Functional characterization and NMR spectroscopy on full-length Vpu from HIV-1 prepared by total chemical synthesis

Vpu is an 81-residue integral membrane protein encoded in the HIV-1 genome that is of considerable interest because it plays important roles in the release of virus particles from infected cells and in the degradation of the cellular receptor. We report here the total chemical synthesis of full-length Vpu(1-81) as well as a site-specifically (15)N-labeled analogue, Vpu(2-81), using native chemical ligation methodologies and also report a structural and functional comparison of these constructs with recombinant protein obtained via bacterial expression. The structures of the synthetic and expressed polypeptides were similar in lipid micelles using solution NMR spectroscopy. Solid-state NMR spectra of the polypeptides in aligned hydrated lipid bilayers indicated that their overall topologies were also very comparable. Further, the channel activity of the synthetic protein was found to be analogous to that previously characterized for the recombinant protein. We have thus demonstrated that using solid phase peptide synthesis and chemical ligation it is feasible to obtain large quantities of a purified and homogeneous membrane protein in a structurally and functionally relevant form for future structural and characterization studies.     

Conformations and 13C NMR chemical shifts of some polyamides in the solid state as studied by high-resolution 13C NMR spectroscopy

High-resolution ¹³Carbon nuclear magnetic resonance (NMR) spectra of Nylons 4, 6, and 66 in the solid state were measured over a wide range of temperature. From the results, it was found that resonance lines of crystalline and noncrystalline components were separable and their chemical shifts were determined. The ¹³C chemical shift behavior is closely related to their conformation. The origin of the conformational effects on the chemical shifts is discussed.     

QSAR studies of phenylhydrazine-substituted tetronic acid derivatives based on the 1H NMR and 13C NMR chemical shifts

The quantitative structure–activity relationship models of 40 phenylhydrazine-substituted tetronic acid derivatives were established between the ¹H nuclear magnetic resonance (NMR) and ¹³C NMR chemical shifts and the antifungal activity against Fusarium graminearum, Botrytis cinerea, Rhizoctonia cerealis, and Colletotrichum capsici. The models were validated by R, R², R_A², variance inflation factor, F, and P values testing and residual analysis. It was concluded from the models that the ¹³C NMR chemical shifts of C8, C10, C7, and the ¹H NMR chemical shifts of Ha contributed positively to the activity against Fusarium graminearum, Botrytis cinerea, Colletotrichum capsici, and Rhizoctonia cerealis, respectively. The models indicated that decreasing the election cloud density of specific nucleuses in compounds, for example, by the substituting of electron withdrawing groups, would improve the antifungal activity. These models demonstrated the practical application meaning of chemical shifts in the quantitative structure–activity relationship study. Furthermore, a practical guide was provided for further structural optimization of the antifungal phenylhydrazine-substituted tetronic acid derivatives based on the ¹H NMR and ¹³C NMR chemical shifts.     

13C isotope effects on 1H chemical shifts: NMR spectral analysis of 13C‐labelled D‐glucose and some 13C‐labelled amino acids

The one‐ and two‐bond ¹³C isotope shifts, typically ?1.5 to ?2.5 ppb and ?0.7 ppb respectively, in non‐cyclic aliphatic systems and up to ?4.4 ppb and ?1.0 ppb in glucose cause effects that need to be taken into account in the adaptive NMR spectral library‐based quantification of the isotopomer mixtures. In this work, NMR spectral analyses of some ¹³C‐labelled amino acids, D ‐glucose and other small compounds were performed in order to obtain rules for prediction of the ¹³C isotope effects on ¹H chemical shifts. It is proposed that using the additivity rules, the isotope effects can be predicted with a sufficient accuracy for amino acid isotopomer applications. For glucose the effects were found strongly non‐additive. The complete spectral analysis of fully ¹³C‐labelled D ‐glucose made it also possible to assign the exocyclic proton signals of the glucose. Copyright © 2009 John Wiley & Sons, Ltd.     

High-speed synthesis of potent C2-symmetric HIV-1 protease inhibitors by in-situ aminocarbonylations

Two novel series of C2-symmetric HIV-1 protease inhibitors were synthesized by microwave-promoted, palladium-catalyzed aminocarbonylations of the o-iodo- and m-bromobenzyloxy P1/P1' substituted core structures. Molybdenum hexacarbonyl was used as a convenient solid source of carbon monoxide in these transformations. After the initial high-speed library generation, biological testing identified highly active HIV-1 protease inhibitors. Selected ortho- and meta-decorated inhibitors were subsequently resynthesized on a larger scale and retested for their affinity toward HIV-1 protease, showing micromolar to low nanomolar inhibition. The discovery of highly active inhibitors containing large phenyl amide ortho substituents in the P1/P1' positions indicates that larger groups than previously believed are tolerated in this part of the S1/S1' pocket.     

13C NMR chemical shift and electronic structure of polyoxymethylene in the solid state

High-resolution ¹³C NMR spectra of polyoxymethylene (POM) in the solid state have been measured in order to obtain a relationship between the conformation and ¹³C NMR chemical shift tensor (δ₁₁, δ₂₂ and δ₃₃) and its isotropic average. It was found that the ¹³C isotropic chemical shift of POM in the crystalline region appears upfield with respect to that in the noncrystalline region and that the width Δδ ( = δ₁₁ - δ₃₃) in the crystalline region is much larger than that in the noncrystalline region. These experimental findings can be reasonably explained by a theoretical calculation for an infinite POM chain based on a tight-binding molecular orbital calculation within the CNDO/2 framework.     

Towards the total synthesis of Calyculin C: preparation of the C13-C25 spirocyclic core

A stereoselective synthesis of the C₁₃-C₂₅ of Calyculin C is described. Key steps involve the coupling of a terminal acetylene with a thiol ester and subsequent spirocyclisation using a double intramolecular hetero-Michael addition.     

Synthetic studies of the HIV-1 protease inhibitive didemnaketals: stereocontrolled synthesis of an ester side chain

The stereocontrolled synthesis of the C₁-C₈ portion, the ester side chain of the HIV-1 protease inhibitive didemnaketals from the ascidian Didemnum sp., has been carried out through 15 steps starting from (S)-carvone as the chiral template. This approach involved the diastereoselective construction of three conjoint chiral centers by intramolecular chiral inducement, and generation of allylic alcohol intermediate through a key Grob fragmentation reaction.     

NMR studies in the heterocyclic series XXIV—1H, 13C and 15N study of 15N labelled indazoles

The ¹⁵N chemical shifts and ¹H? ¹⁵N and ¹³C? ¹⁵N coupling constants of nine monolabelled indazoles were measured and assigned. The experimental values are discussed in terms of the indazolic and iso-indazolic structures, and compared with literature data for other related heterocycles. All the results are consistent with an N-1(H) tautomeric structure for indazole in DMSO-d₆.     

Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease

Two possible mechanisms of the irreversible inhibition of HIV-1 protease by epoxide inhibitors are investigated on an enzymatic model using ab initio (MP2) and density functional theory (DFT) methods (B3LYP, MPW1K and M05-2X). The calculations predict the inhibition as a general acid-catalyzed nucleophilic substitution reaction proceeding by a concerted SN2 mechanism with a reaction barrier of ca. 15-21 kcal mol(-1). The irreversible nature of the inhibition is characterized by a large negative reaction energy of ca. -17-(-24) kcal mol(-1). A mechanism with a direct proton transfer from an aspartic acid residue of the active site onto the epoxide ring has been shown to be preferred compared to one with the proton transfer from the acid catalyst facilitated by a bridging catalytic water molecule. Based on the geometry of the transition state, structural data important for the design of irreversible epoxide inhibitors of HIV-1 protease were defined. Here we also briefly discuss differences between the epoxide ring-opening reaction in HIV-1 protease and epoxide hydrolase, and the accuracy of the DFT method used.     

13C and 15N NMR chemical shifts of 1-(2',4'-dinitrophenyl) and 1-(2',4',6'-trinitrophenyl) pyrazoles in the solid state and in solution

The (13)C and (15)N CPMAS NMR spectra of 18 pyrazoles substituted at position 1 by dinitrophenyl and trinitrophenyl (picryl) groups have been recorded. To help in the assignments, some of these compounds were studied in DMSO-d(6) solution. Phenomena such as the conformation of the N-aryl groups and broadening of splittings due to quadrupolar nuclei are discussed.     

1H and 13C NMR chemical shift assignments of spiro-cycloalkylidenehomo- and methanofullerenes by the DFT-GIAO method

The (1)H and (13)C NMR chemical shifts of spiro-cycloalkylidene[60]fullerenes were assigned using experimental NMR data and the Density Functional Theory (DFT)-Gauge Independence Of Atomic Orbitals method (GAIO) calculation method in the Perdew Burke Ernzerhof (PBE)/3z approach. The calculated values of the (13)C NMR chemical shifts adequately reproduce the experimental values at this quantum chemistry approach. Similar assignments will be helpful for (13)C NMR spectral analysis of homo- and methano[60]fullerene derivatives for structure elucidation and to determine the influence of fullerene frames on substituents and the influence of substituents on fullerene cores.     

Synthetic studies of the HIV-1 protease inhibitive didemnaketals: precise and stereocontrolled synthesis of the key mother spiroketal

The precise and stereocontrolled synthesis of the C₉-C₂₃ portion, the key mother spiroketal of the HIV-1 protease inhibitive didemnaketals from the ascidian Didemnum sp., has been carried out through multisteps starting from (R)-pulegone as the chiral template. This approach involved the distereoselective construction of eight chiral centers by intramolecular chiral inducement and the coupling of two fragments by Julia reaction.     

13C and1H NMR spectra of substituted dihydropyrroles prepared by the reaction of 2-aminooxazoles and maleimide

Substituted dihydropyrroles were characterized by¹³C and¹H NMR spectra. The spectral patterns of these compounds and reversible hydrogen—deuterium exchange are discussed. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 697–700, April, 2000.     

1H and 13C NMR studies of the protonation of isomeric methoxysulmazole analogues

The major protonation sites of six cardiotonic isomeric 2-aryl-n-methoxy-1H-imidazo[4,5-b]- and -[4,5-c]-pyridines (n = 4–7) were determined by ¹H and ¹³C NMR methods. All the 1H-imidazo[4,5-c]pyridines and the 7-methoxy derivative of sulmazole were found to protonate at the pyridyl nitrogen. Protonation occurred at the imidazo nitrogen, however, for the 5- and 6-methoxy derivatives of sulmazole.     

1H and 13C NMR study of cyclopentadienyl metal carbonyls in the solid state

In this paper we deal with some structural and dynamic properties of Cp₂W₂(CO)₆ (I) and Cp₂Ru₂(CO)₄ (II) as shown by solid state ¹³C and ¹H NMR experiments. The IR and ¹³C CPMAS spectra of a polycrystalline sample of I show that this compound possesses the anti rotameric structure found in a previously reported X-ray diffraction study. The analysis of the spinning side-band manifold in the ¹³C CPMAS spectrum of I allows us to assess a different semi-bridging character between two CO-groups not seen from the X-ray results. The spectral features of compound II are fully consistent with the X-ray and solution structures previously reported. In both compounds the cyclopentadienyl ligands are involved in fast reorientation motions which modulate the magnetic interactions responsible for the relaxation of ¹³C resonances. The activation energies (E_a) associated with this reorientation process of the Cp ring along their C₅ coordination axis have been determined to be 15.5 and 10.2 kJ mol⁻¹ for I and II respectively on the basis of ¹H T₁ measurements at different temperatures. Furthermore, we show that an empirical relationship relates E_a values and T_min (the temperature at which proton relaxation is more efficient) in a related series of cyclopentadienyl compounds.     

Solid state 13C NMR studies of methane dehydroaromatization reaction on Mo/HZSM-5 and W/HZSM-5 catalysts

Methane dehydroaromatization on Mo/HZSM-5 and W/HZSM-5 catalysts was studied by solid state 13C NMR spectroscopy, both variation of the state of transition metal component and products such as ethane, benzene, ethene adsorbed on or in zeolite were observed after high temperature (900-1000 K) reaction.     

Characterisation of uniformly 13C, 15N labelled bacteriochlorophyll a and bacteriopheophytin a in solution and in solid state: complete assignment of the 13C, 1H and 15N chemical shifts

In this investigation we report a complete assignment of (13)C, (1)H and (15)N solution and solid state chemical shifts of two bacterial photosynthetic pigments, bacteriochlorophyll (BChl) a and bacteriopheophytin (BPheo) a. Uniform stable-isotope labelling strategies were developed and applied to biosynthetic preparation of photosynthetic pigments, namely uniformly (13)C, (15)N labelled BChl a and BPheo a. Uniform stable-isotope labelling with (13)C, (15)N allowed performing the assignment of the (13)C, (15)N and (1)H resonances. The photosynthetic pigments were isolated from the biomass of photosynthetic bacteria Rhodopseudomonas palustris 17001 grown in uniformly (13)C (99%) and (15)N (98%) enriched medium. Both pigments were characterised by NMR in solution (acetone-d(6)) and by MAS NMR in solid state and their NMR resonances were recorded and assigned through standard liquid 2D (13)C-(13)C COSY, (1)H-(13)C HMQC, (1)H-(15)N HMBC and solid 2D (13)C-(13)C RFDR, (1)H-(13)C FSLG HETCOR and (1)H-(15)N HETCOR correlation techniques at 600 MHz and 750 MHz. The characterisation of pigments is of interest from biochemical to pharmaceutical industries, photosynthesis and food research.     

Stereochemical studies of substituted 6,7- benzomorphan derivatives by 13C and 1H NMR spectroscopy

The ¹³C NMR spectra of a series of 6,7-benzomorphan derivatives variously substituted at C-5 and C-9 by methyl and at C-3 by cyano, alkyl and aralkyl groups, together with certain 3-cyano, 3-allyl or benzyl congeners, are reported and chemical shift data analysed in terms of the configuration of isomeric pairs and compounds isolated as single diastereoisomers. Special attention is given to the consequences of γ-shielding interactions, the effects of the nitrogen lone-pair orbital and anisotropic shielding by the aromatic region of the molecule. Deductions of stereochemistry are supported by ¹H NMR data and the NMR features of the corresponding methiodide salts.