Development Of New Ligands Research Articles

The mechanism insight into the cooperative coordination of Aza-18-crown-6 ether with diglycolamide by p-benzyl as linkers enhancing the selectivity for heavy REEs(III)

The development of new ligands is crucial for the functional application of REEs(III), because the coordination compounds of rare-earth elements (REEs) have many important applications in pharmaceuticals and nuclear medicine. In this paper, a novel ligand (Cr6-Bz-DGA) with the aza-crown ether and diglycolamide (DGA) units was designed to coordinate with light, medium, and heavy REEs(III). It was found that M/L = 2:2 species (aza-crown ether-REEs(III)-DGA connection) was the thermodynamically stable complex. The stability constants of Nd(III), Eu(III), and Ho(III) complexes were determined by UV–Vis and fluorescence titration, respectively, which were logβNd = 7.49 ± 0.019, logβEu = 7.10 ± 0.013 and logβHo = 8.27 ± 0.032. The variation of fluorescence lifetime suggested that the Eu(III) ion was exclusively coordinated by the ligand with coordination number 9 in the inner sphere of the Eu(III) ion. The shifts of 1H NMR revealed that there are different coordination between the ligand and REEs(III). For larger ionic radii La(III), three O atoms of the DGA unit and five O and one N atoms of the aza-crown ether unit were supplied. While, for Y(III)/Lu(III) with smaller ion radii, the ligand supplied three O atoms from the DGA and one N atom and only two O atoms from the aza-crown ether. The displacement experiment of REEs(III) combined with ligand and the fitted stability constants prove that the smaller ionic radii REEs(III) more strongly bind with ligand than larger ionic radius REEs(III). These results may help understand the coordination behavior of REEs(III) and expand their potential applications.

Small lectin ligands as a basis for applications in glycoscience and glycomedicine.

Glycan recognition by lectins mediates important biological events. This Tutorial Review aims to introduce lectin-ligand interactions and show how these molecular recognition events inspire innovations such as: (i) glycomimetic ligands; (ii) multivalent ligand agonists/antagonists; (iii) ligands for precision delivery of therapies to cells, where therapies include vaccines, siRNA and LYTACs (iv) development of diagnostics. A small number of case studies are selected to demonstrate principles for development of new ligands for applications inspired by knowledge of natural glycan ligand structure and function.

Computational Analysis of Histamine Protonation Effects on H1R Binding.

Despite numerous studies investigating histamine and its receptors, the impact of histamine protonation states on binding to the histamine H1-receptor (H1R) has remained elusive. Therefore, we assessed the influence of different histamine tautomers (τ-tautomer, π-tautomer) and charge states (mono- vs. dicationic) on the interaction with the ternary histamine-H1R-Gq complex. In atomistic molecular dynamics simulations, the τ-tautomer formed stable interactions with the receptor, while the π-tautomer induced a rotation of the histamine ring by 180° and formed only weaker hydrogen bonding interactions. This suggests that the τ-tautomer is more relevant for stabilization of the active ternary histamine-H1R-Gq complex. In addition to the two monocationic tautomers, the binding of dicationic histamine was investigated, whose interaction with the H1R had been observed in a previous experimental study. Our simulations showed that the dication is less compatible with the ternary histamine-H1R-Gq complex and rather induces an inactive conformation in the absence of the Gq protein. Our data thus indicate that the charge state of histamine critically affects its interactions with the H1R. Ultimately these findings might have implications for the future development of new ligands that stabilize distinct H1R activation states.

Fluorescence based HTS-compatible ligand binding assays for dopamine D3 receptors in baculovirus preparations and live cells.

Dopamine receptors are G-protein-coupled receptors that are connected to severe neurological disorders. The development of new ligands targeting these receptors enables gaining a deeper insight into the receptor functioning, including binding mechanisms, kinetics and oligomerization. Novel fluorescent probes allow the development of more efficient, cheaper, reliable and scalable high-throughput screening systems, which speeds up the drug development process. In this study, we used a novel Cy3B labelled commercially available fluorescent ligand CELT-419 for developing dopamine D3 receptor-ligand binding assays with fluorescence polarization and quantitative live cell epifluorescence microscopy. The fluorescence anisotropy assay using 384-well plates achieved Z' value of 0.71, which is suitable for high-throughput screening of ligand binding. The assay can also be used to determine the kinetics of both the fluorescent ligand as well as some reference unlabeled ligands. Furthermore, CELT-419 was also used with live HEK293-D3Rcells in epifluorescence microscopy imaging for deep-learning-based ligand binding quantification. This makes CELT-419 quite a universal fluorescence probe which has the potential to be also used in more advanced microscopy techniques resulting in more comparable studies.

DFT Prediction of Radiolytic Stability of Conformationally Flexible Ligands

Radiolytic stability is one of the main requirements of the ligands for the reprocessing of spent nuclear fuel. The prediction of radiation stability based only on the 2D molecular structural formula allows us to accelerate and simplify the development of new ligands. Here, we used quantum chemistry to investigate the radiolytic behavior of water-soluble diglycolamides as one of the most popular ligands for spent nuclear fuel reprocessing. The accurate accounting of conformational mobility in the descriptors based on the Frontier Orbital Fukui theory allowed us to obtain a good correlation between theoretical and experimental data.

Screening for New Inhibitors of Glycine Transporter 1 and 2 by Means of MS Binding Assays.

A straightforward screening of a compound library comprising 2439 substances for the identification of new inhibitors for the neurotransmitter transporters GlyT1 and GlyT2 is described. Screening and full‐scale competition experiments were performed using recently developed GlyT1 and GlyT2 MS Binding Assays. That way for both targets, GlyT1 and GlyT2, ligands were identified, which exhibited affinities (pK i values) in the low micromolar to sub‐micromolar range. The majority of these binders exhibit new chemical scaffolds in the class of GlyT1 and GlyT2 inhibitors, which could be of interest for the development of new ligands with improved affinities for the target proteins. Additionally, compounds with excellent fluorescent properties were found for GlyT2, which renders them promising compounds for future fluorescence‐based techniques. All in all, this study demonstrates that MS Binding Assays represent a powerful technology platform also well suited for the screening of compound libraries in a highly reliable and effective manner.

Cryo-EM structures of tau filaments from Alzheimer\u2019s disease with PET ligand APN-1607

Tau and Aβ assemblies of Alzheimer’s disease (AD) can be visualized in living subjects using positron emission tomography (PET). Tau assemblies comprise paired helical and straight filaments (PHFs and SFs). APN-1607 (PM-PBB3) is a recently described PET ligand for AD and other tau proteinopathies. Since it is not known where in the tau folds PET ligands bind, we used electron cryo-microscopy (cryo-EM) to determine the binding sites of APN-1607 in the Alzheimer fold. We identified two major sites in the β-helix of PHFs and SFs and a third major site in the C-shaped cavity of SFs. In addition, we report that tau filaments from posterior cortical atrophy (PCA) and primary age-related tauopathy (PART) are identical to those from AD. In support, fluorescence labelling showed binding of APN-1607 to intraneuronal inclusions in AD, PART and PCA. Knowledge of the binding modes of APN-1607 to tau filaments may lead to the development of new ligands with increased specificity and binding activity. We show that cryo-EM can be used to identify the binding sites of small molecules in amyloid filaments.

Chapter 22 - Melatonin and the circadian system: Keys for health with a focus on sleep

Melatonin (MLT), secreted during the night by the pineal gland, is an efferent hormonal signal of the master circadian clock located in the suprachiasmatic nucleus (SCN). Consequently, it is a reliable phase marker of the SCN clock. If one defines as "chronobiotic," a drug able to influence the phase and/or the period of the circadian clock, MLT is a very potent one. The most convincing data obtained so far come from studies on totally blind individuals. Exogenous MLT administered daily entrains the sleep-wake cycle of these individuals to a 24-h cycle. MLT, however, is not essential to sleep. In nocturnally, active mammals, MLT is released during the night concomitantly with the daily period of wakefulness. Therefore, MLT cannot be simply considered as a sleep hormone, but rather as a signal of darkness. Its role in the circadian system is to reinforce nighttime physiology, including timing of the sleep-wake cycle and other circadian rhythms. MLT exerts its effects on the sleep cycle especially by a direct action on the master circadian clock. The sleep-wake cycle is depending not only on the circadian clock but also on an orchestrated network of different centers in the brain. Thus, the control of sleep-wake rhythm might be explained by a parallel and concomitant action of MLT on the master clock (chronobiotic effect) and on sleep-related structures within the brain. MLT acts through two high-affinity membrane receptors (MT1 and MT2) with striking differences in their distribution pattern. MLT is a powerful synchronizer of human circadian rhythms, thus justifying the use of MLT and MLT agonists in clinical medicine as pharmacological tools to manipulate the sleep-wake cycle, and to treat sleep disorders and other circadian disorders. Available MLT analogs/drugs are all nonspecific MT1/MT2 agonists. The development of new ligands which are highly selectivity for each subtype is clearly a new challenge for the field and will be at the root of new therapeutic agents for curing specific pathologies, including sleep disorders.

Development of Force Field Parameters for p-Carborane to Investigate the Structural Influence of Carborane Derivatives on Drug Targets by Complex Formation.

Androgen receptor (AR) has a key role in the development and progression of prostate cancer, and AR antagonists are used for its remedy. Recently, carborane derivatives, which are carbon-containing boron clusters have attracted attention as new AR ligands. Here we determined the force field parameters of 10-vertex and 12-vertex p-carborane to facilitate in silico drug design of boron clusters. Then, molecular dynamics (MD) simulations of complexes of AR-carborane derivatives were performed to evaluate the parameters and investigate the influences of carborane derivatives on the three-dimensional structure of AR. Energy profiles were obtained using quantum chemical calculations, and the force-field parameters were determined by curve fitting of the energy profiles. The results of MD simulations indicated that binding of the antagonist-BA341 changed some hydrogen-bond formations involved in the structure and location of helix 12. Those results were consistent with previously reported data. The determined parameters are also useful for refining the structure of the carborane-receptor complex obtained by docking simulations and development of new ligands with carborane cages not only for AR but also for various receptors.

Rational design of specific ligands for human serum albumin separation and applications.

Human serum albumin is widely used in clinical practice, and the development of new ligands with high affinity is beneficial to improve its separation efficiency. The Site II of human serum albumin is an active binding site of various molecules such as l-tryptophan, which was studied with molecular simulation to obtain insights for the design of new ligands. The results showed that the carboxyl and indolyl groups of l-tryptophan were critical for the binding on Site II. Seven ligands containing carboxyl groups and indolyl groups were designed, and molecular simulation showed that indole-3-pentanoic acid was the best ligand. A new ligand combined indole-3-acetic acid and cysteine was designed for easier resin preparation, and molecular simulation also indicated that the new ligand bound strongly to Site II. Resins with the new ligand designed was prepared and static adsorption experiments indicated that the new resin had high adsorption capacity of human serum albumin and strong salt tolerance. Finally, recombinant human serum albumin was separated from yeast broth with high purity of 90.4% and recovery of 94.2%, which indicated that the new resin had good adsorption selectivity and strong potential for applications.

Microwave-assisted Carbon-carbon and Carbon-heteroatom Cross-coupling Reactions in Organic Synthesis

Conventionally, the organic reactions are accomplished by conductive heating with an external heat source like an oil bath. On the contrary, since its inception, the application of microwave irradiation is growing as a suitable alternate heating method in organic synthesis. Microwave heating considerably reduces the reaction time without promoting any side reactions. The fundamental synthetic organic chemistry majorly deals with transition-metal-catalyzed C–C and C–heteroatom bond formation reactions. It is one of the most important methods in contemporary chemistry resulting in a tremendous increment in the applications of these reactions during the last few years. This field has been acknowledged with a number of Nobel Prizes during the last decade (2001, 2005 and 2010). A considerable effort has been done on the continuous development of new ligands and catalysts as well as an increased understanding of the mechanisms for the improvement of the reaction condition. This review focuses on some of the latest developments in the area of cross-coupling reactions aided by microwave irradiation.

Direct (hetero)arylation polymerization: toward defect-free conjugated polymers

In a very short time, direct (hetero)arylation polymerization (DHAP) has established itself as a valuable and atom-economical alternative to traditional cross-coupling methods such as the Migita–Stille and Suzuki-Miyaura polymerizations for the synthesis of low cost and efficient conjugated polymers for organic electronics. Because of sustained research efforts combining in-depth theoretical calculations, the development of new ligands and the careful fine-tuning of polymerization conditions, selectivity and reactivity issues should be soon a thing of the past. This focus review highlights the recent advances that lead to defect-free polymeric semiconductors and conductors and the current limitations and challenges of DHAP as it moves toward simultaneously becoming an industrially feasible, environmentally friendly, and synthetically powerful polymerization technique. The implementation of Direct Heteroarylation Polymerization (DHAP) in the synthesis of well-defined and defect-free materials for organic electronics is still in its early stages but giant leaps have been made over the past few years to improve and stir the selectivity of the reaction to avoid unwanted side-reaction such as β-branching or homocoupling. DHAP has proven to be an efficient, cost-effective, green and scalable polymerization method now competing or even surpassing well-established Suzuki-Miyaura or Migita–Stille cross-coupling polymerization methods. This focus review puts emphasis on the synthetic strategies that made DHAP successful.

Structure and dynamics of dynorphin peptide and its receptor.

Dynorphin is a neuropeptide involved in pain, addiction and mood regulation. It exerts its activity by binding to the kappa opioid receptor (KOP) which belongs to the large family of G protein-coupled receptors. The dynorphin peptide was discovered in 1975, while its receptor was cloned in 1993. This review will describe: (a) the activities and physiological functions of dynorphin and its receptor, (b) early structure-activity relationship studies performed before cloning of the receptor (mostly pharmacological and biophysical studies of peptide analogues), (c) structure-activity relationship studies performed after cloning of the receptor via receptor mutagenesis and the development of recombinant receptor expression systems, (d) structural biology of the opiate receptors culminating in X-ray structures of the four opioid receptors in their inactive state and structures of MOP and KOP receptors in their active state. X-ray and EM structures are combined with NMR data, which gives complementary insight into receptor and peptide dynamics. Molecular modeling greatly benefited from the availability of atomic resolution 3D structures of receptor-ligand complexes and an example of the strategy used to model a dynorphin-KOP receptor complex using NMR data will be described. These achievements have led to a better understanding of the complex dynamics of KOP receptor activation and to the development of new ligands and drugs.

Synthesis, antimicrobial activity, attenuation of aminoglycoside resistance in MRSA, and ribosomal A-site binding of pyrene-neomycin conjugates

The development of new ligands that have comparable or enhanced therapeutic efficacy relative to current drugs is vital to the health of the global community in the short and long term. One strategy to accomplish this goal is to functionalize sites on current antimicrobials to enhance specificity and affinity while abating resistance mechanisms of infectious organisms. Herein, we report the synthesis of a series of pyrene-neomycin B (PYR-NEO) conjugates, their binding affinity to A-site RNA targets, resistance to aminoglycoside-modifying enzymes (AMEs), and antibacterial activity against a wide variety of bacterial strains of clinical relevance. PYR-NEO conjugation significantly alters the affinities of NEO for bacterial A-site targets. The conjugation of PYR to NEO significantly increased the resistance of NEO to AME modification. PYR-NEO conjugates exhibited broad-spectrum activity towards Gram-positive bacteria, including improved activity against NEO-resistant methicillin-resistant Staphylococcus aureus (MRSA) strains.

A Structure- and Ligand-Based Virtual Screening of a Database of "Small" Marine Natural Products for the Identification of "Blue" Sigma-2 Receptor Ligands.

Sigma receptors are a fascinating receptor protein class whose ligands are actually under clinical evaluation for the modulation of opioid analgesia and their use as positron emission tomography radiotracers. In particular, peculiar biological and therapeutic functions are associated with the sigma-2 (σ2) receptor. The σ2 receptor ligands determine tumor cell death through apoptotic and non-apoptotic pathways, and the overexpression of σ2 receptors in several tumor cell lines has been well documented, with significantly higher levels in proliferating tumor cells compared to quiescent ones. This acknowledged feature has found practical application in the development of cancer cell tracers and for ligand-targeting therapy. In this context, the development of new ligands that target the σ2 receptors is beneficial for those diseases in which this protein is involved. In this paper, we conducted a search of new potential σ2 receptor ligands among a database of 1517 “small” marine natural products constructed by the union of the Seaweed Metabolite and the Chemical Entities of Biological Interest (ChEBI) Databases. The structures were passed through two filters that were constituted by our developed two-dimensional (2D) and three-dimensional Quantitative Structure-Activity Relationship (3D-QSAR) statistical models, and successively docked upon a σ2 receptor homology model that we built according to the FASTA sequence of the σ2/TMEM97 (SGMR2_HUMAN) receptor.

Structural insights into serotonin receptor ligands polypharmacology

Identifying desired interactions with a target receptor is often the first step when designing new active compounds. However, attention should also be focused on contacts with other proteins that result in either selective or polypharmacological compounds. Here, the search for the structural determinants of selectivity between selected serotonin receptor subtypes was carried out. Special attention was focused on 5-HT7R and the cross-interactions between its ligands and the 5-HT1AR, 5-HT1BR, 5-HT2AR, 5-HT2BR, and 5-HT6R subtypes. Selective and non-selective compounds for each pair of 5-HT7/5-HTx receptors were docked to the respective 5-HTR homology models and 5-HT1B/5-HT2BR crystal structures. The contacts present in the ligand-receptor complexes obtained by docking were characterized by the structural interaction fingerprint and statistically analyzed in terms of their frequency. The results allowed for the identification of amino acids that discriminate between selective and non-selective compounds for each 5-HT7/5-HTx receptor pair, which was further compared with available mutagenesis data. Interaction pattern characteristics for compounds with particular activity profiles can constitute the basis for the coherent selectivity theory within a considered set of proteins, supporting the ongoing development of new ligands targeting these receptors. The in silico results were used to analyze prospective virtual screening results towards the 5-HT7 receptor in which compounds of different chemotypes to known 5-HT7R ligands, with micromolar level activities were identified. The findings in this study not only confirm the legitimacy of the approach but also constitute a great starting point for further studies on 5-HT7R ligands selectivity.

Recent Advances in Zirconium-89 Chelator Development.

The interest in zirconium-89 (89Zr) as a positron-emitting radionuclide has grown considerably over the last decade due to its standardized production, long half-life of 78.2 h, favorable decay characteristics for positron emission tomography (PET) imaging and its successful use in a variety of clinical and preclinical applications. However, to be utilized effectively in PET applications it must be stably bound to a targeting ligand, and the most successfully used 89Zr chelator is desferrioxamine B (DFO), which is commercially available as the iron chelator Desferal®. Despite the prevalence of DFO in 89Zr-immuno-PET applications, the development of new ligands for this radiometal is an active area of research. This review focuses on recent advances in zirconium-89 chelation chemistry and will highlight the rapidly expanding ligand classes that are under investigation as DFO alternatives.

The Adenosinergic System as a Therapeutic Target in the Vasculature: New Ligands and Challenges.

Adenosine is an adenine base purine with actions as a modulator of neurotransmission, smooth muscle contraction, and immune response in several systems of the human body, including the cardiovascular system. In the vasculature, four P1-receptors or adenosine receptors—A1, A2A, A2B and A3—have been identified. Adenosine receptors are membrane G-protein receptors that trigger their actions through several signaling pathways and present differential affinity requirements. Adenosine is an endogenous ligand whose extracellular levels can reach concentrations high enough to activate the adenosine receptors. This nucleoside is a product of enzymatic breakdown of extra and intracellular adenine nucleotides and also of S-adenosylhomocysteine. Adenosine availability is also dependent on the activity of nucleoside transporters (NTs). The interplay between NTs and adenosine receptors’ activities are debated and a particular attention is given to the paramount importance of the disruption of this interplay in vascular pathophysiology, namely in hypertension., The integration of important functional aspects of individual adenosine receptor pharmacology (such as in vasoconstriction/vasodilation) and morphological features (within the three vascular layers) in vessels will be discussed, hopefully clarifying the importance of adenosine receptors/NTs for modulating peripheral mesenteric vascular resistance. In recent years, an increase interest in purine physiology/pharmacology has led to the development of new ligands for adenosine receptors. Some of them have been patented as having promising therapeutic activities and some have been chosen to undergo on clinical trials. Increased levels of endogenous adenosine near a specific subtype can lead to its activation, constituting an indirect receptor targeting approach either by inhibition of NT or, alternatively, by increasing the activity of enzymes responsible for ATP breakdown. These findings highlight the putative role of adenosinergic players as attractive therapeutic targets for cardiovascular pathologies, namely hypertension, heart failure or stroke. Nevertheless, several aspects are still to be explored, creating new challenges to be addressed in future studies, particularly the development of strategies able to circumvent the predicted side effects of these therapies.

Development of New Ligands for the Recyclable Catalytic Asymmetric Transfer Hydrogenation in Ionic Liquid

Development of New Ligands for the Recyclable Catalytic Asymmetric Transfer Hydrogenation in Ionic Liquid

An LP1 analogue, selective MOR agonist with a peculiar pharmacological profile, used to scrutiny the ligand binding domain

The hypothesis that central analgesia with reduced side effects is obtainable by occupying an ‘allosteric’ site in the MOR ligand binding domain requires the development of new ligands with peculiar pharmacological profile to be used as tools. New benzomorphan derivatives, analogues of LP1, a multitarget MOR agonist/DOR antagonist, were designed to examine in depth MOR ligand binding domain. Compound 5, bearing a diphenylic N-substituent on the benzomorphan nucleus, showed an affinity (Kiμ=0.5±0.2nM) comparable to that of LP1 and a better selectivity versus DOR and KOR. It elicits antinociceptive effects in ex vivo (GPI) and in vivo. This new compound engages receptor amino acidic residues not reached by LP1 and by other established MOR ligands. Molecular modeling studies, conducted on 5 and on several reference compounds, allowed us to propose possible residues in the MOR ligand binding domain essential for their interactions with ‘orthosteric’ and ‘allosteric’ binding sites.