Design, synthesis, and characterization of a potent, nonpeptide, cell-permeable, bivalent Smac mimetic that concurrently targets both the BIR2 and BIR3 domains in XIAP

XIAP is a central apoptosis regulator that inhibits apoptosis by binding to and inhibiting the effectors caspase-3/-7 and an initiator caspase-9 through its BIR2 and BIR3 domains, respectively. Smac protein in its dimeric form effectively antagonizes XIAP by concurrently targeting both its BIR2 and BIR3 domains. We report the design, synthesis, and characterization of a nonpeptide, cell-permeable, bivalent small-molecule (SM-164) which mimics Smac protein for targeting XIAP. Our study shows that SM-164 binds to XIAP containing both BIR domains with an IC50 value of 1.39 nM, being 300 and 7000 times more potent than its monovalent counterparts and the natural Smac AVPI peptide, respectively. SM-164 concurrently interacts with both BIR domains in XIAP and functions as an ultrapotent antagonist of XIAP in both cell-free functional and cell-based assays. SM-164 targets cellular XIAP and effectively induces apoptosis at concentrations as low as 1 nM in the HL-60 leukemia cell line. The potency of bivalent SM-164 in binding, functional, and cellular assays is 2-3 orders of magnitude higher than its corresponding monovalent Smac mimetics.     

A mechanistic insight into caspase-7 inhibition by BIR1-2 domains of XIAP and cIAP1

Previous studies failed to demonstrate any role for the BIR1 domain of the inhibitor of apoptosis proteins (IAPs) in inhibition of executioner caspases. In this study, XIAP-BIR1-2 and c-IAP1-BIR1-2 domains have been used to investigate the role of BIR1 in the inhibition of caspase-7. Kinetic analysis confirmed that caspase-7 was inhibited in an uncompetitive manner at lower concentrations of XIAP-BIR1-2, whereas the inhibition was switched to the mixed type mode at higher concentrations of the inhibitor. In contrast, cIAP1-BIR1-2 inhibited caspase-7 in a mixed type mode at all examined concentrations. These data suggest that the presence of BIR1 is essential for inhibition of caspase-7 by cIAP1. Far-UV CD and fluorescence spectroscopy experiments showed that despite similar secondary structures, XIAP-BIR1-2 and cIAP1-BIR1-2 have different biophysical properties. BIR1-2 domain of XIAP was found to be more flexible than cIAP1, which may be the reason behind differences in their kinetic properties.     

Synthesis, NMR and vibrational spectroscopic characterization, and computational study of the cis-IO2F3 2- anion

The N(CH3)4(+) salt of the cis-IO2F3(2-) anion was synthesized from [N(CH 3)4][IO2F2] and excess [N(CH3)4][F] in CH3CN solvent. The [N(CH3)4] 2[IO2F3] salt was characterized by Raman, infrared, and (19)F solid-state MAS NMR spectroscopy. Geometry optimization and calculation of the vibrational frequencies at the DFT level of theory corroborated the experimental finding that the IO2F3(2-) anion exists as a single isomer with a cis-dioxo and mer-trifluoro arrangement. The fluorine atom in IO2F3(2-) that is trans to one of the oxygen atoms is weakly bound with a calculated bond length of 228.1 pm. The IO2F3(2-) anion is only the second example of an AEO 2F 3 species after XeO2F3(-).     

A computational NPA and NMR study of Li-capped armchair GaN nanotubes

The geometrical structure, the nuclear magnetic resonance (NMR) parameters and natural population analysis (NPA) of the H-capped (raw) and Li-capped armchair single-walled gallium nitride nanotubes (GaNNTs) are computed and reported for the first time. Our results show that the variation of isotropic chemical shielding (ICS) parameters at the sites of ¹⁵N and ⁷¹Ga along the length of both models-raw and Li-capped- are reversed. The calculations were carried out with B3LYP-DFT method and 6–31G (d) standard basis sets using the Gaussian 03 suite of programs.      

Dynamic NMR and computational study of 5,5-dimethyl-3,4-di-p-tolyl-2-cylopenten-1-one

The restricted rotation of p-tolyl moiety in 5,5-dimethyl-3,4-di-p-tolyl-2-cyclopenten-1-one was studied by variable temperature NMR spectroscopy at a temperature range of 218-368 K. A free rotation, in NMR time scale, was observed at temperatures higher than 368 K; while, the rotation froze below 248 K. From dynamic NMR analysis, the Arrhenius energy of activation ΔG? was calculated as 56.37 kJ mol(-1). The experimental results were confirmed by theoretical calculation using the density functional theory method B3LYP with basis sets, 6-31G and 6-31+G.     

Exploring symmetry as an avenue to the computational design of large protein domains

It has been demonstrated previously that symmetric, homodimeric proteins are energetically favored, which explains their abundance in nature. It has been proposed that such symmetric homodimers underwent gene duplication and fusion to evolve into protein topologies that have a symmetric arrangement of secondary structure elements--"symmetric superfolds". Here, the ROSETTA protein design software was used to computationally engineer a perfectly symmetric variant of imidazole glycerol phosphate synthase and its corresponding symmetric homodimer. The new protein, termed FLR, adopts the symmetric (βα)(8) TIM-barrel superfold. The protein is soluble and monomeric and exhibits two-fold symmetry not only in the arrangement of secondary structure elements but also in sequence and at atomic detail, as verified by crystallography. When cut in half, FLR dimerizes readily to form the symmetric homodimer. The successful computational design of FLR demonstrates progress in our understanding of the underlying principles of protein stability and presents an attractive strategy for the in silico construction of larger protein domains from smaller pieces.     

Solid-state NMR and computational studies of 4-methyl-2-nitroacetanilide

Studies on the solid-state structure of two polymorphs of 4-methyl-2-nitroacetanilide (MNA) were conducted using magic-angle spinning (13)C, (15)N and (1)H NMR spectroscopy, together with first-principles computations of NMR shielding (including use of a program that takes explicit account of the translational symmetry inherent in crystalline structures). The effects on (13)C chemical shifts of side-chain rotations have been explored. Information derived from these studies was then incorporated within a systematic space-search methodology for elucidation of trial crystallographic structures from powder XRD.     

NQR and NMR study of hydrogen bonding interactions in anhydrous and monohydrated guanine cluster model: A computational study

In this paper extensive systematic computational study has been carried out to justify hydrogen bonding interactions and their influence on the oxygen, nitrogen and hydrogen NQR and NMR parameters of the anhydrous and monohydrated guanine crystal structures at two different levels, B3LYP and MP2, using 6-311++G** and D95** basis sets. These theoretical data have been compared with experimental NMR and NQR measurements. For further investigation, results of cluster calculation have been compared with that of a single molecule. Our theoretical NQR and NMR parameters of ¹⁷O, ¹⁵N and ²H atoms of anhydrous and monohydrated guanine exhibited extreme sensitivity to electron distribution around mentioned nuclei caused by cooperative influences of various types of hydrogen bonding interactions. Fortunately, our calculated isotropic shielding values and CS tensors for the ¹⁷O and ¹⁵N nuclei as well as obtained ¹⁴N-NQR parameters are in excellent agreement with experimental data. Therefore, we can undoubtedly conclude that for anhydrous and monohydrated guanine tetrameric clusters including intermolecular interactions, our theoretical estimates are in better agreement with observed experimental values than those in which these interactions have been ignored.     

Aromatic-carbohydrate interactions: an NMR and computational study of model systems

The interactions of simple carbohydrates with aromatic moieties have been investigated experimentally by NMR spectroscopy. The analysis of the changes in the chemical shifts of the sugar proton signals induced upon addition of aromatic entities has been interpreted in terms of interaction geometries. Phenol and aromatic amino acids (phenylalanine, tyrosine, tryptophan) have been used. The observed sugar-aromatic interactions depend on the chemical nature of the sugar, and thus on the stereochemistries of the different carbon atoms, and also on the solvent. A preliminary study of the solvation state of a model monosaccharide (methyl beta-galactopyranoside) in aqueous solution, both alone and in the presence of benzene and phenol, has also been carried out by monitoring of intermolecular homonuclear solvent-sugar and aromatic-sugar NOEs. These experimental results have been compared with those obtained by density functional theory methods and molecular mechanics calculations.     

Solid-state NMR and computational chemistry study of mononucleotides adsorbed to alumina

Solid-state NMR spectroscopy and ab initio computational chemistry are used to determine the structure of the complex formed upon adsorption of the mononucleotide 2'-deoxyadenosine 5'-monophosphate (dAMP) to the surface of a mesoporous alumina. In this multi-technique approach, rotational-echo double-resonance NMR results reveal that the phosphate group of dAMP interacts predominantly with octahedrally coordinated aluminum species at the surface, and therefore, adsorption is modeled with both mono- and bidentate sorption of the nucleotide phosphate group with octahedral aluminum. 31P chemical shielding tensors are calculated from the structure of the lowest energy conformations, and these results are compared to tensor values extracted from analysis of spinning-sideband patterns in the experimental 31P cross-polarization magic-angle-spinning NMR spectrum. The chemical shift anisotropy and asymmetry parameter indicate that the binding is via a monodentate, inner-sphere complex.     

A computational study of the oxidation of SO2 to SO3 by gas-phase organic oxidants

We have studied the oxidation of SO(2) to SO(3) by four peroxyradicals and two carbonyl oxides (Criegee intermediates) using both density functional theory, B3LYP, and explicitly correlated coupled cluster theory, CCSD(T)-F12. All the studied peroxyradicals react very slowly with SO(2) due to energy barriers (activation energies) of around 10 kcal/mol or more. We find that water molecules are not able to catalyze these reactions. The reaction of stabilized Criegee intermediates with SO(2) is predicted to be fast, as the transition states for these oxidation reactions are below the free reactants in energy. The atmospheric relevance of these reactions depends on the lifetimes of the Criegee intermediates, which, at present, is highly uncertain.     

Thermochemistry of 2- and 3-acetylthiophenes: calorimetric and computational study

The relative stabilities of 2- and 3-acetylthiophenes have been evaluated by experimental thermochemistry and the results compared to high-level ab initio calculations. The enthalpies of combustion, vaporization, and sublimation were measured by rotating-bomb combustion calorimetry, Calvet microcalorimetry, correlation gas chromatography, and Knudsen effusion techniques and the gas-phase enthalpies of formation, at T = 298.15 K, were determined. Standard ab initio molecular orbital calculations at the G2 and G3 levels were performed, and a theoretical study on the molecular and electronic structures of the compounds studied has been conducted. Calculated enthalpies of formation using atomization and isodesmic reactions are compared with the experimental data. Experimental and theoretical results show that 2-acetylthiophene is thermodynamically more stable than the 3-isomer. A comparison of the substituent effect of the acetyl group in benzene and thiophene rings has been carried out.     

A computational study of the formation and dimerization of benzothiet-2-one

A computational B3LYP/6-31G(d,p) study of the formation of benzothiet-2-one (4) from benzothiophenedione (2) and its subsequent dimerization to 5 was performed. The proposed intermediate ketene 3 has no gas-phase barrier to ring closure to 4. Three transition structures for dimerization were located. The geometry of the lowest energy one (TS8a) has a geometry corresponding to a two atom + two atom, face-to-face addition of the two thiolactone moieties. The orbital interactions suggest that the reaction is pseudopericyclic.     

An experimental NMR and computational study of 4-quinolones and related compounds

Abstract  

We report the synthesis and structural study of eight compounds, either quinolin-4(1H)-ones or quinolines. Tautomerism as well as (E) → (Z) and rotational isomerism were studied both experimentally (¹H and ¹³C NMR) and theoretically [B3LYP/6-311++G(d,p)].     

Deuterium isotope effects in A:T and A:U base pairs: a computational NMR study

Recent measurements of trans-hydrogen bond deuterium isotope effects (DIEs) on 13C chemical shifts in nucleic acids (Vakonakis, I.; LiWang, A. C. J. Biomol. NMR 2004, 29, 65; J. Am. Chem. Soc. 2004, 126, 5688) have led to intriguing results: (i) the DIEs of A:T pairs in DNA are about 5 ppb smaller than those of A:U in RNA and (ii) A:T DIEs vary by as much as 13 ppb among the oligonucleotides. The first observation suggests that inter-base H-bonds in RNA may be stronger than those in DNA, while the second indicates that the conformation of the base pair modulates the transmission of the isotope effect across the hydrogen bond. In an effort at providing a rationale--so far unknown--for the observed DIEs in nucleic acids, density functional theory and hybrid Car-Parrinello/molecular mechanical calculations of DIEs on nucleosides and nucleotides in the gas phase and in aqueous solution have been performed. The calculations suggest that (i) the DIE in an isolated A:T base pair differs from that in an A:U base pair because of the changes in the magnetic properties caused by the replacement of a methyl group on passing from U to T, (ii) the DIEs depend crucially on the conformation of the base pairs, and (iii) the DIEs are strongly affected by magnetic and electrostatic interactions with the surrounding environment.     

A 13C NMR study of β-carboline alkaloids

The ¹³C NMR spectra of β-carboline alkaloids were determined, and unambiguous assignments of the spectra were carried out from the long-range coupling constants.     

Restricted rotation of the amino group and ring inversion in highly substituted anilines. A dynamic NMR and computational study

The reaction of cyclic ylidene malononitriles with acetylene (di)carboxylic acid esters led to the production of nine bicyclic systems incorporating highly substituted (5/6) anilines. The free energy of activation (ΔG^#) for the restricted rotation about the aniline-NH₂ bond was experimentally measured in each case and a correlation was evident between the increase in steric strain in the ground state, the electron withdrawing capabilities of the ring substituents, and a reduction in the rotational barrier. For four of the compounds, the slow ring interconversion (chair?chair) for the annelated saturated seven-membered ring that formed part of the bicyclic system was also evident. In these four compounds, both dynamic processes were also studied theoretically using ab initio methods whilst the ring interconversion was additionally studied using molecular dynamic simulations. The interconversion between the two stable chair forms was deemed to occur via a conformation series consisting of chair?boat?twist-boat?boat?chair.     

Four-component relativistic computational NMR study of ferrous,cobalt and nickel bisglycinates

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Conformational study of 1,2-cycloundecadiene by dynamic NMR spectroscopy and computational methods

Solutions of 1,2-cycloundecadiene in propane were studied by low-temperature (13)C NMR spectroscopy. A total of 17 peaks were observed at -166.7 degrees C, corresponding to two conformations of similar populations, one of C(1) symmetry (11 peaks) and the other of C(2) symmetry. The line shapes show that the predominant pathway for exchange of the topomers (C(1) and C(1)') of the C(1) conformation does not include the C(2) conformation. From the (13)C spectra, free-energy barriers of 8.38 +/- 0.15, 9.45 +/- 0.15, and 9.35 +/- 0.15 kcal/mol were determined for the C(1) to C(1)', (C(1) + C(1)') to C(2), and C(2) to (C(1) + C(1)') conversions, respectively, at -72.2 degrees C. The NMR results for this compound are discussed in terms of the conformations predicted by molecular mechanics calculations obtained with Allinger's MM3 program. Ab initio calculations of free energies are also reported at the HF/ 6-311G level for 25 conformations.