Role of Halogen Bonds in Thyroid Hormone Receptor Selectivity: Pharmacophore-Based 3D-QSSR Studies

Expanding chalcogen bonds in thiophenes to interactions with halogens

Compounds containing the thiophene moiety find several applications in physics and chemistry, such as electrical conduction, which depends on specific conformations to properly exhibiting the desired properties. In turn, chalcogen bonding has found to modulate the conformation of some N-thiophen-2-ylfomamides. Since halogens participate in a kin interaction (halogen bonding) and are abundant in agrochemicals, pharmaceuticals, and materials, we have quantum-chemically explored the interaction between organic halogen and thiophene as a conformational modulator in some model compounds. Although such interaction indeed appears, as demonstrated by atoms in molecules and natural bond orbital analysis, it is inefficient to control the conformational equilibrium. An energy decomposition analysis scheme demonstrated that halomethane and thiophene tend to move away from one another due to a core component (Pauli repulsion and exchange), which is mainly due to a deformation term. Therefore, chalcogen bonds with halogens appear weaker than with other chalcogens.

Rational Supramolecular Strategy via Halogen Bonding for Effective Halogen Recognition in Molecular Imprinting

Halogen bonding is a highly directional interaction and a potential tool in functional material design through self-assembly. Herein, we describe two fundamental supramolecular strategies to synthesize molecularly imprinted polymers (MIPs) with halogen bonding-based molecular recognition sites. In the first method, the size of the σ-hole was increased by aromatic fluorine substitution of the template molecule, enhancing the halogen bonding in the supramolecule. The second method involved sandwiching hydrogen atoms of a template molecule between iodo substituents, which suppressed competing hydrogen bonding and enabled multiple recognition patterns, improving the selectivity. The interaction mode between the functional monomer and the templates was elucidated by ¹H NMR, ¹³C NMR, X-ray absorption spectroscopy, and computational simulation. Finally, we succeeded in the effective chromatographic separation of diiodobenzene isomers on the uniformly sized MIPs prepared by multi-step swelling and polymerization. The MIPs selectively recognized halogenated thyroid hormones via halogen bonding and could be applied to screening endocrine disruptors.

Hydrogen- and halogen bond synergy in the self-assembly of 3,5-dihalo-tyrosines: structural and theoretical insights

Halogenation, generally introduced on aromatic aminoacids, is becoming a key supramolecular tool in peptides. Herein, we report the crystal structures and DFT study of two bis-halogenated tyrosines showing the subtle...

Cooperation/Competition between Halogen Bonds and Hydrogen Bonds in Complexes of 2,6-Diaminopyridines and X-CY3 (X = Cl, Br; Y = H, F)

The DFT calculations have been performed on a series of two-element complexes formed by substituted 2,6-diaminopyridine (R−PDA) and pyridine (R−Pyr) with X−CY3 molecules (where X = Cl, Br and Y = H, F). The primary aim of this study was to examine the intermolecular hydrogen and halogen bonds in the condition of their mutual coexistence. Symmetry/antisymmetry of the interrelation between three individual interactions is addressed. It appears that halogen bonds play the main role in the stabilization of the structures of the selected systems. However, the occurrence of one or two hydrogen bonds was associated with the favourable geometry of the complexes. Moreover, the impact of different substituent groups attached in the para position to the aromatic ring of the 2,6-diaminopyridine and pyridine on the character of the intermolecular hydrogen and halogen bonds was examined. The results indicate that the presence of electron-donating substituents strengthens the bonds. In turn, the presence of electron-withdrawing substituents reduces the strength of halogen bonds. Additionally, when hydrogen and halogen bonds lose their leading role in the complex formation, the nonspecific electrostatic interactions between dipole moments take their place. Analysis was based on geometric, energetic, and topological parameters of the studied systems.

Rising trend on the halogen and non-halogen derivatives (Br, Cl, CF3, F, CH3 and NH2) in ruminal β-d-Xylopyranose - a quantum chemical perspective

The utmost aim of the current study is to find significance of the binding affinity in the halogen and non-halogen derivatives: Br, Cl, CF₃, F, CH₃ and NH₂ of β-d-Xylopyranose with the hinge region amino acids of ruminant-β-glycosidase. The interaction energy analysis was carried out in detail through various density functional studies as M062X/def2-QZVP, M062X/LANL2DZ, B3LYP/LANL2DZ and M06HF/LANL2DZ level of theories. The total interaction energy of halogen derivatives: Br, Cl, F and CF₃ are -618.21, -599.00, -720.45 and -553.08 kcal/mol respectively, and non-halogen derivative: amine group (NH₂) is -87.96 kcal/mol at M062X/def2-QZVP level of theory, which exist with strong binding affinity. Ligand properties: dipole moment, polarizability, volume, molecular mass, electrostatic potential map was evaluated to understand its electrostatic and structural behavior. The nature of the bonds was inferred from the electrostatic potential map for all the halogen and non-halogen derivatives ligand. The stabilization energy from NBO analysis reveals the stability of single hydrogen and halogen bonds (N-H…Br, C-Br…O, N-H…Cl, C-Cl…O, O-H…F, C-H…F, N-H…F, C-F…O, N-H…O, O-H…O, N-H…N, O-H…N) in β-d-Xylopyranose and its derivatives. Overall, this study paves way for scientist and medicinal chemist in modelling new drugs. Further, it suggests mutations that increase the binding and may enhance the catalytic action and strengthen the complex diet in animals and hence recommended for experimental synthesis.Communicated by Ramaswamy H. Sarma.

Limited Chemical Structural Diversity Found to Modulate Thyroid Hormone Receptor in the Tox21 Chemical Library

BACKGROUND

Thyroid hormone receptors (TRs) are critical endocrine receptors that regulate a multitude of processes in adult and developing organisms, and thyroid hormone disruption is of high concern for neurodevelopmental and reproductive toxicities in particular. To date, only a small number of chemical classes have been identified as possible TR modulators, and the receptors appear highly selective with respect to the ligand structural diversity. Thus, the question of whether TRs are an important screening target for protection of human and wildlife health remains.

OBJECTIVE

Our goal was to evaluate the hypothesis that there is limited structural diversity among environmentally relevant chemicals capable of modulating TR activity via the collaborative interagency Tox21 project.

METHODS

We screened the Tox21 chemical library (8,305 unique structures) in a quantitative high-throughput, cell-based reporter gene assay for TR agonist or antagonist activity. Active compounds were further characterized using additional orthogonal assays, including mammalian one-hybrid assays, coactivator recruitment assays, and a high-throughput, fluorescent imaging, nuclear receptor translocation assay.

RESULTS

Known agonist reference chemicals were readily identified in the TR transactivation assay, but only a single novel, direct agonist was found, the pharmaceutical betamipron. Indirect activation of TR through activation of its heterodimer partner, the retinoid-X-receptor (RXR), was also readily detected by confirmation in an RXR agonist assay. Identifying antagonists with high confidence was a challenge with the presence of significant confounding cytotoxicity and other, non-TR-specific mechanisms common to the transactivation assays. Only three pharmaceuticals-mefenamic acid, diclazuril, and risarestat-were confirmed as antagonists.

DISCUSSION

The results support limited structural diversity for direct ligand effects on TR and imply that other potential target sites in the thyroid hormone axis should be a greater priority for bioactivity screening for thyroid axis disruptors. https://doi.org/10.1289/EHP5314.

Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases

Halogen bonding (or X bonding) has attracted increasing interest due to its significant role in molecular recognition in biological systems. Trypsin-like serine proteases have many physiological and pathophysiological functions. There is therefore extensive interest in generating specific inhibitors for pharmacological intervention in their enzymatic activity. We study here if it is possible to use halogenated compounds as the P1 group to bind to the S1 specificity pocket of trypsin-like serine proteases to avoid the low bioavailability of the amidine or guanidine P1 group that is typically used in many inhibitors. We used 4-chlorobenzylamine (ClBA), 4-bromobenzylamine (BrBA) and 4-iodobenzylamine (IBA) as probes to test their binding modes to a trypsin-like serine protease, urokinase-type plasminogen activator (uPA), which has been recognized as a marker for breast cancer and an important target for inhibitor development. The results showed that these compounds inhibited uPA with stronger efficacies compared with their non-halogenated analogues. We also determined the high-resolution crystal structures of uPA in complex with BrBA and IBA, respectively. The structures revealed that BrBA bound to the S1 pocket of uPA via halogen bonds, but IBA did not make halogen bonds with uPA, demonstrating that the iodine may not be the best choice as a target moiety for serine proteases. These results advocate halogen bonding, especially bromine bonding, as an efficient strategy for the future design of novel inhibitors against trypsin-like serine proteases to provide strong potency and promote bioavailability.

The Affinity of Brominated Phenolic Compounds for Human and Zebrafish Thyroid Receptor β: Influence of Chemical Structure

Brominated phenolic compounds (BPCs) are found in the environment, and in human and wildlife tissues, and some are considered to have endocrine disrupting activities. The goal of this study was to determine how structural differences of 3 BPC classes impact binding affinities for the thyroid receptor beta (TRβ) in humans and zebrafish. BPC classes included halogenated bisphenol A derivatives, halogenated oxidative transformation products of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), and brominated phenols. Affinities were assessed using recombinant TRβ protein in competitive binding assays with 125I-triiodothyronine (125I-T3) as the radioligand. Zebrafish and human TRβ displayed similar binding affinities for T3 (Ki = 0.40 and 0.49 nM) and thyroxine (T4, Ki = 6.7 and 6.8 nM). TRβ affinity increased with increasing halogen mass and atomic radius for both species, with the iodinated compounds having the highest affinity within their compound classes. Increasing halogen mass and radius increases the molecular weight, volume, and hydrophobicity of a compound, which are all highly correlated with increasing affinity. TRβ affinity also increased with the degree of halogenation for both species. Human TRβ displayed higher binding affinities for the halogenate bisphenol A compounds, whereas zebrafish TRβ displayed higher affinities for 2,4,6-trichlorophenol and 2,4,6-trifluorophenol. Observed species differences may be related to amino acid differences within the ligand binding domains. Overall, structural variations impact TRβ affinities in a similar manner, supporting the use of zebrafish as a model for TRβ disruption. Further studies are necessary to investigate how the identified structural modifications impact downstream receptor activities and potential in vivo effects.

Molecular modeling and structure-activity relationships for a series of benzimidazole derivatives as cruzain inhibitors

AIM

Chagas disease is endemic in Latin America and no effective treatment is available. Efforts in drug research have focused on several enzymes from Trypanosoma cruzi, among which cruzain is a validated pharmacological target.

METHODOLOGY

Chemometric analyses were performed on the data set using the hologram quantitative structure-activity relationship, comparative molecular field analysis and comparative molecular similarity index analysis methods. Docking simulations were executed using the crystallographic structure of cruzain in complex with a benzimidazole inhibitor. The top-scoring enzyme-inhibitor complexes were selected for the development of the 3D quantitative structure-activity relationship (QSAR) models and to assess the inhibitor binding modes and intermolecular interactions.

RESULTS

Benzimidazole derivatives as cruzain inhibitors were used in molecular docking and QSAR studies. Significant statistical indicators were obtained, and the best models demonstrated high predictive ability for an external test set (r ²_pred = 0.65, 0.94 and 0.82 for hologram QSAR, comparative molecular field analysis and comparative molecular similarity index analysis, respectively). Additionally, the graphical information of the chemometric analyses demonstrated substantial complementarity with the enzyme-binding site.

CONCLUSION

These results demonstrate the relevance of the QSAR models to guide the design of structurally related benzimidazole derivatives with improved potency.

Increasing Thyromimetic Potency through Halogen Substitution

Sobetirome is one of the most studied thyroid hormone receptor β (TRβ)-selective thyromimetics in the field due to its excellent selectivity and potency. A small structural change-replacing the 3,5-dimethyl groups of sobetirome with either chlorine or bromine-produces significantly more potent compounds, both in vitro and in vivo. These halogenated compounds induce transactivation of a TRβ-mediated cell-based reporter with an EC50 value comparable to that of T3, access the central nervous system (CNS) at levels similar to their parent, and activate an endogenous TR-regulated gene in the brain with an EC50 value roughly five-fold lower than that of sobetirome. Previous studies suggest that this apparent increase in affinity can be explained by halogen bonding between the ligand and a backbone carbonyl group in the receptor. This makes the new analogues potential candidates for treating CNS disorders that may respond favorably to thyroid-hormone-stimulated pathways.

The Halogen Bond

The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

A halogen bond does not dictate the conformational preferences of cis-1,3-disubstituted cyclohexanes

A halogen bond is unlikely to control the conformation of cis-1,3-disubstituted cyclohexanes. In addition, polarization rather than the σ-hole effect describes this weak interaction more appropriately.

A cryospectroscopic infrared and Raman study of the CX⋯π halogen bonding motif: complexes of the CF3Cl, CF3Br, and CF3I with ethyne, propyne and 2-butyne

Experimental information on the C-X⋯π halogen bonding motif was obtained by studying the formation of molecular complexes of CF3Cl, CF3Br and CF3I with ethyne, propyne and 2-butyne in liquid krypton, using FTIR and Raman spectroscopy. For CF3Br, experimental evidence was found for the formation of 1:1 complexes with propyne and 2-butyne only, while for CF3I spectroscopic features confirming the existence of the halogen bonded complexes were observed for ethyne, propyne and 2-butyne. In addition, at higher concentrations of CF3I and 2-butyne, weak absorptions due to a 2:1 complex were also observed. The experimental complexation enthalpies, obtained by using spectra recorded at temperatures between 120 K and 140 K, are -5.9(3) kJ mol(-1) for CF3I.ethyne, -5.6(3) kJ mol(-1) for CF3Br.propyne, -8.1(2) kJ mol(-1) for CF3I.propyne, -7.3(2) kJ mol(-1) for CF3Br.2-butyne, -10.9(2) kJ mol(-1) for CF3I.2-butyne and -20.9(7) kJ mol(-1) for (CF3I)2.2-butyne. The experimental study is supported by theoretical data obtained from ab initio calculations at the MP2/aug-cc-pVDZ(-PP) and MP2/aug-cc-pVTZ(-PP) levels, and Monte Carlo Free Energy Perturbation (MC-FEP) simulations. The experimental and theoretical values on the C-X⋯π halogen-bonding motifs studied are compared with previously reported data for the complexes with ethene and propene and with preliminary results obtained for benzene and toluene.

Biomolecular halogen bonds

Halogens are atypical elements in biology, but are common as substituents in ligands, including thyroid hormones and inhibitors, which bind specifically to proteins and nucleic acids. The short-range, stabilizing interactions of halogens - now seen as relatively common in biology - conform generally to halogen bonds characterized in small molecule systems and as described by the σ-hole model. The unique properties of biomolecular halogen bonds (BXBs), particularly in their geometric and energetic relationship to classic hydrogen bonds, make them potentially powerful tools for inhibitor design and molecular engineering. This chapter reviews the current research on BXBs, focusing on experimental studies on their structure-energy relationships, how these studies inform the development of computational methods to model BXBs, and considers how BXBs can be applied to the rational design of more effective inhibitors against therapeutic targets and of new biological-based materials.

Halogen bonding (X-bonding): a biological perspective

The concept of the halogen bond (or X-bond) has become recognized as contributing significantly to the specificity in recognition of a large class of halogenated compounds. The interaction is most easily understood as primarily an electrostatically driven molecular interaction, where an electropositive crown, or σ-hole, serves as a Lewis acid to attract a variety of electron-rich Lewis bases, in analogous fashion to a classic hydrogen bonding (H-bond) interaction. We present here a broad overview of X-bonds from the perspective of a biologist who may not be familiar with this recently rediscovered class of interactions and, consequently, may be interested in how they can be applied as a highly directional and specific component of the molecular toolbox. This overview includes a discussion for where X-bonds are found in biomolecular structures, and how their structure-energy relationships are studied experimentally and modeled computationally. In total, our understanding of these basic concepts will allow X-bonds to be incorporated into strategies for the rational design of new halogenated inhibitors against biomolecular targets or toward molecular engineering of new biological-based materials.

Using in vivo electroporation to identify hepatic LDL receptor promoter elements and transcription factors mediating activation of transcription by T3

The technique of in vivo electroporation was adapted to investigate the promoter elements and transcription factors mediating the rapid induction of hepatic LDL receptor expression in response to thyroid hormone. Direct comparisons between wild type and mutant promoter constructs were made within the same animal. It was demonstrated that both TREs at bp − 612 and − 156 were required for the l-triiodothyronine (T₃) response. ChIP analysis showed that binding of TRβ1 to the − 612 and − 156 TREs was markedly stimulated by T₃in vivo. Introduction of siRNAs against TRβ1/RXRα with LDL receptor promoter-luciferase construct by in vivo electroporation demonstrated that these transcription factors play the major physiological role in the activation of hepatic LDL receptor transcription. The findings agree with those made by transfecting H4IIE cells in vitro thus validating this technique for in vivo studies of mechanisms of transcriptional regulation. The findings reported herein also indicated, for the first time, that PPARα and USF-2 were required for maximum transcriptional activation of the LDL receptor in response to T₃ treatment.

3D-QSAR and 3D-QSSR models of negative allosteric modulators facilitate the design of a novel selective antagonist of human α4β2 neuronal nicotinic acetylcholine receptors

Subtype selective molecules for α4β2 neuronal nicotinic acetylcholine receptors (nAChRs) have been sought as novel therapeutics for nicotine cessation. α4β2 nAChRs have been shown to be involved in mediating the addictive properties of nicotine while other subtypes (i.e., α3β4 and α7) are believed to mediate the undesired effects of potential CNS drugs. To obtain selective molecules, it is important to understand the physiochemical features of ligands that affect selectivity and potency on nAChR subtypes. Here we present novel QSAR/QSSR models for negative allosteric modulators of human α4β2 nAChRs and human α3β4 nAChRs. These models support previous homology model and site-directed mutagenesis studies that suggest a novel mechanism of antagonism. Additionally, information from the models presented in this work was used to synthesize novel molecules; which subsequently led to the discovery of a new selective antagonist of human α4β2 nAChRs.

Is halogen bonding the basis for iodothyronine deiodinase activity?

Density functional theory studies of S...X and Se...X (X = Br, I) halogen-bonding interactions are used to interpret the selection of selenium and iodine for thyroid hormone signaling. A new mechanism for dehalogenation in terms of halogen bonding is proposed. The activation barriers for deiodination of an aromatic iodide by MeSeH and MeSH (17.6 and 19.8 kcal/mol) are consistent with the relative rates of deiodination by iodothyronine deiodinase and its cysteine mutant.

Directional Weak Intermolecular Interactions: σ-Hole Bonding

The prototypical directional weak interactions, hydrogen bonding and σ-hole bonding (including the special case of halogen bonding) are reviewed in a united picture that depends on the anisotropic nature of the molecular electrostatic potential around the donor atom. Qualitative descriptions of the effects that lead to these anisotropic distributions are given and examples of the importance of σ-hole bonding in crystal engineering and biological systems are discussed.