Binding of synthetic carbohydrate receptors to enveloped virus glycans: Insights from molecular dynamics simulations.

Can envelope glycans be targeted to stop viral pandemics? Here we address this question by using molecular dynamics simulations to study the binding between 10 synthetic carbohydrate receptors (SCRs) and the 33 N-glycans most commonly found on the surfaces of enveloped viruses, including Zika virus and SARS-CoV-2. Based on association quotients derived from these simulations, we classified the SCRs as weak binders, promiscuous binders, or selective binders. The SCRs almost exclusively associate at the Man3GlcNAc2 core, which is common to all N-glycans, but the binding affinity between the SCR⋅glycan pair depends on the noncovalent interactions between the heterocycle rings and the glycan antennae. Systematic variations in the glycan and SCR structures reveal relationships that could guide the design of SCRs to attain affinity and selectivity towards a chosen envelope glycan target. With these results, envelope glycans, which are currently considered "undruggable", could become viable targets for new therapeutic strategies.

Regioselectivity in the Scholl Reaction: Mono and Double [7]Helicenes.

We employed the density functionaly theory (DFT)-predicted regioselectivity of the intramolecular Scholl reaction in phenanthrene and dibenzo[g,p]chrysene frameworks to obtain π-extended mono and double [7]helicenes, respectively. The formation of these helical structures occurs despite the buildup of a large strain energy up to 30 kcal/mol compared with their most stable isomers. The twisted and strained structures were characterized and analyzed by experimental (NMR, UV-vis, emission, electrochemistry, and single-crystal X-ray diffraction) techniques and were further supported by DFT calculations.

Regiochemical Effects on the Carbohydrate Binding and Selectivity of Flexible Synthetic Carbohydrate Receptors with Indole and Quinoline Heterocyclic Groups.

Synthetic carbohydrate receptors (SCRs) that bind cell-surface carbohydrates could be used for disease detection, drug-delivery, and therapeutics, or for the site-selective modification of complex carbohydrates but their potential has not been realized because of remaining challenges associated with binding affinity and substrate selectivity. We have reported recently a series of flexible SCRs based upon a biaryl core with four pendant heterocyclic groups that bind glycans selectively through noncovalent interactions. Here we continue to explore the role of heterocycles on substrate selectivity by expanding our library to include a series of indole and quinoline heterocycles that vary in their regiochemistry of attachment to the biaryl core. The binding of these SCRs to a series of biologically-relevant carbohydrates was studied by 1H NMR titrations in CD2Cl2 and density-functional theory calculations. We find SCR030, SCR034 and SCR037 are selective, SCR031, SCR032, and SCR039 are strong binders, and SCR033, SCR035, SCR036, and SCR038 are promiscuous and bind weakly. Computational analysis reveals the importance of C-H⋯π and H-bonding interactions in defining the binding properties of these new receptors. By combining these data with those obtained from our previous studies on this class of flexible SCRs, we develop a series of design rules that account for the binding of all SCRs of this class and anticipate the binding of future, not-yet imagined tetrapodal SCRs.

Electron-Transfer-Induced Self-Assembly of a Molecular Tweezer Platform.

The design and synthesis of a new molecular tweezer (T-tmp) with electron-rich pincers are reported. The stable monocationic radicals and self-assembled dimeric radicals of this molecular tweezer platform were prepared by chemical oxidative titration. With the aid of DFT calculations, it was found that the dimeric radicals with syn-syn-syn conformer has the most stable structure, with the hole primarily delocalized between parallel stacked pyrenyl groups.

Synthesis of Doubly Annulated m-Terphenyl-Based Molecular Tweezers and Their Charge-Transfer Complexes with DDQ as a Guest.

The synthesis of a doubly-annulated m-terphenyl-based tweezer platform has been developed, which affords ready incorporation of various pincer units from monobenzenoid to polybenzenoid electron donors. The complexation study with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as guest has been carried out, and the crystal structure of T-Py∩DDQ reveals the sandwich-type binding mode in the solid state.

Serendipitous discovery of light-induced (In Situ) formation of an Azo-bridged dimeric sulfonated naphthol as a potent PTP1B inhibitor.

BACKGROUND: Protein tyrosine phosphatases (PTPs) like dual specificity phosphatase 5 (DUSP5) and protein tyrosine phosphatase 1B (PTP1B) are drug targets for diseases that include cancer, diabetes, and vascular disorders such as hemangiomas. The PTPs are also known to be notoriously difficult targets for designing inihibitors that become viable drug leads. Therefore, the pipeline for approved drugs in this class is minimal. Furthermore, drug screening for targets like PTPs often produce false positive and false negative results. RESULTS: Studies presented herein provide important insights into: (a) how to detect such artifacts, (b) the importance of compound re-synthesis and verification, and (c) how in situ chemical reactivity of compounds, when diagnosed and characterized, can actually lead to serendipitous discovery of valuable new lead molecules. Initial docking of compounds from the National Cancer Institute (NCI), followed by experimental testing in enzyme inhibition assays, identified an inhibitor of DUSP5. Subsequent control experiments revealed that this compound demonstrated time-dependent inhibition, and also a time-dependent change in color of the inhibitor that correlated with potency of inhibition. In addition, the compound activity varied depending on vendor source. We hypothesized, and then confirmed by synthesis of the compound, that the actual inhibitor of DUSP5 was a dimeric form of the original inhibitor compound, formed upon exposure to light and oxygen. This compound has an IC50 of 36 µM for DUSP5, and is a competitive inhibitor. Testing against PTP1B, for selectivity, demonstrated the dimeric compound was actually a more potent inhibitor of PTP1B, with an IC50 of 2.1 µM. The compound, an azo-bridged dimer of sulfonated naphthol rings, resembles previously reported PTP inhibitors, but with 18-fold selectivity for PTP1B versus DUSP5. CONCLUSION: We report the identification of a potent PTP1B inhibitor that was initially identified in a screen for DUSP5, implying common mechanism of inhibitory action for these scaffolds.

Isolation of a chiral anthracene cation radical: X-ray crystallography and computational interrogation of its racemization.

Chiral cation-radical salts hold significant promise as charge-transfer materials, chiroptical switches, and electron-transfer catalysts for enantioselective synthesis. Herein we demonstrate that the readily-available chiral 9,10-diphenyleanthracene derivative (i.e.SANT) forms a robust cation radical, whose structure was elucidated by X-ray crystallography and DFT calculations. While SANT was observed to racemize on a timescale (t1/2) of 1.1 hours, a computational conformational search and kinetic analysis of the racemization pathway led us to identify a simple methyl substituted SANT derivative, which does not racemize (racemization t1/2 1013-1017 years).

A search for blues brothers: X-ray crystallographic/spectroscopic characterization of the tetraarylbenzidine cation radical as a product of aging of solid magic blue.

Magic blue (MB+˙ SbCl6− salt), i.e. tris-4-bromophenylamminium cation radical, is a routinely employed one-electron oxidant that slowly decomposes in the solid state upon storage to form so called 'blues brothers', which often complicate the quantitative analyses of the oxidation processes. Herein, we disclose the identity of the main 'blues brother' as the cation radical and dication of tetrakis-(4-bromophenyl)benzidine (TAB) by a combined DFT and experimental approach, including isolation of TAB+˙ SbCl6− and its X-ray crystallography characterization. The formation of TAB in aged magic blue samples occurs by a Scholl-type coupling of a pair of MB followed by a loss of molecular bromine. The recognition of this fact led us to the rational design and synthesis of tris(2-bromo-4-tert-butylphenyl)amine, referred to as 'blues cousin' (BC: Eox1 = 0.78 V vs. Fc/Fc+, λmax(BC+˙) = 805 nm, εmax = 9930 cm−1 M−1), whose oxidative dimerization is significantly hampered by positioning the sterically demanding tert-butyl groups at the para-positions of the aryl rings. A ready two-step synthesis of BC from triphenylamine and the high stability of its cation radical (BC+˙) promise that BC will serve as a ready replacement for MB and an oxidant of choice for mechanistic investigations of one-electron transfer processes in organic, inorganic, and organometallic transformations.

From Wires to Cables: Attempted Synthesis of 1,3,5-Trifluorenylcyclohexane as a Platform for Molecular Cables.

Multiple molecular wires braided together in a single assembly, termed as molecular cable, are promising next-generation materials for effective long-range charge transport. As an example of the platform for constructing molecular cables, 1,3,5-trifluorenylcyclohexane (TFC) and its difluorenyl analogues (DFCs) were systematically investigated both experimentally (X-ray crystallography) and theoretically (DFT calculations). Although the syntheses of DFCs were successfully achieved, the synthesis of TFC, which involved a similar intramolecular Friedel-Crafts cyclization as the last step, was unsuccessful. An exhaustive study of the conformational landscape of cyclohexane ring of TFC and DFCs revealed that TFC is a moderately strained molecule (∼17 kcal/mol), and computational studies of the reaction profile show that this steric strain, present in the transition state, is responsible for the unusually high (∼5 years) reaction half-life. A successful synthesis of TFC will require that the steric strain is introduced in multiple steps, and such alternative strategies are being currently explored.

Electrochemistry and electrogenerated chemiluminescence of π-stacked poly(fluorenemethylene) oligomers. Multiple, interacting electron transfers.

The electrochemistry, spectroscopy, and electrogenerated chemiluminescence (ECL) of a series of π-stacked poly(fluorenemethylene) oligomers (Fn, n = 1-6) were investigated. The pendant cofacially oriented fluorene moieties are essentially in contact with each other by Van der Waals interaction promoting electronic delocalization in these species. All six compounds give successive cyclic voltammetric one-electron (1e) oxidations in 1:1 acetonitrile/benzene (MeCN/Bz), and the multiple 1e transfer properties of all these compounds were confirmed by chronoamperometric experiments with an ultramicroelectrode and digital simulations. The potentials for oxidation of the successive 1e transfers can be explained in terms of electrostatic interactions among the fluorenes. The monomer (F1) shows one irreversible wave, while F2 shows two reversible 1e waves. F3 shows only two reversible 1e oxidation waves, which is consistent with the large energy to remove a third electron because of the greater electrostatic repulsion, so the third wave is shifted toward more positive potentials. Both F4 and F5 show three reversible 1e oxidation waves, while F6 shows four reversible 1e waves. The removal of the first electron from an oligomer becomes easier as n increases. The stability of the radical cations also increases with n. The removal of consecutive electrons from Fn can be correlated with the distance between fluorene moieties. No reduction peaks were observed except for some broad ones at ~-3.2 V vs SCE in THF, which is consitent with the wide highest occupied molecular orbital-lowest unoccupied molecular orbital gap in these compounds (absorbance at about 300 nm). No characteristic annihilation ECL signal was observed for these compounds in 1:1 MeCN/Bz mixed solvent. However, the ECL of F6 in the presence of the coreactant C(2)O(4)(2-) showed a long-wavelength ECL emission that was proposed to be electrolyzed byproduct from the radical cation.

Charge delocalization in self-assembled mixed-valence aromatic cation radicals.

The spontaneous assembly of aromatic cation radicals (D(+•)) with their neutral counterpart (D) affords dimer cation radicals (D(2)(+•)). The intermolecular dimeric cation radicals are readily characterized by the appearance of an intervalence charge-resonance transition in the NIR region of their electronic spectra and by ESR spectroscopy. The X-ray crystal structure analysis and DFT calculations of a representative dimer cation radical (i.e., the octamethylbiphenylene dimer cation radical) have established that a hole (or single positive charge) is completely delocalized over both aromatic moieties. The energetics and the geometrical considerations for the formation of dimer cation radicals is deliberated with the aid of a series of cyclophane-like bichromophoric donors with drastically varied interplanar angles between the cofacially arranged aryl moieties. X-ray crystallography of a number of mixed-valence cation radicals derived from monochromophoric benzenoid donors established that they generally assemble in 1D stacks in the solid state. However, the use of polychromophoric intervalence cation radicals, where a single charge is effectively delocalized among all of the chromophores, can lead to higher-order assemblies with potential applications in long-range charge transport. As a proof of concept, we show that a single charge in the cation radical of a triptycene derivative is evenly distributed on all three benzenoid rings and this triptycene cation radical forms a 2D electronically coupled assembly, as established by X-ray crystallography.

Sequential oxidative transformation of tetraarylethylenes to 9,10-diarylphenanthrenes and dibenzo[g,p]chrysenes using DDQ as an oxidant.

Tetraarylethylenes can be sequentially transformed into 9,10-diarylphenanthrenes and dibenzo[g,p]chrysenes using 1 and 2 equiv of DDQ, respectively, in CH(2)Cl(2) containing methanesulfonic acid, in excellent yields. Efficient access to substituted dibenzochrysenes from tetraarylethylenes establishes the versatility of this procedure over the existing multistep syntheses of dibenzochrysenes. Moreover, the ready regeneration of DDQ from easily recovered reduced DDQ-H(2) continues to advance the use of DDQ/H(+) for the oxidative C-C bond forming reactions.

ortho-Phenylenes: unusual conjugated oligomers with a surprisingly long effective conjugation length.

ortho-Phenylenes represent a fundamental but relatively unexplored class of conjugated molecular architecture. We have developed a robust synthetic approach to monodisperse o-phenylene oligomers which we have demonstrated by synthesizing a homologous series up to the dodecamer. The o-phenylenes exhibit complex conformational behavior but are biased toward a specific 2-fold-symmetric conformation which we believe corresponds to a stacked helix. Surprisingly, the series exhibits long-range delocalization, as measured by bathochromic shifts in UV/vis spectra. Although the overall magnitude of the shifts is modest (but comparable to some other classes of conjugated materials), the effective conjugation length of the series is approximately eight repeat units. The oligomers also exhibit an unusual hypsochromic shift in their fluorescence spectra with increasing length. The origin of these trends is discussed in the context of conformational analysis and DFT calculations of the frontier molecular orbitals for the series.

Direct observation of electron-transfer-induced conformational transformation (molecular actuation) in a bichromophoric electron donor.

With the aid of laser-flash photolysis, the one-electron oxidation of conformationally mobile tetramethoxydibenzobicyclo[4.4.1]undecane (1), using photoexcited chloranil as an oxidant, allows us to show that extended 1(+•) undergoes a conformational transformation to π-stacked folded 1(+•) on a microsecond time scale (τ ≈ 1 µs), which is at least six times longer than that found for the conformationally locked model compound.