Trifunctional Molecules Research Articles

Simulations of the 2D self-assembly of tripod-shaped building blocks.

We introduce a molecular dynamics (MD) coarse-grained model for the description of tripod building blocks. This model has been used by us already for linear, V-shape, and tetratopic molecules. We wanted to further extend its possibilities to trifunctional molecules to prove its versatility. For the chosen systems we have also compared the MD results with Monte Carlo results on a triangular lattice. We have shown that the constraints present in the latter method can enforce the formation of completely different structures, not reproducible with off-lattice simulations. In addition to that, we have characterized the obtained structures regarding various parameters such as theoretical diffraction pattern and average association number.

PHOTACs enable optical control of protein degradation.

PROTACs (PROteolysis TArgeting Chimeras) are bifunctional molecules that target proteins for ubiquitylation by an E3 ligase complex and subsequent degradation by the proteasome. They have emerged as powerful tools to control the levels of specific cellular proteins. We now introduce photoswitchable PROTACs that can be activated with the spatiotemporal precision that light provides. These trifunctional molecules, which we named PHOTACs (PHOtochemically TArgeting Chimeras), consist of a ligand for an E3 ligase, a photoswitch, and a ligand for a protein of interest. We demonstrate this concept by using PHOTACs that target either BET family proteins (BRD2,3,4) or FKBP12. Our lead compounds display little or no activity in the dark but can be reversibly activated with different wavelengths of light. Our modular approach provides a method for the optical control of protein levels with photopharmacology and could lead to new types of precision therapeutics that avoid undesired systemic toxicity.

Facile assembly of three cycloalkyne-modules onto a platform compound bearing thiophene S,S-dioxide moiety and two azido groups.

An efficient method to assemble three cycloalkyne-modules onto a platform compound bearing a thiophene S,S-dioxide moiety and two azido groups has been developed. The sequential reactions without catalysis or additives enabled the facile preparation of trifunctional molecules by a simple procedure. One-pot assembly was also achieved using the platform and three cycloalkynes.

Exploring the Photochemical Reactivity of Multifunctional Photocaged Dienes in Continuous Flow

AbstractFlow reactors become more and more automated by enabling on‐line reaction monitoring and adjusting the process parameters. On‐line monitoring of chemical processes is a valuable tool to steer processes, leading to precise engineering of macromolecular materials. Detailed information about specific product patterns, end‐group functionality or material composition can be obtained by coupling a flow reactor to a mass spectrometer (e. g. ESI‐MS). In this work, we study the deprotection of maleimides and its subsequent photoenol functionalization to synthesize complex macromolecules using a photo flow reactor coupled to an ESI‐MS. Using a trapping agent (TA), furan is efficiently removed from the maleimide Diels−Alder adduct within just minutes at 175 °C and quantitatively converted into an unreactive species that does not interfere with further reactions of the maleimide. The photoenol reaction was likewise shown to be highly effective to proceed in microreactors, reaching quantitative conversion of trifunctional molecules in as little as 2 min.

Convergent synthesis of trifunctional molecules by three sequential azido-type-selective cycloadditions.

A facile strategy for the synthesis of trifunctional molecules involving three sequential selective triazole-forming reactions is proposed. This method exploits three kinds of mechanistically different azido-type-selective cycloadditions. Three different azidophiles could be efficiently connected to a triazido platform molecule with three types of azido groups in a consecutive manner, which rendered a practical trifunctional molecule readily available.

Chemisorption of Organic Triols on Ge(100)-2 × 1 Surface: Effect of Backbone Structure on Adsorption of Trifunctional Molecules

The effect of backbone on the adsorption mechanism of homo-trifunctional molecules on Ge(100)-2 × 1 has been studied. The chemisorption of the triols 1,3,5-benzenetriol and 2-hydroxymethyl-1,3-propanediol on Ge(100)-2 × 1 was investigated by means of Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and density functional theory calculations. Both triol molecules undergo an O–H dissociation reaction with the Ge dimers, with experiments showing that the fraction of O–H groups that dissociates per molecule is the same for 2-hydroxymethyl-1,3-propanediol and 1,3,5-benzenetriol. Experimental results suggest that for both molecules there is a mix of products formed at saturation, with evidence of trifold adsorbates. The flexibility of the backbone is shown to influence surface coverage and dimer occupancy, with the flexible backbone able to pack the surface more easily. DFT calculations support these results by showing favorable pathways for all reactions through single, double, and tr...

Dasatinib, imatinib and staurosporine capture compounds — Complementary tools for the profiling of kinases by Capture Compound Mass Spectrometry (CCMS)

Capture Compound Mass Spectrometry (CCMS) is a platform technology for the functional isolation of subproteomes. Here we report the synthesis of two new kinase Capture Compounds (CCs) based on the tyrosine-kinase specific inhibitors dasatinib and imatinib and compare their interaction profiles to that of our previously reported staurosporine-CCs. CCs are tri-functional molecules: they comprise a sorting function (e.g. the small molecule or drug of interest) which interacts with target proteins, a photo-activatable reactivity function to covalently trap the interacting proteins, and a sorting function to isolate the CC-protein conjugates from complex biological samples for protein identification by liquid chromatography/mass spectrometry (LC-MS/MS). We present data of CCMS experiments from human HepG2 cells and compare the profiles of the kinases isolated with dasatinib, imatinib and staurosporine CC, respectively. Dasatinib and imatinib have a more selective kinase binding profile than staurosporine. Moreover, the new CCs allow isolation and identification of additional kinases, complementing the staurosporine CC. The family of kinase CCs will be a valuable tool for the proteomic profiling of this important protein class. Besides sets of expected kinases we identified additional specific interactors; these off-targets may be of relevance in the view of the pharmacological profile of dasatinib and imatinib.

Trifunctional99mTc based radiopharmaceuticals: metal-mediated conjugation of a peptide with a nucleus targeting intercalator

The development of molecular imaging agents with multiple functions has become a major trend in radiopharmaceutical chemistry. We present herein the syntheses of trifunctional compounds, combining an acridine orange (AO) based intercalator with a GRP receptor specific bombesin like peptide (BBN). Metal-mediated conjugation of these two functions via the [2 + 1] approach to the third function, the [M(CO)(3)](+) (M = (99m)Tc, Re) moiety, yielded the final trifunctional molecules. The strongly fluorescent acridine orange, a nuclear targeting agent, has been derivatised with 4-imidazolecarboxylate as a bidentate ligand and bombesin with an isonitrile group as a monodentate ligand. For cell and nuclear uptake studies, [Re(L(1)-BBN)(L(2)-Ical)(CO)(3)] type complexes were synthesized and characterized. For radiopharmaceutical purposes, the (99m)Tc analogues have been prepared in a stepwise synthesis. Fluorescence microscopy studies on PC-3 cells, bearing the BBN receptor, showed high and rapid uptake into the cytoplasm. For the bifunctional molecule, lacking the BBN peptide, no internalization was observed.

The cAMP Capture Compound Mass Spectrometry as a Novel Tool for Targeting cAMP-binding Proteins : FROM PROTEIN KINASE A TO POTASSIUM/SODIUM HYPERPOLARIZATION-ACTIVATED CYCLIC NUCLEOTIDE-GATED CHANNELS

The profiling of subproteomes from complex mixtures on the basis of small molecule interactions shared by members of protein families or small molecule interaction domains present in a subset of proteins is an increasingly important approach in functional proteomics. Capture CompoundTM Mass Spectrometry (CCMS) is a novel technology to address this issue. CCs are trifunctional molecules that accomplish the reversible binding of target protein families to a selectivity group (small molecule), covalent capturing of the bound proteins by photoactivated cross-linking through a reactivity group, and pullout of the small molecule-protein complexes through a sorting function, e.g. biotin. Here we present the design, synthesis, and application of a new Capture Compound to target and identify cAMP-binding proteins in complex protein mixtures. Starting with modest amounts of total protein mixture (65–500 μg), we demonstrate that the cAMP-CCs can be used to isolate bona fide cAMP-binding proteins from lysates of Escherichia coli, mammalian HepG2 cells, and subcellular fractions of mammalian brain, respectively. The identified proteins captured by the cAMP-CCs range from soluble cAMP-binding proteins, such as the catabolite gene activator protein from E. coli and regulatory subunits of protein kinase A from mammalian systems, to cAMP-activated potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channels from neuronal membranes and specifically synaptosomal fractions from rat brain. The latter group of proteins has never been identified before in any small molecule protein interaction and mass spectrometry-based proteomics study. Given the modest amount of protein input required, we expect that CCMS using the cAMP-CCs provides a unique tool for profiling cAMP-binding proteins from proteome samples of limited abundance, such as tissue biopsies.

Capture Compound Mass Spectrometry: A Technology for the Investigation of Small Molecule Protein Interactions

One of the major hurdles in the post-genomic era is to understand the function of genes and the interplay of many different cellular proteins. This is especially important for drug development. Capture compound mass spectrometry (CCMS) addresses this challenge by selectively reducing the complexity of the proteome. Capture compounds are trifunctional molecules: a selectivity function reversibly interacts via affinity with proteins; a reactivity function irreversibly forms a covalent bond outside the affinity binding site; and a sorting/pullout function allows the captured protein(s) to be isolated from cellular lysate for mass spectrometric analysis and characterization by database queries. In the present study, we demonstrate the use of a CCMS capture compound with a sulfonamide drug analog as its selectivity function, isolating an expected target protein from cell lysates containing a large excess of other "non-target" proteins. A future application of CCMS is to define or confirm drug target proteins and their mechanisms of drug action, or to discover off-target proteins that cause side effects, enabling subsequent drug structure optimization.

Anomalous behaviour within a systematic series of barium sulfate growth modifiers

The generally accepted view that phosphonate derivatives are more potent than the analogous carboxylates as crystal growth modifiers for barium sulfate has been systematically studied by using trifunctional molecules varying from the triphosphonate through to the analogous tricarboxylate; the results suggest that predictions based on simple structural features should be made with caution.

Inframolecular acid–base properties of myo-inositol 1,2,6-trisphosphate analogues: influence of the hydroxyl groups, phosphate configuration and intracyclic atom substitution

Abstract The microscopic acid–base properties of analogues of d - myo -inositol 1,2,6-trisphosphate 1 are reported. These analogues differ by the hydroxyl configuration ( l - chiro -inositol 1,2,3-trisphosphate 2 ) or the replacement of the inositol ring by a ring containing an atom of oxygen (1,5-anhydro- d -arabinitol 2,3,4-trisphosphate 3 and 1,5-anhydroxylitol 2,3,4-trisphosphate 4 ) or an atom of nitrogen (1,5-anhydro-1,5-imino- d -arabinitol 2,3,4-trisphosphate 5 ). In addition, the discussion includes the analogue of 1 where all three hydroxyls were removed ( 6 ). The studies, performed by potentiometric and 31 P-NMR titrations in a 0.2 M KCl medium at 37 °C, allowed the resolution without approximation of the microprotonation scheme of the trifunctional molecules. The constants as well as the chemical shifts of the phosphorus nuclei that characterize each individual phosphate group are analyzed in terms of hydration and hydrogen bonding. Thus, for 2 , the loss of a hydrogen bonding possibility between P-1 and OH-6 leads to an increase of the P-1 basicity with regard to 1 . Also, by comparing 3 and 4 it appears that the lower basicity of P-2 for 4 with regard to 3 may be attributed to a more favourable interaction between P-1 and P-2 in 3 when the two possible chair forms are allowed. Moreover, for 5 , the addition of the first equivalent of protons will protonate only about 75% of the amine, thus indicating that for polyfunctional molecules a given macroscopic protonation constant can hardly be attributed to a specific protonation site.

Effect of monomer purity on functionality distribution of ISRO polyol

The functionality distribution of ISRO polyol, a condensation polymer derived from 12-hydroxy stearic acid (THSA) and trimethylol propane (TMP), which is used as a binder in solid propellant has been studied by a dual detector analytical gel permeation Chromatographie (DDAGPC) method. The results show difference in the amounts of non-, mono-, di- and trifunctional molecules present in the samples prepared from commercial THSA and purified THSA. The difference in functionality distribution has been attributed to the presence of monofunctional stearic acid impurity in THSA. Polyol, prepared after removal of the stearic acid impurity, contained more than 50% trifunctional molecules and could be cured with a difunctional curator like toluene diisocyanate (TDI), whereas the polyols prepared with commercial THSA were found to contain more than 90% difunctional molecules and no trifunctional ones. These samples needed considerable quantity of trifunctional curator like TMP to get a crosslinked product with TDI. Thus a knowledge of the functionality distribution is necessary to determine the amount of crosslinker needed to form a good polymer network.

Analysis of the distribution of functionality types and the mechanism of hydroxyoligobutadiene formation in lithium-initiated polymerization

By the chromatographic method, under near to critical conditions, the distribution of functionality types was studied with hydroxyoligobutadienes synthesized with an initiator prepared by reaction of lithium with 2,4-hexadiene. It was shown that already at the stage of initiator synthesis, besides the required dilithium molecules, also mono- and trilithium compounds are formed in the reaction mixture, and in consequences of this the resulting oligomers contain mono-, bi- and trifunctional molecules. The number-average functionality of the oligomers can reach a value near to two, although the content of the bifunctional fraction does not exceed 60%. It was found that the solution of the initiator contains paramagnetic particles with a very narrow singlet EPR signal. Assumptions concerning possible mechanisms of functionality redistribution in the initiator solution are presented, including transmetallation processes and (or) reactions involving free-radical centres.

Study of change in the molecular mass distributions and compositions of linear and cyclic copolymerization products of octamethylcyclotetrasiloxane and α-, ω-dihydroxypolymethylphenyl siloxane using two-detector gel permeation chromatography

Change in the mean composition and MMD of the dimethylmethylphenylsiloxane copolymer during its preparation under the influence of an alkaline catalyst by the interaction of octamethylcyclotetrasiloxane and α,ω-dihydroxypolymethylphenyl siloxane, the dependence of the composition of the copolymer on the MM and also change in the composition and quantity of cyclic products present in the reaction mixture have been studied. Two-detector GPC has established that splitting of the starting oligomer takes place at the highest rate from the very start of the process with formation of phenyl-containing cyclosiloxanes with simultaneous copolymerization of octamethylcyclotetrasiloxane and the newly formed cycles with unsplit residues of the oligomer and redistribution of the units. The equilibrium distribution of methylphenylsiloxane units and the cycle-polymer equilibrium are achieved within 4 h of the start of the reaction. The character of the change in the MMD of the copolymer indicates the presence in the oligomer of a certain number of trifunctional molecules.