Structure elucidation of uniformly 13C labeled small molecule natural products

Utilization of ²H, ¹³C, and ¹⁵N isotopically labeled proteins and peptides is now routine in biomolecular NMR investigations. The widespread availability of inexpensive, uniformly ¹³C enriched glucose now makes it possible to isolate uniformly ¹³C labeled natural products from microbial fermentation. We now wish to describe an approach for the rapid structural characterization of uniformly ¹³C labeled natural products that avoids the pitfalls of relying on parameters typically employed in biomolecular NMR studies. Copyright © 2015 John Wiley & Sons, Ltd.     

Real‐Time Interrogation of Aspirin Reactivity,Biochemistry, and Biodistribution by Hyperpolarized Magnetic Resonance Spectroscopy

Hyperpolarized magnetic resonance spectroscopy enables quantitative, non‐radioactive, real‐time measurement of imaging probe biodistribution and metabolism in vivo. Here, we investigate and report on the development and characterization of hyperpolarized acetylsalicylic acid (aspirin) and its use as a nuclear magnetic resonance (NMR) probe. Aspirin derivatives were synthesized with single‐ and double‐¹³C labels and hyperpolarized by dynamic nuclear polarization with 4.7 % and 3 % polarization, respectively. The longitudinal relaxation constants (T₁) for the labeled acetyl and carboxyl carbonyls were approximately 30 seconds, supporting in vivo imaging and spectroscopy applications. In vitro hydrolysis, transacetylation, and albumin binding of hyperpolarized aspirin were readily monitored in real time by ¹³C‐NMR spectroscopy. Hyperpolarized, double‐labeled aspirin was well tolerated in mice and could be observed by both ¹³C‐MR imaging and ¹³C‐NMR spectroscopy in vivo.     

Real‐Time Interrogation of Aspirin Reactivity,Biochemistry, and Biodistribution by Hyperpolarized Magnetic Resonance Spectroscopy

Hyperpolarized magnetic resonance spectroscopy enables quantitative, non‐radioactive, real‐time measurement of imaging probe biodistribution and metabolism in vivo. Here, we investigate and report on the development and characterization of hyperpolarized acetylsalicylic acid (aspirin) and its use as a nuclear magnetic resonance (NMR) probe. Aspirin derivatives were synthesized with single‐ and double‐¹³C labels and hyperpolarized by dynamic nuclear polarization with 4.7 % and 3 % polarization, respectively. The longitudinal relaxation constants (T₁) for the labeled acetyl and carboxyl carbonyls were approximately 30 seconds, supporting in vivo imaging and spectroscopy applications. In vitro hydrolysis, transacetylation, and albumin binding of hyperpolarized aspirin were readily monitored in real time by ¹³C‐NMR spectroscopy. Hyperpolarized, double‐labeled aspirin was well tolerated in mice and could be observed by both ¹³C‐MR imaging and ¹³C‐NMR spectroscopy in vivo.     

Participation of the BC Loop in the Correct Folding of Bacteriorhodopsin as Revealed by Solid‐state NMR†

Structural changes in bacteriorhodopsin (bR) in two different processes of retinal reconstitutions were investigated by observing the ¹³C and ¹⁵N solid‐state NMR spectra of [1‐¹³C]Val‐ and [¹⁵N]Pro‐labeled bR. We found that NMR signals of the BC loop were sensitive to changes in protein structure and dynamics, from wild‐type (WT) bR to bacterio‐opsin (bO), regenerated bR and E1001 bR. Regenerated bR was prepared following the addition of retinal into bO obtained from photobleached WT‐bR. E1001 bR was cultured from a retinal‐deficient strain termed E1001 following the addition of retinal to growing cells. ¹⁵N NMR signal at Pro70 in the BC loop in WT‐bR was observed at 122.4 p.p.m., whereas signals were not apparent or partly suppressed in bO and regenerated bR, respectively. Similarly, the ¹³C NMR signal at Val69 in the BC loop at 172.0 p.p.m. that was observed in WT‐bR was significantly decreased in both regenerated bR and bO. These results suggest that the dynamic structure of the BC loop in bO was substantially altered following the removal of retinal. As a consequence, the correct protein structure failed to be recovered via the regenerating process of retinal to bO. On the other hand, ¹³C and ¹⁵N NMR signals at the BC loop in E1001 bR appeared at positions identical to those of WT‐bR. The results of the current study indicate that the BC loop may not always fold correctly in the regenerated bR, which leads to different properties in the regenerated bR compared to that of WT‐bR.     

Spatially Selective Heteronuclear Multiple‐Quantum Coherence Spectroscopy for Biomolecular NMR Studies

Spatially selective heteronuclear multiple‐quantum coherence (SS HMQC) NMR spectroscopy is developed for solution studies of proteins. Due to “time‐staggered” acquisitioning of free induction decays (FIDs) in different slices, SS HMQC allows one to use long delays for longitudinal nuclear spin relaxation at high repetition rates. To also achieve high intrinsic sensitivity, SS HMQC is implemented by combining a single spatially selective ¹H excitation pulse with nonselective ¹H 180° pulses. High‐quality spectra were obtained within 66 s for a 7.6 kDa uniformly ¹³C,¹⁵N‐labeled protein, and within 45 and 90 s for, respectively, two proteins with molecular weights of 7.5 and 43 kDa, which were uniformly ²H,¹³C,¹⁵N‐labeled, except for having protonated methyl groups of isoleucine, leucine and valine residues.     

An Approach to NMR Assignment of Intrinsically Disordered Proteins

An efficient approach to NMR assignments in intrinsically disordered proteins is presented, making use of the good dispersion of cross peaks observed in [¹⁵N,¹³C′]‐ and [¹³C′,¹H^N]‐correlation spectra. The method involves the simultaneous collection of {3D (H)NCO(CAN)H and 3D (HACA)CON(CA)HA} spectra for backbone assignments via sequential H^N and H^α correlations and {3D (H)NCO(CACS)HS and 3D (HS)CS(CA)CO(N)H} spectra for side‐chain ¹H and ¹³C assignments, employing sequential ¹H data acquisitions with direct detection of both the amide and aliphatic protons. The efficacy of the approach for obtaining resonance assignments with complete backbone and side‐chain chemical shifts is demonstrated experimentally for the 61‐residue [¹³C,¹⁵N]‐labelled peptide of a voltage‐gated potassium channel protein of the Kv1.4 channel subunit. The general applicability of the approach for the characterisation of moderately sized globular proteins is also demonstrated.     

Natural Abundance 15N NMR by Dynamic Nuclear Polarization: Fast Analysis of Binding Sites of a Novel Amine‐Carboxyl‐Linked Immobilized Dirhodium Catalyst

A novel heterogeneous dirhodium catalyst has been synthesized. This stable catalyst is constructed from dirhodium acetate dimer (Rh₂(OAc)₄) units, which are covalently linked to amine‐ and carboxyl‐bifunctionalized mesoporous silica (SBA‐15?NH₂?COOH). It shows good efficiency in catalyzing the cyclopropanation reaction of styrene and ethyl diazoacetate (EDA) forming cis‐ and trans‐1‐ethoxycarbonyl‐2‐phenylcyclopropane. To characterize the structure of this catalyst and to confirm the successful immobilization, heteronuclear solid‐state NMR experiments have been performed. The high application potential of dynamic nuclear polarization (DNP) NMR for the analysis of binding sites in this novel catalyst is demonstrated. Signal‐enhanced ¹³C CP MAS and ¹⁵N CP MAS techniques have been employed to detect different carboxyl and amine binding sites in natural abundance on a fast time scale. The interpretation of the experimental chemical shift values for different binding sites has been corroborated by quantum chemical calculations on dirhodium model complexes.     

NMR “Crystallography” for Uniformly (13C, 15N)‐Labeled Oriented Membrane Proteins

In oriented‐sample (OS) solid‐state NMR of membrane proteins, the angular‐dependent dipolar couplings and chemical shifts provide a direct input for structure calculations. However, so far only ¹H–¹⁵N dipolar couplings and ¹⁵N chemical shifts have been routinely assessed in oriented ¹⁵N‐labeled samples. The main obstacle for extending this technique to membrane proteins of arbitrary topology has remained in the lack of additional experimental restraints. We have developed a new experimental triple‐resonance NMR technique, which was applied to uniformly doubly (¹⁵N, ¹³C)‐labeled Pf1 coat protein in magnetically aligned DMPC/DHPC bicelles. The previously inaccessible ¹H_α–¹³C_α dipolar couplings have been measured, which make it possible to determine the torsion angles between the peptide planes without assuming α‐helical structure a priori. The fitting of three angular restraints per peptide plane and filtering by Rosetta scoring functions has yielded a consensus α‐helical transmembrane structure for Pf1 protein.     

1H, 13C and 15N NMR assignments for N‐ and O‐acylethanolamines,important family of naturally occurring bioactive lipid mediators

The complete ¹H, ¹³C and ¹⁵N NMR signal assignments of some N‐ and O‐acylethanolamines, important family of naturally occurring bioactive lipid mediators, were achieved using one‐dimensional and two‐dimensional experiments (gs‐HMQC and gs‐HMBC). Copyright © 2012 John Wiley & Sons, Ltd.     

Synthesis of [18,19,21,22‐13C4]‐Labeled Tautomycin as an NMR Probe of Protein Phosphatase Inhibitor

We have accomplished the synthesis of ¹³C‐labeled tautomycin at the C18, C19, C21, and C22 positions starting from 100 % [¹³C]triethylphosphonoacetate for the purpose of elucidating the dynamics and conformation of the C17–C26 moiety. NMR spectroscopy of ¹³C‐labeled tautomycin revealed strong binding with protein phosphatase type 1 and new features in the ¹³C NMR spectrum, such as the very small three‐bond coupling constants (²J).     

Fast Proton Exchange in Histidine: Measurement of Rate Constants through Indirect Detection by NMR Spectroscopy

Owing to its imidazole side chain, histidine participates in various processes such as enzyme catalysis, pH regulation, metal binding, and phosphorylation. The determination of exchange rates of labile protons for such a system is important for understanding its functions. However, these rates are too fast to be measured directly in an aqueous solution by using NMR spectroscopy. We have obtained the exchange rates of the NH₃⁺ amino protons and the labile NH^ε2 and NH^δ1 protons of the imidazole ring by indirect detection through nitrogen‐15 as a function of temperature (272 K<T<293 K) and pH (1.3<pH<4.9) of uniformly nitrogen‐15‐ and carbon‐13‐labeled L ‐histidine ? HCl ? H₂O. Exchange rates up to 8.5×10⁴ s^?1 could be determined (i.e., lifetimes as short as 12 μs). The three chemical shifts δ_Hi of the invisible exchanging protons H_i and the three one‐bond scalar coupling constants ¹J(N,H_i) could also be determined accurately.     

Solid‐State and Solution Structural Studies of 4‐{[C(E)]‐1H‐Azol‐1‐ylimino)methyl}pyridin‐3‐ols

The new N‐salicylideneheteroarenamines 1 – 4 were prepared by reacting the biologically relevant 3‐hydroxy‐4‐pyridinecarboxaldehyde ( 5 ) with 1H‐imidazol‐1‐amine ( 6 ), 1H‐pyrazol‐1‐amine ( 7 ), 1H‐1,2,4‐triazol‐1‐amine ( 8 ), and 1H‐1,3,4‐triazol‐1‐amine ( 9 ). Solution ¹H‐, ¹³C‐, and ¹⁵N‐NMR were used to establish that the hydroxyimino form A is the predominant tautomer. A combination of ¹³C‐ and ¹⁵N‐CPMAS‐NMR with X‐ray crystallographic studies confirms that the same form is present in the solid state. The stabilities and H‐bond geometries of the different forms, tautomers and rotamers, are discussed by using B3LYP/6‐31G** calculations.     

Crystal Effects on Mesobilirubin: A Combined NMR Spectroscopic and Density Functional Theory Study

We report solid‐state NMR investigations of crystal effects in powdered mesobilirubin‐IXα, an open‐chain tetrapyrrole that is structurally related to bilirubin‐IXα but hydrogenated at the 3‐ and 18‐vinyl groups. ¹³C and ¹⁵N cross‐polarization magic‐angle spinning (CP/MAS) NMR experiments were performed on the compound at natural abundance. To facilitate the spectral analysis, density functional calculations were carried out at the B3LYP/6‐311G(d,p) level of theory, using an enneameric cluster to simulate the solid. The ¹H, ¹³C and ¹⁵N chemical shift data calculated for the enneamer are in a good agreement with those observed in the experimental spectra, and the relative order of the calculated resonances was thus used to confirm the tentative assignments obtained mainly from the heteronuclear correlation spectra. The observed signal splittings of a small subset of the ¹³C resonances in the peripheral regions of the two terminal rings provide evidence for microcrystalline heterogeneity of the powdered compound.     

Imines in the Titanium Coordination Sphere – Transformation of Imidoyl Chlorides to Nitrilium Ions

In the reaction of TiCl₄ in benzene as solvent with the imidoyl chloride p‐Tolyl(Cl)C=NPh ( 1 ) the abstraction of the chloride substituent is observed, leading to the nitrilium salt [p‐Tolyl–C≡N–Ph]⁺[Ti₂Cl₉]^– ( 2 ) in quantitative yield. The highly electrophilic salt 2 is characterized by IR‐ and NMR spectroscopy. The observed band for the C≡N stretching mode of 2 clearly indicates the formation of a nitrilium ion. Especially a characteristic line broadening of the ¹³C{¹H}‐NMR signals related to carbon atoms next to the nitrogen is observed. By ¹⁵N,¹H‐HMBC NMR experiments it is shown that the nitrogen signal of 2 is significantly shifted to high‐field in relation to nitriles and imines. The molecular structure of 2 was confirmed by single‐crystal X‐ray diffraction. The C≡N bond length and the linearity of the C–C≡N–C unit in 2 confirm the triple bond character of this bond.     

hNCOcanH pulse sequence and a robust protocol for rapid and unambiguous assignment of backbone (1HN, 15N and 13C′) resonances in 15 N/13C‐labeled proteins

A three‐dimensional nuclear magnetic resonance (NMR) pulse sequence named as hNCOcanH has been described to aid rapid sequential assignment of backbone resonances in ¹⁵N/¹³C‐labeled proteins. The experiment has been derived by a simple modification of the previously described HN(C)N pulse sequence [Panchal et al., J. Biomol. NMR 20 (2001) 135–147]; t₂ evolution is used to frequency label ¹³C′ rather than ¹⁵N (similar trick has also been used in the design of hNCAnH pulse sequence from hNcaNH [Frueh et al., JACS, 131 (2009) 12880–12881]). The modification results in a spectrum equivalent to HNCO, but in addition to inter‐residue correlation peaks (i.e. H_i, C_i?1), the spectrum also contains additional intra‐residue correlation peaks (i.e. H_i?1, C_i?1) in the direct proton dimension which has maximum resolution. This is the main strength of the experiment and thus, even a small difference in amide ¹H chemical shifts (5–6 Hz) can be used for establishing a sequential connectivity. This experiment in combination with the HNN experiment described previously [Panchal et al., J. Biomol. NMR 20 (2001) 135–147] leads to a more robust assignment protocol for backbone resonances (¹H^N, ¹⁵N) than could be derived from the combination of HNN and HN(C)N experiments [Bhavesh et al., Biochemistry, 40 (2001) 14727–14735]. Further, this new protocol enables assignment of ¹³C′ resonances as well. We believe that the experiment and the protocol presented here will be of immense value for structural—and functional—proteomics research by NMR. Performance of this experiment has been demonstrated using ¹³C/¹⁵N labeled ubiquitin. Copyright © 2011 John Wiley & Sons, Ltd.     

Unexpected Spiroproducts from the Reaction of N‐Benzoylglycine with Ortho‐Formylbenzoic Acids −3,5′‐Dioxo‐2′‐Phenyl‐1,3‐Dihydrospiro[Indene‐2,4′‐[1,3]Oxazol]‐1‐yl Acetates: Establishments of Their Structure

This paper describes a method of preparation of new 3,5′‐dioxo‐2′‐phenyl‐1,3‐dihydrospiro[indene‐2,4′‐[1,3]oxazol]‐1‐yl acetate and its 5‐chloro‐ and bromoderivatives as products of interaction of N‐benzoylglycine (hippuric acid) with corresponding ortho‐formylbenzoic acids. The reaction carried out in acetic anhydride media in the presence of piperidine as catalyst. The novel spirocompounds were purified by column chromatography from multicomponent reaction mixtures. The composition of the spiro‐products was confirmed by C, H, N element analysis. The structure was established by IR, MS, ¹H‐ and ¹³C‐NMR analysis including COSY ¹H‐¹³C experiments.     

Structural Revision and Elucidation of the Biosynthesis of Hypodoratoxide by 13C,13C COSY NMR Spectroscopy

Feeding of (2,3,4,5,6‐¹³C₅)mevalonolactone to the fungus Hypomyces odoratus resulted in a completely labeled sesquiterpene ether. The connectivity of the carbon atoms was easily deduced from a ¹³C,¹³C COSY spectrum, revealing a structure that was different from the previously reported structure of hypodoratoxide, even though the reported ¹³C NMR data matched. A structural revision of hypodoratoxide is thus presented. Its absolute configuration was tentatively assigned from its co‐metabolite cis‐dihydroagarofuran. Its biosynthesis was investigated by feeding of (3‐¹³C)‐ and (4,6‐¹³C₂)mevalonolactone, which gave insights into the complex rearrangement of the carbon skeleton during terpene cyclization by analysis of the ¹³C,¹³C couplings.     

On the Solution Structure of PHB: Preparation and NMR Analysis of Isotopically Labeled Oligo[(R)‐3‐hydroxybutanoic Acids] (OHBs)

While the chain conformation of poly‐ and oligo[(R)‐3‐hydroxybutanoate] (PHB, OHB) is known to be 2₁‐ and 3₁‐helical in stretched fibers and in the crystalline state, respectively (Fig. 2), the structure in solution is unknown. To be able to determine the NMR‐solution structure, specifically labeled linear oligomers have been prepared: a 16‐mer consisting of alternating pairs of fully ¹³C‐labeled and non‐labeled residues ( 1 ) and a 20‐mer containing an O‐¹³CH(¹³CH₂D)‐¹³CHD^Si‐¹³CO residue in position 9 (from the O‐terminus) and a fully ¹³C‐labeled residue in position 12 ( 2 ), both with (t‐Bu)Ph₂Si protection at the O‐ and Bn protection at the C‐terminus. The labeled (R)‐3‐hydroxybutanoic acid building blocks were prepared by Noyori hydrogenation of the ethyl ester of fully ¹³C‐labeled acetoacetic acid, and the D‐atoms were incorporated by D₂/Pd‐C reduction of a previously reported dibromo‐1,3‐dioxinone 8 (Scheme 1). The oligomers were obtained by a series of fragment couplings (Schemes 2 and 3). 600‐MHz NMR COSY, HSQC, ROESY, and cross‐correlated relaxation measurements (Figs. 4 – 6, 9, and 12, and Tables 1 – 3) at different temperatures and interpretations thereof led to assignments of all resonances, including those from the diastereotopic C(2)H₂ protons, and to determination of the conformationally averaged dihedral angles ϕ₂ and ϕ₃ (Figs. 2, 7, and 8) in the chain of the oligoester. The conclusions are: all but five or six terminal residues adopt the same conformation; the 2₁ helix is not the predominant secondary structure; the structure of the HB chain is averaged, even at –30°. Our investigation confirms the high flexibility of the polyester chain, a property that has been deduced previously from biological studies of PHB in membranes, in ion channels, and as appendage of proteins.     

Assignment of the 15N resonances of the antifungal agent posaconazole

The structurally complex antifungal agent posaconazole has been well characterized by conventional ¹H‐ and ¹³C‐NMR studies. In contrast, ¹⁵N resonance assignments have never been reported. We now wish to report the assignment of the eight ¹⁵N resonances of posaconazole using two‐dimensional long‐range ¹H‐¹⁵N GHMBCAD NMR data. The ¹⁵N resonance assignments were undertaken to facilitate the evaluation of the impact of ¹H‐¹⁵N heteronuclear shift correlation data in the Computer‐Assisted Structure Elucidation (CASE) of complex molecular structures. J. Heterocyclic Chem., (2011).     

Stereospecificity of 1H, 13C and 15N shielding constants in the isomers of methylglyoxal bisdimethylhydrazone: problem with configurational assignment based on 1H chemical shifts

In the ¹³C NMR spectra of methylglyoxal bisdimethylhydrazone, the ¹³C‐5 signal is shifted to higher frequencies, while the ¹³C‐6 signal is shifted to lower frequencies on going from the EE to ZE isomer following the trend found previously. Surprisingly, the ¹H‐6 chemical shift and ¹J(C‐6,H‐6) coupling constant are noticeably larger in the ZE isomer than in the EE isomer, although the configuration around the –CH═N– bond does not change. This paradox can be rationalized by the C–H?N intramolecular hydrogen bond in the ZE isomer, which is found from the quantum‐chemical calculations including Bader's quantum theory of atoms in molecules analysis. This hydrogen bond results in the increase of δ(¹H‐6) and ¹J(C‐6,H‐6) parameters. The effect of the C–H?N hydrogen bond on the ¹H shielding and one‐bond ¹³C–¹H coupling complicates the configurational assignment of the considered compound because of these spectral parameters. The ¹H, ¹³C and ¹⁵N chemical shifts of the 2‐ and 8‐(CH₃)₂N groups attached to the –C(CH₃)═N– and –CH═N– moieties, respectively, reveal pronounced difference. The ab initio calculations show that the 8‐(CH₃)₂N group conjugate effectively with the π‐framework, and the 2‐(CH₃)₂N group twisted out from the plane of the backbone and loses conjugation. As a result, the degree of charge transfer from the N‐2– and N‐8– nitrogen lone pairs to the π‐framework varies, which affects the ¹H, ¹³C and ¹⁵N shieldings. Copyright © 2012 John Wiley & Sons, Ltd.