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In DNA-encoded library synthesis, amine-substituted building blocks are prevalent. We explored isocyanide multicomponent reactions to diversify DNA-tagged amines and reported the Ugi-azide reaction with high yields and a good substrate scope. In addition, the Ugi-aza-Wittig reaction and the Ugi-4-center-3-component reaction, which used bifunctional carboxylic acids to provide lactams, were explored. Five-, six-, and seven-membered lactams were synthesized from solid support-coupled DNA-tagged amines and bifunctional building blocks, providing access to structurally diverse scaffolds., Competing Interests: The authors declare the following competing financial interest(s): AB declares a competing financial interest as co-founder of Serengen GmbH, a company that provides DEL services., (© 2024 The Authors. Published by American Chemical Society.)

Monoterpene indole alkaloids (MIAs) are endowed with high structural and spatial complexity and characterized by diverse biological activities. Given this complexity-activity combination in MIAs, rapid and efficient access to chemical matter related to and with complexity similar to these alkaloids would be highly desirable, since such compound classes might display novel bioactivity. We describe the design and synthesis of a pseudo-natural product (pseudo-NP) collection obtained by the unprecedented combination of MIA fragments through complexity-generating transformations, resulting in arrangements not currently accessible by biosynthetic pathways. Cheminformatic analyses revealed that both the pseudo-NPs and the MIAs reside in a unique and common area of chemical space with high spatial complexity-density that is only sparsely populated by other natural products and drugs. Investigation of bioactivity guided by morphological profiling identified pseudo-NPs that inhibit DNA synthesis and modulate tubulin. These results demonstrate that the pseudo-NP collection occupies similar biologically relevant chemical space that Nature has endowed MIAs with., (© 2023 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Circularly polarized luminescent (CPL) films with high dissymmetry factors hold great potential for optoelectronic applications. Herein, we propose a strategy for achieving strongly dissymetric CPL in nanocomposite films based on chirality induction and energy transfer to semiconductor nanocrystals. First, focusing on a purely organic system, aggregation-induced emission (AIE) and CPL activity of organic liquid crystals (LCs) forming helical nanofilaments was detected, featuring green emission with high dissymmetry factors g lum . The handedness of helical filaments, and thus the sign of CPL, was controlled via minute amounts of a small chiral organic dopant. Second, nanocomposite films were fabricated by incorporating InP/ZnS semiconductor quantum dots (QDs) into the LC matrix, which induced the chiral assembly of QDs and endowed them with chiroptical properties. Due to the spectral matching of the components, energy transfer (ET) from LC to QDs was possible enabling a convenient way of tuning CPL wavelengths by varying the LC/QD ratio. As obtained, composite films exhibited absolute -2 . The handedness of helical filaments, and thus the sign of CPL, was controlled via minute amounts of a small chiral organic dopant. Second, nanocomposite films were fabricated by incorporating InP/ZnS semiconductor quantum dots (QDs) into the LC matrix, which induced the chiral assembly of QDs and endowed them with chiroptical properties. Due to the spectral matching of the components, energy transfer (ET) from LC to QDs was possible enabling a convenient way of tuning CPL wavelengths by varying the LC/QD ratio. As obtained, composite films exhibited absolute g and thermally on/off switchable luminescence. Overall, we demonstrate the induction of chiroptical properties by the assembly of nonchiral building QDs on the chiral organic template and energy transfer from organic films to QDs, representing a simple and versatile approach to tune the CPL activity of organic materials.lum values up to ∼10 -2 and thermally on/off switchable luminescence. Overall, we demonstrate the induction of chiroptical properties by the assembly of nonchiral building QDs on the chiral organic template and energy transfer from organic films to QDs, representing a simple and versatile approach to tune the CPL activity of organic materials.

DNA-encoded libraries (DELs) offer great promise for the discovery of new ligands for proteins. Many current reactions used for DEL synthesis do not proceed efficiently over a wide range of substrates. Combining a diverse array of multicomponent reactions with micellar-promoted Suzuki-Miyaura cross-coupling provides a strategy for synthesizing highly diverse DELs with exceptionally high fidelity. These results demonstrate that the micellar Suzuki-Miyaura reaction has exceptional functional group tolerance and broad applicability.

Knowledge about interrelationships between different proteins is crucial in fundamental research for the elucidation of protein networks and pathways. Furthermore, it is especially critical in chemical biology to identify further key regulators of a disease and to take advantage of polypharmacology effects. Here, we present a new concept that combines a scaffold-based analysis of bioactivity data with a subsequent screening to identify novel inhibitors for a protein target of interest. The initial scaffold-based analysis revealed a flavone-like scaffold that can be found in ligands of different unrelated proteins indicating a similarity in ligand binding. This similarity was further investigated by testing compounds on bromodomain-containing protein 4 (BRD4) that were similar to known ligands of the other identified protein targets. Several new BRD4 inhibitors were identified and proven to be validated hits based on orthogonal assays and X-ray crystallography. The most important discovery was an unexpected relationship between BRD4 and peroxisome-proliferator activated receptor gamma (PPARγ). Both proteins share binding site similarities near a common hydrophobic subpocket which should allow the design of a polypharmacology-based ligand targeting both proteins. Such dual-BRD4-PPARγ modulators open up new therapeutic opportunities, because both are important drug targets for cancer therapy and many more important diseases. Thereon, a complex structure of sulfasalazine was obtained that involves two bromodomains and could be a potential starting point for the design of a bivalent BRD4 inhibitor.

The development of DNA-compatible reaction methodologies is a central theme to advance DNA-encoded screening library technology. Recently, we were able to show that sulfonic acid-functionalized block copolymer micelles facilitated Brønsted acid-promoted reactions such as the Povarov reaction on DNA-coupled starting materials with minimal DNA degradation. Here, the impact of polymer composition on micelle shape, and reaction conversion was investigated. A dozen sulfonic acid-functionalized block copolymers of different molar mass and composition were prepared by RAFT polymerization and were tested in the Povarov reaction, removal of the Boc protective group, and the Biginelli reaction. The results showed trends in the polymer structure-micellar catalytic activity relationship. For instance, micelles composed of block copolymers with shorter acrylate ester chains formed smaller particles and tended to provide faster reaction kinetics. Moreover, fluorescence quenching experiments as well as circular dichroism spectroscopy showed that DNA-oligomer-conjugates, although highly water-soluble, accumulated very effectively in the micellar compartments, which is a prerequisite for carrying out a DNA-encoded reaction in the presence of polymer micelles., (© 2021 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

Understanding the ligandability of a target protein, defined as the capability of a protein to bind drug-like compounds on any site, can give important stimuli to drug-development projects. For instance, inhibition of protein-protein interactions usually depends on the identification of protein surface binders. DNA-encoded chemical libraries (DELs) allow scanning of protein surfaces with large chemical space. Encoded library selection screens uncovered several protein-protein interaction inhibitors and compounds binding to the surface of G protein-coupled receptors (GPCRs) and kinases. The protein surface-binding chemotypes from DELs are predominantly chemically modified and cyclized peptides, and functional small-molecule peptidomimetics. Peptoid libraries and structural peptidomimetics have been less studied in the DEL field, hinting at hitherto less populated chemical space and suggesting alternative library designs. Roughly a third of bioactive molecules evolved from smaller, target-focused libraries. They showcase the potential of encoded libraries to identify more potent molecules from weak, for example, fragment-like, starting points., (© 2020 The Authors. ChemMedChem published by Wiley-VCH GmbH.)

The combination of shape-complementary bis-monodentate ligands L A and L B with Pd II cations yields heteroleptic cages cis-[Pd 2 L A 2 ] by self-sorting. Herein, we report how such assemblies can be diversified by introduction of covalent backbone bridges between two L B units. Together with solvent and guest effects, the flexibility of these linkers can modulate nuclearity, topology, and number of cavities in a family of four structurally diverse assemblies. Ligand L 2 ] by self-sorting. Herein, we report how such assemblies can be diversified by introduction of covalent backbone bridges between two L A units. Together with solvent and guest effects, the flexibility of these linkers can modulate nuclearity, topology, and number of cavities in a family of four structurally diverse assemblies. Ligand L A1 counterpart to a tetranuclear dimer D1. In DMSO, however, a trinuclear pseudo-tetrahedron T1 is formed. The product of L 3 , with rigid linker, looks similar to D1, but with a rotated ligand arrangement. In presence of an anionic guest, this dimer D2 transforms and a hexanuclear prismatic barrel P2 crystallizes. We demonstrate how controlling a ligand's coordination mode can trigger structural differentiation and increase complexity in metallo-supramolecular assembly.B counterpart to a tetranuclear dimer D1. In DMSO, however, a trinuclear pseudo-tetrahedron T1 is formed. The product of L A2 , with rigid linker, looks similar to D1, but with a rotated ligand arrangement. In presence of an anionic guest, this dimer D2 transforms and a hexanuclear prismatic barrel P2 crystallizes. We demonstrate how controlling a ligand's coordination mode can trigger structural differentiation and increase complexity in metallo-supramolecular assembly., (© 2020 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Metal-binding DNA structures with catalytic function are receiving increasing interest. Although a number of metalloDNAzymes have been reported to be highly efficient, the exact coordination/position of their catalytic metal center is often unknown. Here, we present a new approach to rationally develop metalloDNAzymes for Lewis acid-catalyzed reactions such as enantioselective Michael additions. Our strategy relies on the predictable folding patterns of unimolecular DNA G-quadruplexes, combined with the concept of metal-mediated base-pairing. Transition-metal coordination environments were created in G-quadruplex loop regions, accessible by substrates. Therefore, protein-inspired imidazole ligandoside L was covalently incorporated into a series of G-rich DNA strands by solid-phase synthesis. Iterative rounds of DNA sequence design and catalytic assays allowed us to select tailored metalloDNAzymes giving high conversions and excellent enantioselectivities (≥99%). Based on their primary sequence, folding pattern, and metal coordination mode, valuable information on structure-activity relationships could be extracted. Variation of the number and position of ligand L within the sequence allowed us to control the formation of ( S ) and ( R ) enantiomeric reaction products, respectively.

A strategy to implement four members of the classic coal-tar dye family, Michler's ketone, methylene blue, rhodamine B, and crystal violet, into [Pd 2 L 4 ] self-assemblies is introduced. Chromophores were incorporated into bis-monodentate ligands using piperazine linkers that allow to retain the auxochromic dialkyl amine functionalities required for intense colors deep in the visible spectrum. Upon palladium coordination, ligands with pyridine donors form lantern-shaped dinuclear cages while quinoline donors lead to strongly twisted [Pd 2 L 4 ] helicates in solution. In one case, single crystal X-ray diffraction revealed rearrangement to a [Pd 3 L 6 ] ring structure in the solid state. For nine examined derivatives, showing colors from yellow to deep violet, CD spectroscopy discloses different degrees of chiral induction by an enantiomerically pure guest. Ion mobility mass spectrometry allows to distinguish two binding modes. Self-assemblies based on this new ligand class promise application in chiroptical recognition, photo-redox catalysis and optical materials., (© 2020 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

DNA G-quadruplexes show a pronounced tendency to form higher-order structures, such as π-stacked dimers and aggregates with aromatic binding partners. Reliable methods for determining the structure of these non-covalent adducts are scarce. Here, we use artificial square-planar Cu(pyridine) 4 complexes, covalently incorporated into tetramolecular G-quadruplexes, as rigid spin labels for detecting dimeric structures and measuring intermolecular Cu 2+ -Cu 2+ distances via pulsed dipolar EPR spectroscopy. A series of G-quadruplex dimers of different spatial dimensions, formed in tail-to-tail or head-to-head stacking mode, were unambiguously distinguished. Measured distances are in full agreement with results of molecular dynamics simulations. Furthermore, intercalation of two well-known G-quadruplex binders, PIPER and telomestatin, into G-quadruplex dimers resulting in sandwich complexes was investigated, and previously unknown binding modes were discovered. Additionally, we present evidence that free G-tetrads also intercalate into dimers. Our transition metal labeling approach, combined with pulsed EPR spectroscopy, opens new possibilities for examining structures of non-covalent DNA aggregates., (© 2020 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

We report on the synthesis of core-shell microparticles (CSMs) with an acid catalyst in the core and a base catalyst in the shell by surfactant-free emulsion polymerization (SFEP). The organocatalytic monomers were separately copolymerized in three synthetic steps allowing the spatial separation of incompatible acid and base catalysts within the CSMs. Importantly, a protected and thermo-decomposable sulfonate monomer was used as acid source to circumvent the neutralization of the base catalyst during shell formation, which was key to obtain stable, catalytically active CSMs. The catalysts showed excellent performance in an established one-pot model cascade reaction in various solvents (including water), which involved an acid-catalyzed deacetalization followed by a base-catalyzed Knoevenagel condensation. The CSMs are easily recycled, modified, and their synthesis is scalable, making them promising candidates for organocatalytic applications., (© 2020 The Authors. Published by Wiley-VCH GmbH.)

A series of copper(I) complexes bearing a cyclic (amino)(aryl)carbene (CAArC) ligand with various complex geometries have been investigated in great detail with regard to their structural, electronic, and photophysical properties. Comparison of [CuX(CAArC)] (X = Br ( 1 ), Cbz ( 2 ), acac ( 3 ), Ph 2 acac ( 4 ), Cp ( 5 ), and Cp* ( 6 )) with known Cu I complexes bearing cyclic (amino)(alkyl), monoamido, or diamido carbenes (CAAC, MAC, or DAC, respectively) as chromophore ligands reveals that the expanded π-system of the CAArC leads to relatively low energy absorption maxima between 350 and 550 nm in THF with high absorption coefficients of 5-15 × 10 3 M -1 cm -1 for 1 - 6 . Furthermore, 1 - 5 show intense deep red to near-IR emission involving their triplet excited states in the solid state and in PMMA films with λ em max = 621-784 nm. Linear [Cu(Cbz)( Dipp CAArC)] ( 2 ) has been found to be an exceptional deep red (λ max = 621 nm, ϕ = 0.32, τ av of ca. 9 × 10 k r , exceeding those of commercially employed Ir 5 s -1 -based emitters. Time-resolved transient absorption and fluorescence upconversion experiments complemented by quantum chemical calculations employing Kohn-Sham density functional theory and multireference configuration interaction methods as well as temperature-dependent steady-state and time-resolved luminescence studies provide a detailed picture of the excited-state dynamics of III . To demonstrate the potential applicability of this new class of low-energy emitters in future photonic applications, such as nonclassical light sources for quantum communication or quantum cryptography, we have successfully conducted single-molecule photon-correlation experiments of II -based emitters. Time-resolved transient absorption and fluorescence upconversion experiments complemented by quantum chemical calculations employing Kohn-Sham density functional theory and multireference configuration interaction methods as well as temperature-dependent steady-state and time-resolved luminescence studies provide a detailed picture of the excited-state dynamics of 2 . To demonstrate the potential applicability of this new class of low-energy emitters in future photonic applications, such as nonclassical light sources for quantum communication or quantum cryptography, we have successfully conducted single-molecule photon-correlation experiments of 2 , showing distinct antibunching as required for single-photon emitters.

Ten-eleven-translocation (TET) dioxygenases catalyze the oxidation of 5-methylcytosine (5mC), the central epigenetic regulator of mammalian DNA. This activity dynamically reshapes the epigenome and transcriptome by depositing oxidized 5mC derivatives and initiating active DNA demethylation. However, studying this dynamic is hampered by the inability to selectively activate individual TETs with temporal control in cells. We report activation of TETs in mammalian cells by incorporation of genetically encoded 4,5-dimethoxy-2-nitrobenzyl-l-serine as a transient active-site block, and its subsequent deprotection with light. Our approach enables precise insights into the impact of cancer-associated TET2 mutations on the kinetics of TET2 catalysis in vivo , and allows time-resolved monitoring of target gene activation and transcriptome reorganization. This sets a basis for dissecting the order and kinetics of chromatin-associated events triggered by TET catalysis, ranging from DNA demethylation to chromatin and transcription regulation.

A series of seven homoleptic Cu I complexes based on hetero-bidentate P^N ligands was synthesized and comprehensively characterized. In order to study structure-property relationships, the type, size, number and configuration of substituents at the phosphinooxazoline (phox) ligands were systematically varied. To this end, a combination of X-ray diffraction, NMR spectroscopy, steady-state absorption and emission spectroscopy, time-resolved emission spectroscopy, quenching experiments and cyclic voltammetry was used to assess the photophysical and electrochemical properties. Furthermore, time-dependent density functional theory calculations were applied to also analyze the excited state structures and characteristics. Surprisingly, a strong dependency on the chirality of the respective P^N ligand was found, whereas the specific kind and size of the different substituents has only a minor impact on the properties in solution. Most importantly, all complexes except C3 are photostable in solution and show fully reversible redox processes. Sacrificial reductants were applied to demonstrate a successful electron transfer upon light irradiation. These properties render this class of photosensitizers as potential candidates for solar energy conversion issues., (© 2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

We present a small molecule pK a prediction tool entirely written in Python. It predicts the macroscopic pK a value and is trained on a literature compilation of monoprotic compounds. Different machine learning models were tested and random forest performed best given a five-fold cross-validation (mean absolute error=0.682, root mean squared error=1.032, correlation coefficient r 2 =0.82). We test our model on two external validation sets, where our model performs comparable to Marvin and is better than a recently published open source model. Our Python tool and all data is freely available at https://github.com/czodrowskilab/Machine-learning-meets-pKa., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Baltruschat M and Czodrowski P.)

For metal-mediated host compounds, the development of strategies to reduce symmetry and introduce multiple functionalities in a non-statistical way is a challenging task. We show that the introduction of steric stress around the coordination environment of square-planar Pd II cations and bis-monodentate nitrogen donor ligands allows to control the size and shape of the assembled product, from [Pd 2 L 4 ] cages over [Pd 2 L 3 ] bowl-shaped structures to [Pd 2 L 2 ] rings. Therefore, banana-shaped ligand backbones were equipped with pyridines, two different quinoline isomers and acridine, the latter three introducing steric congestion through hydrogen substituents on annelated benzene rings. Differing behavior of the four resulting hosts towards the binding of C 60 and C 70 fullerenes was studied and related to structural differences by NMR spectroscopy, mass spectrometry and single crystal X-ray diffraction. The three cages based on pyridine, 6-quinoline or 3-quinoline donors were found to either bind C 60 , C 70 or no fullerene at all., (© 2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

Two types of imidazole ligands were introduced both at the end of tetramolecular and into the loop region of unimolecular DNA G-quadruplexes. The modified oligonucleotides were shown to complex a range of different transition-metal cations including Ni II , Cu II , Zn II and Co II , as indicated by UV/Vis absorption spectroscopy and ion mobility mass spectrometry. Molecular dynamics simulations were performed to obtain structural insight into the investigated systems. Variation of ligand number and position in the loop region of unimolecular sequences derived from the human telomer region (htel) allows for a controlled design of distinct coordination environments with fine-tuned metal affinities. It is shown that Cu II , which is typically square-planar coordinated, has a higher affinity for systems offering four ligands, whereas Ni II prefers G-quadruplexes with six ligands. Likewise, the positioning of ligands in a square-planar versus tetrahedral fashion affects binding affinities of Cu II and Zn II cations, respectively. Gaining control over ligand arrangement patterns will spur the rational development of transition-metal-modified DNAzymes. Furthermore, this method is suited to combine different types of ligands, for example, those typically found in metalloenzymes, inside a single DNA architecture., (© 2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

Isocyanide multicomponent reactions play a prominent role in drug discovery. This chemistry has hardly been investigated for compatibility with DNA-encoded combinatorial synthesis. The Ugi, Ugi-azide, and Groebke-Blackburn-Bienaymé reactions are well-tolerated by DNA on the solid phase and show a broad scope. However, an oxadiazole-forming variant of the Ugi reaction caused DNA depurination, requiring a more stable hexathymidine DNA for encoded library synthesis. Cheminformatic analysis revealed that isocyanide multicomponent-reaction-based encoded libraries cover a diverse chemical space.

The translation of well-established molecular biology methods such as genetic coding, selection, and DNA sequencing to combinatorial organic chemistry and compound identification has made extremely large compound collections, termed DNA-encoded libraries, accessible for drug screening. However, the reactivity of the DNA imposes limitations on the choice of chemical methods for encoded library synthesis. For example, strongly acidic reaction conditions must be avoided because they damage the DNA by depurination, i.e. the cleavage of purine bases from the oligomer. Application of micellar catalysis holds much promise for encoded chemistry. Aqueous micellar dispersions enabled compound synthesis under often appealingly mild conditions. Amphiphilic block copolymers covalently functionalized with sulfonic acid moieties in the lipophilic portion assemble in water and locate the Brønsted catalyst in micelles. These acid nanoreactors enabled the reaction of DNA-conjugated aldehydes to diverse substituted tetrahydroquinolines and aminoimidazopyridines by Povarov and Groebke-Blackburn-Bienaymé reactions, respectively, and the cleavage of tBoc protective groups from amines. The polymer micelle design was successfully translated to the Cu/Bipyridine/TEMPO system mediating the oxidation of DNA-coupled alcohols to the corresponding aldehydes. These results suggest a potentially broad applicability of polymer micelles for encoded chemistry.

Autophagy ensures cellular homeostasis by the degradation of long-lived proteins, damaged organelles and pathogens. This catabolic process provides essential cellular building blocks upon nutrient deprivation. Cellular metabolism, especially mitochondrial respiration, has a significant influence on autophagic flux, and complex I function is required for maximal autophagy. In Parkinson's disease mitochondrial function is frequently impaired and autophagic flux is altered. Thus, dysfunctional organelles and protein aggregates accumulate and cause cellular damage. In order to investigate the interdependency between mitochondrial function and autophagy, novel tool compounds are required. Herein, we report the discovery of a structurally novel autophagy inhibitor (Authipyrin) using a high content screening approach. Target identification and validation led to the discovery that Authipyrin targets mitochondrial complex I directly, leading to the potent inhibition of mitochondrial respiration as well as autophagy., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Fullerenes and their derivatives are of tremendous technological relevance. Synthetic access and application are still hampered by tedious purification protocols, peculiar solubility, and limited control over regioselective derivatization. We present a modular self-assembly system based on a new low-molecular-weight binding motif, appended by two palladium(II)-coordinating units of different steric demands, to either form a [Pd 2 L 1 4 ] 4+ cage or an unprecedented [Pd 2 L 2 3 (MeCN) 2 ] 4+ bowl (with L 1 . The latter, owing to its more open structure, also allows binding of C 2 and fullerene derivatives. By exposing only a fraction of the bound guests' surface, the bowl acts as fullerene protecting group to control functionalization, as demonstrated by exclusive monoaddition of anthracene. In a hierarchical manner, sterically low-demanding dicarboxylates were found to bridge pairs of bowls into pill-shaped dimers, able to host two fullerenes. The hosts allow transferring bound fullerenes into a variety of organic solvents, extending the scope of possible derivatization and processing methodologies.60 . The latter, owing to its more open structure, also allows binding of C 70 and fullerene derivatives. By exposing only a fraction of the bound guests' surface, the bowl acts as fullerene protecting group to control functionalization, as demonstrated by exclusive monoaddition of anthracene. In a hierarchical manner, sterically low-demanding dicarboxylates were found to bridge pairs of bowls into pill-shaped dimers, able to host two fullerenes. The hosts allow transferring bound fullerenes into a variety of organic solvents, extending the scope of possible derivatization and processing methodologies.

3D electron diffraction has reached a stage where the structures of chemical compounds can be solved productively. Instrumentation is lagging behind this development, and to date dedicated electron diffractometers for data collection based on the rotation method do not exist. Current studies use transmission electron microscopes as a workaround. These are optimized for imaging, which is not optimal for diffraction studies. The beam intensity is very high, it is difficult to create parallel beam illumination and the detectors used for imaging are of only limited use for diffraction studies. In this work, the combination of an EIGER hybrid pixel detector with a transmission electron microscope to construct a productive electron diffractometer is described. The construction not only refers to the combination of hardware but also to the calibration of the system, so that it provides rapid access to the experimental parameters that are necessary for processing diffraction data. Until fully integrated electron diffractometers become available, this describes a setup for productive and efficient operation in chemical crystallography., (open access.)

The identification of possible targets for a known bioactive compound is of the utmost importance for drug design and development. Molecular docking is one possible approach for in-silico protein target prediction, whereas a molecule is docked into several different protein structures to identify potential targets. This reverse docking approach is hampered by the limitation of current scoring functions to correctly discriminate between targets and nontargets. In this work, a development of target-specific scoring functions is described that showed improved prediction performances for the correct target prediction of both actives and decoys on three validation data sets. In contrast to pure ligand-based approaches, that are in general faster and include a greater target space, docking-based approaches can cover also unknown chemical space that lies outside the known bioactivity data. These target-specific scoring functions are based on known bioactivity data retrieved from ChEMBL and supervised machine learning approaches. Neural Networks and Support Vector Machines (SVMs) models were trained for 20 different protein targets. Our protein-ligand interaction fingerprint PADIF (Protein Atom Score Contributions Derived Interaction Fingerprint) represents the input for training, whereas the PADIFs are calculated based on docking poses of active and inactive compounds. Different data sets of previously unseen molecules were used for the final evaluation and analysis of the prediction performance of the created models. For a single-target selectivity data set, the correct target model returns in most of the cases the highest probabilities scores for their active molecules and with statistically significant differences from the other targets. These probability scores were also predicted and successfully used to rank the targets for molecules of a multitarget data set with activity data described simultaneously for two, three, and four to seven protein targets.

Photochromic [Pd 2 L 4 ] coordination cages based on dithienylethene (DTE) ligands L allow triggering guest uptake and release by irradiation with light of different wavelengths. The process involves four consecutive electrocyclic reactions to convert all chromophores between their open and closed photoisomeric forms. So far, guest affinity of the fully switched species was elucidated, but mechanistic details concerning the intermediate steps remained elusive. Now, a new member of the DTE cage family allows unprecedented insight into the interplay between photoisomerization steps and guest location inside/outside the cavity. Therefore, the intrinsic chirality of the DTE backbones was used as reporter for monitoring the fate of a chiral guest. In its "open" photoisomeric form ( o-L, [Pd 2 ( o-L) 4 ] = o-C), the C 2 -symmetric DTE chromophore quickly converts between energetically degenerate P and M helical conformations. After binding homochiral 1 R-( -) or 1 S-( +) camphor sulfonate ( R-CSA or S-CSA), guest-to-host chirality transfer was observed via a circular dichroism (CD) signal for the cage-centered absorption. Irradiating the R/S-CSA@ o-C host-guest complexes at 313 nm produced configurationally stable "closed" photoisomers, thus locking the induced chirality with an enantiomeric excess close to 25%. This value (corresponding to chiral induction for one out of four ligands), together with DOSY NMR, ion mobility mass spectrometry, and X-ray structure results, shows that closure of the first photoswitch is sufficient to expel the guest from the cavity.

Protein myristoylation plays key roles in biological processes, for instance, in membrane attachment and activation of proteins and in mediating protein-protein and protein-lipid interactions. Furthermore, myristoylated proteins are involved in disorders, including cancer and viral infections. Therefore, new tools to study protein myristoylation are in high demand. Herein, we report the development of photoactivatable probes, based on a diazirine-substituted analogue of myristic acid. The probes bind to and, upon irradiation, covalently label the lipid-binding chaperone protein uncoordinated 119 (UNC119). UNC119 increases overall solubility and regulates specifically the transport of myristoylated proteins between intercellular membranes. The binding mode of the probes is similar to that of the myristate moiety, and the residues inside the hydrophobic pocket of UNC119 proteins that are critical for covalent binding have been identified. The interaction with UNC119 was also demonstrated in cell lysate by means of affinity enrichment. Moreover, it is shown that the myristate analogue can be incorporated into peptide substrates by N-myristoyl transferases of Leishmania and Trypanosoma protozoan parasites., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Porous nanostructures and materials based on metal-mediated self-assembly have developed into a vibrantly studied subdiscipline of supramolecular chemistry during the past decades. In principle, two branches of such coordination compounds can be distinguished: Metal-organic frameworks (MOFs) on the one side represent infinite porous networks of metals or metal clusters that are connected via organic ligands to give solid-state materials. On the other hand, metal-organic cages (MOCs) are discrete and soluble systems with only a limited number of pores. Formation of a particular structure type is achieved by carefully balancing the donor site angles within the ligands as well as the nature and coordination geometry of the metal component. Years of research on MOFs and MOCs has yielded numerous types of well-defined porous crystals and complex supramolecular architectures. Since various synthetic routes and postsynthetic modification methods have been established, the focus of recent developments has moved toward the preparation of multifunctional systems that are able to mimic the structural and functional complexity of natural enzymes. This Account compares different strategies to prepare multifunctional MOFs and heteroleptic MOCs and gives a perspective on where to move forward. While the preparative toolbox for multifunctional MOFs is already quite mature, pore accessibility and substrate diffusion within the crystal have been identified as major challenges yet to be overcome. Only recently have a set of different strategies for the assembly of heteroleptic MOCs been developed. Such multifunctional cages can be formed from either partially protected or "naked" metal cations. Controlled assembly, producing single products rather than statistical mixtures, leans on assembly-dependent approaches making use of either steric effects or shape complementarity between the ligands. Further strategies include coordination-site engineering and hierarchical assembly of preformed components. The main challenge with heteroleptic, functional MOCs is to find a balance between the required dynamic assembly fidelity and the stability of the resulting system under operating conditions. If these limitations can be overcome in the future, chemists will be able to design multifunctional systems of similar activity and complexity as nature's enzymes from simple and easily accessible synthetic building blocks. Major impacts on chemical sensing, small-molecule recognition and sequestration, drug delivery, and catalysis will be achieved by these materials.

A series of metal-mediated cages, having multiple cavities, was synthesized from Pd II cations and tris- or tetrakis-monodentate bridging ligands and characterized by NMR spectroscopy, mass spectrometry, and X-ray methods. The peanut-shaped [Pd 3 L 1 4 ] cage deriving from the tris-monodentate ligand L 1 could be quantitatively converted into its interpenetrated [5Cl@Pd 6 L 1 Pd} stack as an unprecedented structural motif upon addition of chloride anions. Small-angle neutron scattering (SANS) experiments showed that the cigar-shaped assembly with a length of 3.7 nm aggregates into mono-layered discs of 14 nm diameter via solvophobic interactions between the hexyl sidechains. The hepta-cationic [5Cl@Pd 8 ] dimer featuring a linear {[Pd-Cl-] 5 ] cage was found to interact with polyanionic oligonucleotide double-strands under dissolution of the aggregates in water, rendering the compound class interesting for applications based on non-covalent DNA binding.6 L 1 8 ] cage was found to interact with polyanionic oligonucleotide double-strands under dissolution of the aggregates in water, rendering the compound class interesting for applications based on non-covalent DNA binding., (© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The synthesis and application of three chiral receptors based on the covalent linkage of 1,1'-binaphthylphosphoric acids is reported. The binding of the lysine enantiomers to the chiral receptors was investigated by DOSY-NMR and NMR titrations, revealing that the bisphosphoric acid 1d acts as a highly stereoselective receptor for binding of d-lysine.

A donor-site engineering approach facilitates the formation of heteroleptic [Pd 2 L 2 L' 2 ] 4+ cage structures through a favored cis-'in 2 /out 2 ' spatial configuration of the methyl groups of 5- and 3-substituted bis-monodentate picolyl ligands with flat acridone and bent phenothiazine backbones. The heteroleptic cages were confirmed by ESI-MS and 2D NMR experiments as well as DFT calculations, which pointed toward a cis-configuration being energetically favored. This was further supported by the synthesis and X-ray structure of a previously unreported cis-[Pd(2-picoline) 4 ] 2+ complex. The formation of homoleptic structures, however, was met with considerable steric hindrance at the Pd II centers, as observed by the formation of [Pd 2 L 3 (solvent) 2 ] 4+ and [Pd 2 L 2 (solvent) 4 ] 4+ species when only one type of acridone-based ligand was offered. In contrast, bent phenothiazine ligands with outside-pointing methyl groups showed the ability to form interpenetrated double-cages, as revealed by X-ray crystallography. The general route presented herein enables the assembly of uniform cis-[Pd 2 L 2 L' 2 ] 4+ coordination cages, thus furthering the possibility to increase structural and functional complexity in supramolecular systems., (© 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

Non-natural oligonucleotides represent important (bio)chemical tools and potential therapeutic agents. Backbone modifications altering hybridization properties and biostability can provide useful analogues. Here, we employ an artificial nucleosyl amino acid (NAA) motif for the synthesis of oligonucleotides containing a backbone decorated with primary amines. An oligo-T sequence of this cationic DNA analogue shows significantly increased affinity for complementary DNA. Notably, hybridization with DNA is still governed by Watson-Crick base pairing. However, single base pair mismatches are tolerated and some degree of sequence-independent interactions between the cationic NAA backbone and fully mismatched DNA are observed. These findings demonstrate that a high density of positive charges directly connected to the oligonucleotide backbone can affect Watson-Crick base pairing. This provides a paradigm for the design of therapeutic oligonucleotides with altered backbone charge patterns., (© 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

When used as inhibitors of gene expression in vivo, oligonucleotides require modification of their structures to boost their binding affinity for complementary target RNAs. To date, hundreds of modifications have been designed and tested but few have proven to be useful. Among those investigated are mono- and polyamino-groups. These are positively charged at physiological pH and have been appended to oligonucleotides in an effort to reduce electrostatic repulsion during hybridization to RNAs, but have generally shown relatively minor benefits to binding. We conjugated spermine to uracils in oligonucleotides via a triazole linker so that the polyamine fits in the major groove of a subsequently formed RNA-duplex. The modifications produced large increases in target-binding affinity of the oligonucleotides. Using surface plasmon resonance-based assays, we showed that the increases derived mainly from faster annealing (k on ). We propose that the spermine fragments play a similar role to that of natural polyamines during oligonucleotide-target interactions in cells, and may be advantageous for oligonucleotides that operate catalytic mechanisms., (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

N-Terminal myristoylation facilitates membrane binding and activity of proteins, in particular of Src family kinases, but the underlying mechanisms are only beginning to be understood. The chaperones UNC119A/B regulate the cellular distribution and signaling of N-myristoylated proteins. Selective small-molecule modulators of the UNC119-cargo interaction would be invaluable tools, but have not been reported yet. We herein report the development of the first UNC119-cargo interaction inhibitor, squarunkin A. Squarunkin A selectively inhibits the binding of a myristoylated peptide representing the N-terminus of Src kinase to UNC119A with an IC 50 value of 10 nm. It binds to UNC119 proteins in cell lysate and interferes with the activation of Src kinase. Our results demonstrate that small-molecule inhibition of the UNC119-cargo interaction might provide new opportunities for modulating the activity of Src kinases that are independent of direct inhibition of the enzymatic kinase activity., (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The ever increasing bioactivity data that are produced nowadays allow exhaustive data mining and knowledge discovery approaches that change chemical biology research. A wealth of chemoinformatics tools, web services, and applications therefore exists that supports a careful evaluation and analysis of experimental data to draw conclusions that can influence the further development of chemical probes and potential lead structures. This review focuses on open-source approaches that can be handled by scientists who are not familiar with computational methods having no expert knowledge in chemoinformatics and modeling. Our aim is to present an easily manageable toolbox for support of every day laboratory work. This includes, among other things, the available bioactivity and related molecule databases as well as tools to handle and analyze in-house data.

Due to the inherent difficulties in achieving a defined and exclusive formation of multicomponent assemblies against entropic predisposition, we present the rational assembly of a heteroleptic [Pd 2 L A 2 L B coordination cage achieved through the geometric complementarity of two carefully designed ligands, L 2 and L 4+ coordination cage achieved through the geometric complementarity of two carefully designed ligands, L A and L B . With Pd(II) cations as rigid nodes, the pure distinctly angular components readily form homoleptic cages, a [Pd 2 strained helical assembly and a [Pd A 4 ] 4+ box-like structure, both of which were characterized by X-ray analysis. Combined, however, the two ligands could be used to cleanly assemble a cis-[Pd 4 L B 8 ] 8+ cage with a bent architecture. The same self-sorted product was also obtained by a quantitative cage-to-cage transformation upon mixing of the two homoleptic cages revealing the [Pd 2 L A 2 L B assembly as the thermodynamic minimum. The structure of the heteroleptic cage was examined by ESI-MS, COSY, DOSY, and NOESY methods, the latter of which pointed toward a cis-conformation of ligands in the assembly. Indeed, DFT calculations revealed that the angular ligands and strict Pd(II) geometry strongly favor the cis-[Pd 2 ] 4+ cage with a bent architecture. The same self-sorted product was also obtained by a quantitative cage-to-cage transformation upon mixing of the two homoleptic cages revealing the [Pd 2 L A species. The robust nature of the cis-[Pd 2 L B 2 ] 4+ cage allowed us to probe the accessibility of its cavity, which could be utilized for shape recognition toward stereoisomeric guests. The ability to directly combine two different backbones in a controlled manner provides a powerful strategy for increasing complexity in the family of [Pd 2 L A ] cages and opens up possibilities of introducing multiple functionalities into a single self-assembled architecture.2 L B 2 ] 4+ species. The robust nature of the cis-[Pd 2 L A 2 L B 2 ] 4+ cage allowed us to probe the accessibility of its cavity, which could be utilized for shape recognition toward stereoisomeric guests. The ability to directly combine two different backbones in a controlled manner provides a powerful strategy for increasing complexity in the family of [Pd 2 L 4 ] cages and opens up possibilities of introducing multiple functionalities into a single self-assembled architecture.

Trypanothione synthetase is an essential enzyme for kinetoplastid parasites which cause highly disabling and fatal diseases in humans and animals. Inspired by the observation that N(5)-substituted paullones inhibit the trypanothione synthetase from the related parasite Leishmania infantum, we designed and synthesized a series of new derivatives. Although none of the new compounds displayed strong inhibition of Trypanosoma brucei trypanothione synthetase, several of them caused a remarkable growth inhibition of cultivated Trypanosoma brucei bloodstream forms. The most potent congener 3a showed antitrypanosomal activity in double digit nanomolar concentrations and a selectivity index of three orders of magnitude versus murine macrophage cells., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Photon-powered charge separation is achieved in a supramolecular architecture based on the dense packing of functional building blocks. Therefore, self-assembled dimers of interpenetrated coordination cages consisting of redoxactive chromophors were synthesized in a single assembly step starting from easily accessible ligands and Pd(II) cations. Two backbones consisting of electron rich phenothiazine (PTZ) and electron deficient anthraquinone (ANQ) were used to assemble either homo-octameric or mixed-ligand double cages. The electrochemical and spectroscopic properties of the pure cages, mixtures of donor and acceptor cages and the mixed-ligand cages were compared by steady-state UV-vis and transient absorption spectroscopy, supported by cyclic voltammetry and spectroelectrochemistry. Only the mixed-ligand cages, allowing close intra-assembly communication between the donors and acceptors, showed the evolution of characteristic PTZ radical cation and ANQ radical anion features upon excitation in the transient spectra. In contrast, excitation of the mixtures of the homo-octameric donor and acceptor cages in solution did not lead to any signs of electron transfer. Densely packed photo- and redox-functional self-assemblies promise molecular-level control over the morphology of the charge separation layer in future photovoltaic applications.

Modern rational drug design not only deals with the search for ligands binding to interesting and promising validated targets but also aims to identify the function and ligands of yet uncharacterized proteins having impact on different diseases. Additionally, it contributes to the design of inhibitors with distinct selectivity patterns and the prediction of possible off-target effects. The identification of similarities between binding sites of various proteins is a useful approach to cope with those challenges. The main scope of this perspective is to describe applications of different protein binding site comparison approaches to outline their applicability and impact on molecular design. The article deals with various substantial application domains and provides some outstanding examples to show how various binding site comparison methods can be applied to promote in silico drug design workflows. In addition, we will also briefly introduce the fundamental principles of different protein binding site comparison methods.

Fatty acid amide hydrolase (FAAH) is a serine hydrolase that terminates the analgesic and anti-inflammatory effects of endocannabinoids such as anandamide. Herein, structure-activity relationship studies on a new series of aryl N-(ω-imidazolyl- and ω-tetrazolylalkyl)carbamate inhibitors of FAAH were investigated. As one result, a pronounced increase in inhibitory potency was observed if a phenyl residue attached to the carbamate oxygen atom was replaced by a pyridin-3-yl moiety. The most active compounds exhibited IC50 values in the low nanomolar range. In addition, investigations on the metabolic properties of these inhibitors were performed. In rat liver homogenate and in porcine plasma, the extent of their degradation was shown to be strongly dependent on the kind of aryl residue bound to the carbamate as well as on the length and type of the alkyl spacer connecting the carbamate group with the heterocyclic system. With the aid of esterase inhibitors it was shown that in porcine plasma, carboxylesterase-like enzymes and paraoxonase are involved in carbamate cleavage. Moreover, it was found that highly active pyridin-3-yl carbamates reacted with albumin, which led to covalent albumin adducts., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)