A convergent, enantioselective total synthesis of (+)-guanacastepene N was developed that features a 7-endo Heck cyclization as the key step. In the course of this synthesis, short syntheses of the enantiomerically pure cyclopentenone and cyclohexene building blocks 5 and 6, which constitute A and C ring fragments of guanacastepene N, were developed. These fragments were linked by a challenging conjugate addition reaction that also generated the C11 quaternary carbon stereocenter. Regioselective 7-endo Heck cyclization gave rise to a tricyclic intermediate, which was elaborated to complete the first total synthesis of guanacastepene N and the second enantioselective total synthesis of a guanacastepene natural product.
Heteroleptic copper compounds have been designed and synthesized on solid supports. Chemical redox agents were used to change the oxidation state of the SiO2-immobilized heteroleptic copper compounds from Cu(I) to Cu(II) and then back to Cu(I). Optical spectroscopy of a dimethyl sulfoxide (DMSO) suspension demonstrated the reversibility of the Cu(I)/Cu(II) SiO2-immobilized compounds by monitoring the metal-to-ligand charge transfer (MLCT) peak at about 450 nm. EPR spectroscopy was used to monitor the isomerization of Cu(I) tetrahedral to Cu(II) square planar. This conformational change corresponds to a 90° rotation of one ligand with respect to the other. Conductive AFM (cAFM) and macroscopic gold electrodes were used to study the electrical properties of a p+ Si-immobilized heteroleptic copper compound where switching between the Cu(I)/Cu(II) states occurred at −0.8 and +2.3 V.
The synthesis and operation of a light-operated nanovalve that controls the pore openings of mesoporous silica nanoparticles containing gold cores nanoparticles is described. The nanoparticles, consisting of 20 nm gold cores inside ~150 nm mesoporous silica spheres, were synthesized using a unique one-pot method. The nanovalves are comprised of cucurbituril rings encircling stalks that are attached to the ~2 nm pore openings. Plasmonic heating of the gold core raises the local temperature and decreases the ring-stalk binding constant, thereby unblocking the pore and releasing the cargo molecules that were preloaded inside. Bulk heating of the suspended particles to 60 °C is required to release the cargo, but no bulk temperature change was observed in the plasmonic heating release experiment. High intensity irradiation caused thermal damage to the silica particles, but low intensity illumination caused a sufficient local temperature increase to operate the valves without damaging the nanoparticles containers. These light-stimulated, thermally activated mechanized nanoparticles demonstrate a new system with potential utility for on-command drug release.
We have developed a nickel-catalyzed method for the asymmetric cross-coupling of secondary electrophiles with secondary nucleophiles, specifically, stereoconvergent Negishi reactions of racemic benzylic bromides with achiral cycloalkylzinc reagents. In contrast to most previous studies of enantioselective Negishi cross-couplings, tridentate pybox ligands are ineffective in this process; however, a new, readily available bidentate isoquinoline-oxazoline ligand furnishes excellent ee's and good yields. The use of acyclic alkylzinc reagents as coupling partners led to the discovery of a highly unusual isomerization that generates a significant quantity of a branched cross-coupling product from an unbranched nucleophile.
Nearest-neighbor recognition (NNR) measurements have been made for two lipidated forms of GlyCys, interacting with analogues of cholesterol and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in the liquid-ordered (lo) and liquid-disordered (ld) phases. Interaction free energies that have been determined from these measurements have been used in Monte Carlo simulations to quantify the distribution of the peptides between liquid-ordered and liquid-disordered regions. These simulations have shown that significant differences in the lipid chains have a very weak influence on the partitioning of the peptide between these two phases. They have also revealed an insensitivity of the peptide partition coefficient, Kp, to the size of the lo and ld domains that are present. In a broader context, these findings strongly suggest that the sorting of peripheral proteins in cellular membranes via differential lipidation may be more subtle than previously thought.
Experiments have shown that homologous Ras proteins containing different lipid-modification, which is required for membrane binding, form non-overlapping nanoclusters on the plasma membrane. However, the physical basis for clustering and lateral organization remained poorly understood. We have begun to tackle this issue using coarse-grained molecular dynamics simulations of the H-ras lipid anchor (tH), a triply lipid-modified heptapeptide embedded in a domain-forming mixed bilayer [Janosi L. et al., Proc. Natl. Acad. Sci. U. S. A. 2012 109:8097]. Here we use the same simulation approach to investigate the effect of peptide concentration and bilayer composition on the clustering and lateral distribution of tH. We found no major difference in the clustering behavior of tH above a certain concentration. However, the simulations predict the existence of a critical concentration below which tH does not form nanoclusters. Moreover, our data demonstrate that cholesterol enhances the stability of tH nanoclusters but is not required for their formation. Finally, analyses of peptide distributions and partition free energies allowed us to quantitatively describe how clustering facilitates the accumulation of tH at the interface between ordered and disordered domains of the simulated bilayer systems. These thermodynamic insights represent some of the key elements for a comprehensive understanding of the molecular basis for the formation and stability of Ras signaling platforms.
Ras; nanocluster; lipid anchor; membrane domain; Molecular Dynamics; partitioning
Two synthetic approaches to psymberin have been accomplished. A highly convergent first generation synthesis led to the complete stereochemical assignment and demonstrated that psymberin and irciniastatin A are identical compounds. This synthesis featured a diastereoselective aldol coupling between the aryl fragment and a central tetrahydropyran core, and a novel one-pot procedure to convert an amide, via intermediacy of a sensitive methyl imidate, to the N-acyl aminal reminiscent of psymberin. The highlights of the second generation synthesis include an efficient iridium-catalyzed enantioselective bis-allylation of neopentyl glycol, and a stepwise Sonogashira coupling/cycloisomerization/reduction sequence to construct the dihydroisocoumarin unit. The two synthetic avenues were achieved in 17–18 steps (longest linear sequence, ~14–15 isolations) from 3 fragments prepared in 7–8 steps (1st generation) and 3–8 steps (2nd generation) each. This convergent approach allowed for the preparation of sufficient amounts of psymberin (~ 0.5 g) for follow-up biological studies. Meanwhile, our highly flexible strategy enabled the design and synthesis of multiple analogs, including a psymberin-pederin hybrid termed psympederin that proved crucial to a comprehensive understanding of the chemical biology of psymberin and related compounds that will be described in a subsequent manuscript.
An improved sulfenylation method for the preparation of epidithio-, epitetrathio- and bis-(methylthio)diketopiperazines from diketopiperazines has been developed. Employing NaHMDS and related bases and elemental sulfur or bis[bis(trimethylsilyl)amino]trisulfide (23) in THF, the developed method was applied to the synthesis of a series of natural and designed molecules, including epicoccin G (1), 8,8′-epi-ent-rostratin B (2), gliotoxin (3), gliotoxin G (4), emethallicin E (5) and haematocin (6). Biological screening of selected synthesized compounds led to the discovery of a number of nanomolar anti poliovirus agents (i.e. 46, 2,2′-epi-46 and 61, Table 5) and several low micromolar anti Plasmodium falciparum lead compounds (i.e. 46, 2,2′-epi-46, 58, 61 and 1, Table 5).
Cytochrome P450scc (CYP11A1) catalyzes conversion of cholesterol (CH) to pregnenolone, the precursor to all steroid hormones. This process proceeds via three sequential monooxygenation reactions: two stereospecific hydroxylations with formation first of 22R-hydroxycholesterol (22-HC) and then 20α,22R-dihydroxycholesterol (20,22-DHC), followed by the C20-C22 bond cleavage. Herein we have employed EPR and ENDOR spectroscopy to characterize the intermediates in the first hydroxylation step by 77K radiolytic one-electron cryoreduction and subsequent annealing of the ternary oxy cytochrome P450scc-cholesterol complex. This approach is fully validated by the demonstration that the cryoreduced ternary complex of oxy-P450scc-CH is catalytically competent and hydroxylates cholesterol to form 22R-HC with no detectable formation of 20-HC, just as occurs under physiological conditions. Cryoreduction of the ternary complex trapped at 77K produces predominantly the hydroperoxy-ferriheme P450scc intermediate, along with a minor fraction of peroxo-ferriheme intermediate that converts into a new hydroperoxo-ferriheme species at 145K. This behavior reveals that the distal pocket of the parent oxy-P450scc-cholesterol complex exhibits an efficient proton delivery network, with an ordered water molecule H-bonded to the distal oxygen of the dioxygen ligand. During annealing of the hydroperoxy-ferric P450scc intermediates at 185K they convert to the primary product complex in which CH has been converted to 22-HC. In this process, the hydroperoxy-ferric intermediate decays with a large sKIE, as expected when proton delivery to the terminal O leads to formation of Compound I (Cpd I). 1H ENDOR measurements of the primary product formed in deuterated solvent show that the heme Fe(III) is coordinated to the 22R-O1H of 22-HC, where the 1H is derived from substrate and exchanges to D after annealing at higher temperatures. These observations establish that Cpd I is agent that hydroxylates CH, rather than the hydroperoxy-ferric heme.
The development of enantioselective synthetic routes to (–)-kinamycin F (9) and (–)-lomaiviticin aglycon (6) is described. The diazotetrahydrobenzo[b]fluorene (diazofluorene) functional group of the targets was prepared by fluoride-mediated coupling of a β-trimethylsilylmethyl-α,β-unsaturated ketone (38) with an oxidized naphthoquinone (19), palladium-catalyzed cyclization (39→37), and diazo transfer (37→53). The D-ring precursors 60 and 68 were prepared from m-cresol and 3-ethylphenol, respectively. Coupling of the β-trimethylsilylmethyl-α,β-unsaturated ketone 60 with the juglone derivative 61, cyclization, and diazo transfer, provided the advanced diazofluorene 63, which was elaborated to (–)-kinamycin F (9) in three steps. The diazofluorene 87 was converted to the C2-symmetric lomaiviticin aglycon precursor 91 by enoxysilane formation and oxidative dimerization with manganese tris(hexafluoroacetylacetonate) (94, 26%). The stereochemical outcome is attributed to the steric bias engendered by the mesityl acetal of 87 and contact ion pairing of the intermediates. The coupling product 91 was deprotected (tert-butylhydrogen peroxide, trifluoroacetic acid–dichloromethane) to form the chain isomer of lomaiviticin aglycon 98, which cyclizes to (–)-lomaiviticin aglycon (6, 39–41% overall). The scope of the fluoride-mediated coupling process is delineated (nine products, average yield = 72%, Table 2); a related enoxysilane quinonylation reaction is also described (10 products, average yield = 77%, Table 1). We establish that dimeric diazofluorenes undergo hydrodediazotization 3-fold faster then related monomeric diazofluorenes (Table 6). The simple diazofluorene 103 is a potent inhibitor of ovarian cancer stem cells (IC50 = 500 nM).
The Protein Arginine Deiminases (PADs) catalyze the hydrolysis of peptidyl-arginine to form peptidylcitrulline. Abnormally high PAD activity is observed in a host of human diseases, however, the exact role of protein citrullination in these diseases, as well as the identities of specific citrullinated disease biomarkers, remain unknown, largely due to the lack of readily available chemical probes to detect protein citrullination. For this reason, we developed a citrulline specific chemical probe, rhodamine-phenylglyoxal (Rh-PG), which we show can be used to investigate protein citrullination. This methodology is superior to existing techniques because it possesses higher throughput and excellent sensitivity. Additionally, we demonstrate that this probe can be used to determine the kinetic parameters for a number of protein substrates, monitor drug efficacy, and identify disease biomarkers in an animal model of ulcerative colitis that displays aberrantly increased PAD activity.
One mechanism by which ribozymes can accelerate biological reactions is by adopting folds that favorably perturb nucleobase ionization. Herein we used Raman crystallography to directly measure pKa values for the Ade38 N1-imino group of a hairpin ribozyme in distinct conformational states. A transition-state analogue gave a pKa value of 6.27 ± 0.05, which agrees strikingly well with values measured by pH-rate analyses. To identify the chemical attributes that contribute to the shifted pKa we determined crystal structures of hairpin ribozyme variants containing single-atom substitutions at the active site and measured their respective Ade38 N1 pKa values. This approach led to the identification of a single interaction in the transition-state conformation that elevates the base pKa >0.8 log units relative to the precatalytic state. The agreement of the microscopic and macroscopic pKa values and the accompanying structural analysis support a mechanism in which Ade38 N1(H)+ functions as a general acid in phosphodiester bond cleavage. Overall the results quantify the contribution of a single electrostatic interaction to base ionization, which has broad relevance for understanding how RNA structure can control chemical reactivity.
Addition of biphenylene to the bis(imino)pyridine iron dinitrogen complexes, (iPrPDI)Fe(N2)2 and [(MePDI)Fe(N2)]2(μ2-N2) (RPDI = 2,6-(2,6-R2—C6H3— N=CMe)2C5H3N; R = Me, iPr), resulted in oxidative addition of a C—C bond at ambient temperature to yield the corresponding iron biphenyl compounds, (RPDI)Fe-(biphenyl). The molecular structures of the resulting bis-(imino)pyridine iron metallacycles were established by X-ray diffraction and revealed idealized square pyramidal geometries. The electronic structures of the compounds were studied by Mössbauer spectroscopy, NMR spectroscopy, magnetochemistry, and X-ray absorption and X-ray emission spectroscopies. The experimental data, in combination with broken-symmetry density functional theory calculations, established spin crossover (low to intermediate spin) ferric compounds antiferromagnetically coupled to bis(imino)pyridine radical anions. Thus, the overall oxidation reaction involves cooperative electron loss from both the iron center and the redox-active bis(imino)pyridine ligand.
Water motion probed by intrinsic tryptophan shows the significant slowdown around protein surfaces but it is unknown how the ultrafast internal conversion of two nearly degenerate states of Trp (1La and 1Lb) affects the initial hydration in proteins. Here, we used a mini-protein with ten different tryptophan locations one at a time through site-directed mutagenesis and extensively characterized the conversion dynamics of the two states. We observed all the conversion time scales in 40-80 fs by measurement of their anisotropy dynamics. This result is significant and shows no noticeable effect on the initial observed hydration dynamics and unambiguously validates the slowdown of hydration layer dynamics as shown here again in two mutant proteins.
Total syntheses of HMP-Y1, atrop-HMP-Y1, hibarimicinone, atrop-hibarimicinone, and HMP-P1 are described using a two-directional synthesis strategy. A novel benzyl fluoride Michael–Claisen reaction sequence was developed to construct the complete carbon skeleton of HMP-Y1 and atrop-HMP-Y1 via a symmetrical, two-directional, double annulation. Through efforts to convert HMP-Y1 derivatives to hibarimicinone and HMP-P1, a biomimetic mono-oxidation to desymmetrize protected HMP-Y1 was realized. A two-directional unsymmetrical double annulation and biomimetic etherification were developed to construct the polycyclic and highly-oxidized skeleton of hibarimicinone, atrop-hibarimicinone, and HMP-P1. The use of a racemic biaryl precursor allowed for the synthesis of both hibarimicinone atropisomers and provides the first confirmation of the structure of atrop-hibarimicinone. Additionally, this work documents the first reported full characterization of atrop-hibarimicinone, HMP-Y1, atrop-HMP-Y1, and HMP-P1. Lastly, a pH-dependent rotational barrier about the C2–C2' bond of hibarimicinone was discovered, which provides valuable information necessary to achieve syntheses of the glycosylated congeners of hibarimicinone.
The dynamics of the racemization, catalytic and stoichiometric dynamic resolution of 2-lithio-N-Boc-piperidine, 7, have been investigated. The kinetic order in TMEDA, for both racemization and resolution of the title compound, and the kinetic order in resolving ligands, have been determined. The catalytic dynamic resolution is 0.5-order in chiral ligand 8, 0.265 order in chiral ligand 10, and second order in TMEDA. The X-ray crystal structure of ligand 10 shows it to be an octamer. Dynamic NMR studies of the resolution process were obtained. Some of the requirements for a successful catalytic dynamic resolution by ligand exchange have been identified.
Duplex DNA containing an apurinic/apyrimidinic (AP) lesion undergoes cleavage significantly more rapidly in nucleosome core particles (NCPs) than it does when free. The mechanism of AP cleavage within NCPs was studied through independently generating lesions within them. AP mediated DNA cleavage within NCPs is initiated by DNA-protein crosslink (DPCun) formation followed by β-elimination to give DPCs containing cleaved DNA (DPCcl). Hydrolysis of DPCcl produces a DNA single strand break (SSB). C2-dideuteration of AP showed that deprotonation from this position is involved in the rate determining step. Experiments utilizing NCPs containing mutated histone H4 proteins indicated that lysine residues in the amino terminal tail are involved in both DPC formation and β-elimination steps. Lysines 16 and 20 seem to play a greater role in reacting with AP at superhelical location 1.5 but other amino acids (e.g. lysines 5, 8, and 12) compensate in their absence. The mechanism of rapid double strand breaks in bistranded, clustered AP lesions was studied by independently preparing reaction intermediates within model NCPs. A single strand break on one strand enhances the cleavage of a proximal AP on the opposite strand.
Thermal denaturation profiles of several model oligonucleotides of the human telomere DNA sequence including d[A(GGGTTA)3GGG] (Tel22) were determined using circular dichroism (CD), fluorescence of adenine → 2-aminopurine analogs and fluorescence resonance energy transfer (FRET) to monitor the unfolding process at specific locations within the quadruplex. The resulting optical spectra vs. temperature data matrices were analyzed by singular value decomposition (SVD) to ascertain the minimum number of species required to reproduce the unfolding spectral profiles. Global non-linear least squares fitting of the SVD amplitude vectors was used to estimate thermodynamic parameters and optical spectra of all species for a series of unfolding mechanisms that included one-, two-, and three-step sequential pathways F ⇌ In ⇌ U, n = 0, 1 or 2) as well as two mechanisms with spectroscopically distinct starting structures (F1 and F2). The CD and FRET data for Tel22 unfolding between 4 and 94 °C in 25 mM KCl were best described by a sequential unfolding model with two intermediates, while the 2-aminopurine analogs required one intermediate. The higher melting intermediate I2 had a transition midpoint temperature (Tm) of 61 °C and a CD spectrum with a maximum at ~265 nm and a minimum at ~245 nm. The fluorescence emission spectra of the 2-aminopurine and FRET derivatives suggest greater solvent exposure of the 5′-AGGGTTA- segment in the intermediate compared to the folded state. The spectroscopic properties of the 61 °C intermediate suggest that it may be a triple helical structure.
DNA; quadruplex; telomere; potassium; temperature-dependent denaturation; folding intermediate; circular dichroism; fluorescence; 2-aminopurine; FRET; triple helix
The aggregation and deposition of normally soluble proteins is the hallmark of several devastating neurodegenerative disorders. For proteins such as tau in Alzheimer’s disease and α-synuclein in Parkinson’s disease, aggregation involves a transition from an intrinsically disordered monomer to a highly structured fiber. While understanding the role of these proteins in neurodegeneration requires elucidation of the structural basis of self-association, the conformational heterogeneity of disordered proteins makes their structural characterization inherently challenging. Here we use single molecule Förster resonance energy transfer to measure the conformational ensemble of tau in the absence and presence of heparin to identify critical conformational changes relevant to the initiation of aggregation. We find that different domains of tau display distinct conformational properties that are strongly correlated with their degree of disorder and which may relate to their roles in aggregation. Moreover, we observe that heparin binding induces a distinct two-state structural transition in tau described by a loss of long-range contacts and a concomitant compaction of the microtubule binding domain. Our results describe a conformational intermediate of tau that precedes the formation of aggregates and could serve as a target for tau-focused therapeutics.
microtubule binding protein; tauopathies; neurofibrillary tangles
Potassium 1-(alkoxy/acyloxy)alkyltrifluoroborates have been synthesized through a copper-catalyzed diboration of aldehydes and subsequent conversion of the resulting potassium 1-(hydroxy)alkyltrifluoroborates. The palladium-catalyzed Suzuki-Miyaura reaction employing the potassium 1-(benzyloxy)alkyltrifluoroborates with aryl and heteroaryl chlorides provides access to protected secondary alcohols in high yields. The β-hydride elimination pathway is avoided through use of the benzyl protecting group, which is proposed to stabilize the diorganopalladium intermediate by coordination of the arene to the metal center. This cross-coupling is stereospecific with complete retention of stereochemistry.
The direct amination of alkyl and aryl pinacol boronates is accomplished with lithiated methoxyamine. This reaction directly provides aliphatic and aromatic amines, stereospecifically, and without preactivation of the boronate substrate.