential fields of application of computer models are discussed.

Probing the binding site of the A1 adenosine receptor reengineered for orthogonal recognition by tailored nucleosides

His272 (7.43) in the seventh transmembrane domain (TM7) of the human A3 adenosine receptor (AR) interacts with the 3' position of nucleosides, based on selective affinity enhancement at a H272E mutant A3 AR (neoceptor) of 3'-ureido, but not 3'-OH, adenosine analogues. Here, mutation of the analogous H278 of the human A1 AR to Ala, Asp, Glu, or Leu enhanced the affinity of novel 2'- and 3'-ureido adenosine analogues, such as 10 (N6-cyclopentyl-3'-ureido-3'-deoxyadenosine), by >100-fold, while decreasing the affinity or potency of adenosine and other 3'-OH adenosine analogues. His278 mutant receptors produced a similar enhancement regardless of the charge character of the substituted residue, implicating steric rather than electrostatic factors in the gain of function, a hypothesis supported by rhodopsin-based molecular modeling. It was also demonstrated that this interaction was orientationally specific; i.e., mutations at the neighboring Thr277 did not enhance the affinity for a series of 2'- and 3'-ureido nucleosides. Additionally, H-bonding groups placed on substituents at the N6 or 5' position demonstrated no enhancement in the mutant receptors. These reengineered human A1 ARs revealed orthogonality similar to that of the A3 but not the A2A AR, in which mutation of the corresponding residue, His278, to Asp did not enhance nucleoside affinity. Functionally, the H278D A1 AR was detectable only in a measure of membrane potential and not in calcium mobilization. This neoceptor approach should be useful for the validation of molecular modeling and the dissection of promiscuous GPCR signaling.