Synthesis,biological activity,and conformational analysis of [pGlu6, N-MePhe8, Aib9] substance P (6–11): A selective agonist for the NK-3 receptor

A highly potent and selective agonist to the tachykinin NK-3 receptor, [pGlu⁶, N-MePhe⁸, Aib⁹] substance P (6–11) ( I ), was synthesized via the solid phase method. The ED₅₀ of I was 4n M in the guinea pig ileum in the absence of atropine (NK-1 + NK-3 receptors) and this agonist was 5000-fold less potent in the presence of atropine (NK-1 receptor). The analogue was virtually inactive in the rat vas deferens (NK-2 receptor). A detailed analysis of the solution conformation of this analogue in DMSO-d₆ and in a DMSO-d₆ H₂O cryornixture was carried out by a combination of ¹H-nmr 2D techniques (DQF-COSY, TOCSY, NOESY and ROESY) and model building based on empirical energy calculations. Peptide I exists as a mixture of isomers containing cis and trans Phe-N-MePhe peptide bonds. The main isomer, containing a cis Phe-N-MePhe peptide bond, shows a preferred folded conformation characterized by a type VI β-turn with Phe and N-MePhe in the i + 1 and i + 2 positions. The turn is followed by a helical segment extending to the C-terminal. This conformation is compared to previously reported conformations of other selective tachykinin agonists and may be a promising lead for the design of novel NK-3 agonists with additional conformational constraints. © 1993 John Wiley & Sons, Inc.     

Molecular Structure,Conformation and Interactions of Antitumor Antibiotic Cyanonaphthridinomycin,a Covalent Binder of DNA

Abstract

X-ray, NMR and molecular modeling studies on cyanonaphthridinomycin (C₂₂ H₂₆N₄O₅), a DNA binding antibiotic, have been carried out to study the structure, conformation and interactions with DNA. The crystals belong to the space group P₂₁ with the cell dimensions of a = 5.934(1), b = 20.684(4), c = 16.866(3)A γ = 90.9° and Z = 4(two molecules/asymmetric unit). The structure was solved by direct methods and difference Fourier methods and refined to an R value of 0.087 for 4061 reflections. The conformation of the molecule is compared with that of naphthridinomycin. There are differences in the orientation of the methoxyl group and the saturated oxazole ring. 1 and 2D NMR studies have been carried out and the dihedral angles obtained from coupling constants have been compared with those obtained from the crystal structure. Molecular mechanics studies were carried out to obtain the energy minimized structure and its comparison with X-ray and NMR results. Molecular modelling studies were performed to propose models for drug-DNA interactions. Both partial intercalation and groove-binding models have been proposed.     

Structural Transformation and Physical Properties of a Hydrogel-Forming Peptide Studied by NMR,Transmission Electron Microscopy,and Dynamic Rheometer

Peptide-based hydrogels are attractive biological materials. Study of their self-assembly pathways from their monomer structures is important not only for undertaking the rational design of peptide-based materials, but also for understanding their biological functions and the mechanism of many human diseases relative to protein aggregation. In this work, we have monitored the conformation, morphological, and mechanical properties of a hydrogel-forming peptide during hydrogelation in different dimethylsulfoxide (DMSO)/H₂O solutions. The peptide shows nanofiber morphologies in DMSO/H₂O solution with a ratio lower than 4:1. Increased water percentage in the solution enhanced the hydrogelation rate and gel strength. One-dimensional and two-dimensional proton NMR and electron microscopy studies performed on the peptide in DMSO/H₂O solution with different ratios indicate that the peptide monomer tends to adopt a more helical structure during the hydrogelation as the DMSO/H₂O ratio is reduced. Interestingly, at the same DMSO/H₂O ratio, adding Ca²⁺ not only promotes peptide hydrogelation and gel strength, but also leads to special shear-thinning and recovery properties of the hydrogel. Without changing the peptide conformation, Ca²⁺ binds to the charged Asp residues and induces the change of interfiber interactions that play an important role in hydrogel properties.     

Synthesis, spectroscopic and electrochemical characterization of water soluble [(η-C5H5)2Mo(thionucleobase/thionucleoside)]Cl2 complexes

A series of water soluble molybdenocene complexes of general formula [(η⁵-C₅H₅)₂Mo(L)]Cl₂ (L=6-mercaptopurine (2), 6-mercaptopurine ribose (3), 2-amino-6-mercaptopurine (4), 2-amino-6-mercaptopurine ribose (5)) have been prepared by reacting Cp₂MoCl₂ (1) with the corresponding thionucleobase/thionucleoside in a (2:1) THF/MeOH solvent mixture. The complexes have been characterized by spectroscopic methods (NMR, UV-Vis, IR and MS). ¹H NMR spectroscopic data (DMSO-d₆) on the complexes suggest a S-Mo-N(7) coordination by the thionucleobase/thionucleoside. In buffer solution NMR data suggest that the thionucleobase/thionucleoside remains coordinated to molybdenum probably through S(6) and assisted by either N(7) or N(1) atoms. Intermediate species such as [Cp₂Mo(η¹-L)(H₂O)]^2+/1+ where the L is acting as monodentate ligand are possible in solution. Electrochemical characterization has also been pursued by cyclic voltammetry in DMSO and buffer solution. In DMSO, the complexes including the molybdenocene dichloride exhibit reversible redox behavior. On the other hand, in buffer solution, the oxidation process is irreversible for all the species.     

Two-dimensional NMR studies of [Pro-10] atrial natriuretic factor [7-23

The conformational properties of an analog of atrial naturiuretic factor, [Pro-10] ANF(7-23), were examined in H₂O, H₂O/DMSO-d₆ (2/1), and DMSO-d₆ using two-dimensional nmr techniques. The sequence differs from the native peptide by the absence of the exocyclic N- and C-terminal residues, and the substitution of a proline for a glycine at position 10—a modification expected to reduce the conformational flexibility of this analog. The backbone proton nmr resonances were assigned from two-dimensional correlated spectroscopy (2D-COSY), relayed COSY, and 2D nuclear Overhàuser enhancement (NOE) experiments, and the solution conformation was evaluated from vicinal spin–spin coupling constants and NOE data. Despite the substitution of a proline in the sequence, [Pro-10] ANF(7-23) exhibits a considerable amount of flexibility in all of the solvents employed.     

Interaction of Ni(II) with 2,3-dihydroxybenzoic acid

The reaction of NiCl₂·6H₂O with 2,3-dihydroxybenzoic acid=L in n-PrOH:H₂O=1:1 solution, produced the complex {[Ni₅L₅(OH)₇]K₄·13H₂O}_n. Its structure was investigated using elemental analysis, IR, UV–Vis, NMR and ES MS spectroscopy. The complex is unstable in aqueous solution and its decomposition scheme was proposed on the basis of NMR and ES MS spectra. This may contribute to the understanding of oxidative degradation of catecholic derivatives by Ni(II), as well as to other similar ones.     

An aromatic schiff base stabilised as a coordinated enol iminium zwitterion by complex formation with a series of divalent metal ions

The Schiff base N-(2-hydroxy-3-carboxy-1-naphthylidine)-4-methyl-2-sulphonic acid aniline (bonsaH₃) has been found to react with a range of divalent metal ions (Mg²⁺, Mn²⁺, Co²⁺, Ni²⁺ and Zn²⁺ and UO₂²⁺ to give red-yellow insoluble complexes (bonsaH)_m(H₂O)_n. The solid state diffuse reflectance spectra of all the complexes have an intense visible band at ca. 470 nm. This fact, together with evidence from infrared spectra and room-temperature magnetic-moment measurements, suggests that in all cases the ligand is coordinated to the metal ion in the solid state in the enol-iminium zwitterionic form. The ¹H NMR spectra of the Mg²⁺ and Zn²⁺ complexes in DMSO-d₆ indicate that a different structure is adopted in this solvent. Comparisons with the spectra of bonsa-H₃ and (bonsa-H₂)K·H₂O suggest that the solution structure is that of an enol-imine.     

Secondary Structure and Dynamics of an Intrinsically Unstructured Linker Domain

Abstract

The transient secondary structure and dynamics of an intrinsically unstructured linker domain from the 70 kDa subunit of human replication protein A was investigated using solution state NMR. Stable secondary structure, inferred from large secondary chemical shifts, was observed for a segment of the intrinsically unstructured linker domain when it is attached to an N-terminal protein interaction domain. Results from NMR relaxation experiments showed the rotational diffusion for this segment of the intrinsically unstructured linker domain to be correlated with the N-terminal protein interaction domain. When the N-terminal domain is removed, the stable secondary structure is lost and faster rotational diffusion is observed. The large secondary chemical shifts were used to calculate phi and psidihedral angles and these dihedral angles were used to build a backbone structural model. Restrained molecular dynamics were performed on this new structure using the chemical shift based dihedral angles and a single NOE distance as restraints. In the resulting family of structures a large, solvent exposed loop was observed for the segment of the intrinsically unstructured linker domain that had large secondary chemical shifts.     

A fresh look into VO(salen) chemistry: synthesis, spectroscopy, electrochemistry and crystal structure of [VO(salen)(H2O)]Br · 0.5 CH3CN

The reaction of V^IVO(salen) with [Et₄N][SnBr₃] in air proceeds via an initial reduction to give a [V^III (salen)]⁺ intermediate, which is then oxidised to dark green [V^VO(salen)(H₂O)]Br, 1. As determined by X-ray crystallography, 1 in the solid state contains hexacoordinate vanadium. ⁵¹V NMR spectra indicate that dissociation of the aqua ligand occurs to give a pentacoordinated [V^VO(salen)] cation in methanol-d₄ solution, while in DMSO-d₆ solutions, coordination of the solvent occurs to give [V^VO(salen)(DMSO-d₆)]⁺. The colour of 1 can be accounted for by O_oxo → V^V and phenolate → V^V LMCTs. Results from this study have led to the re-assignment of LMCTs and V-N and V-O_phenolate stretching frequencies in the IR spectrum. Cyclic voltammetry of 1 indicates three redox processes. The first is typical of [VO(salen)]/[VO(salen)]⁺ couple and the other two are bromide oxidations.     

NMR solution structure of human cannabinoid receptor-1 helix 7/8 peptide: Candidate electrostatic interactions and microdomain formation

We report the NMR solution structure of a synthetic 40-mer (T³⁷⁷-E⁴¹⁶) that encompasses human cannabinoid receptor-1 (hCB1) transmembrane helix 7 (TMH7) and helix 8 (H8) [hCB1(TMH7/H8)] in 30% trifluoroethanol/H₂O. Structural features include, from the peptide’s amino terminus, a hydrophobic α-helix (TMH7); a loop-like, 11 residue segment featuring a pronounced Pro-kink within the conserved NPxxY motif; a short amphipathic α-helix (H8) orthogonal to TMH7 with cationic and hydrophobic amino-acid clusters; and an unstructured C-terminal end. The hCB1(TMH7/H8) NMR solution structure suggests multiple electrostatic amino-acid interactions, including an intrahelical H8 salt bridge and a hydrogen-bond network involving the peptide’s loop-like region. Potential cation-π and cation-phenolic OH interactions between Y³⁹⁷ in the TMH7 NPxxY motif and R⁴⁰⁵ in H8 are identified as candidate structural forces promoting interhelical microdomain formation. This microdomain may function as a flexible molecular hinge during ligand-induced hCB1 conformer transitions.     

D-glucose interaction with uranium ion. Synthesis,spectroscopic and structural characterization of uranylglucose adducts and the effect of metal cation binding on the sugar anomeric structures

The interaction of D-glucose with hydrated uranyl salts has been investigated in solution and solid adducts of the type UO₂(D-glucose)X₂·2H₂O, where X = Cl⁻, Br⁻, NO_3⁻ and 0.5 SO_4²⁻ have been isolated. These adducts are characterized by means of FT-IR, ¹H NMR and molar conductivity measurements.Spectroscopic evidence suggested that UO_2²⁺ cation could be bonded to one D-glucose molecule (possibly through O(1)H and O(2)H hydroxyl groups) and to two H₂O, resulting in six-coordination around the uranium ion.The strong sugar H-bonding network is perturbed, on metal ion interaction and the D-glucose α-anomeric structure is favoured, upon uranyl cation coordination.     

Gramicidin S analogs with a D-Ala, Gly, or L-Ala residue in place of the D-Phe residue: molecular conformations and interactions with phospholipid membrane

The proton nmr and CD spectra of gramicidin S (GS) cyclic-(Val^1,1′-Orn^2,2′-Leu^3,3′-D-Phe^4,4′-Pro^5,5′)₂ and of GS analogs—namely, [D-Ala^4,4′]-GS, [Gly^4,4′]-GS, and [L-Ala^4,4′]-GS—were analyzed. The molecular conformation of [D-Ala^4,4′]-GS is similar to that of GS, with the trans form about the D-Ala-Pro peptide bond. The molecular conformation of [Gly^4,4′]-GS depends on the solvent composition of dimethylsulfoxide-d₆/trifluoroethanol (DMSO)-d₆/TFE and DMSO-d₆/H₂O as well as the solute concentration. In DMSO-d₆ solution, [Gly^4,4′]-GS forms the GS-type conformation of the monomer at lower concentration. At higher concentration, the GS-type conformer is converted to the other one that forms molecular aggregates. The cis form about the X-Pro peptide bonds is found for [Gly^4,4′]-GS and [L-Ala^4,4′]-GS in DMSO-d₆ and for [L-Ala^4,4′]-GS in TFE solution. The large temperature dependences of α-proton chemical shifts of [L-Ala^4,4′]-GS in DMSO-d₆ solution indicate that the conformer equilibrium changes with temperature. The GS-type conformation is not formed in [L-Ala^4,4′]-GS. The two active peptide analogs, [D-Ala^4,4′]-GS and [Gly^4,4′]-GS, interact with the phospholipid membrane, taking the GS-type conformation. By contrast, an inactive analog, [L-Ala^4,4′]-GS, does not interact with phospholipid membrane. The activities of GS analogs are found to correlate to the formation of the GS-type conformation upon binding with phospholipid membrane.     

Structure of the O-polysaccharide from the lipopolysaccharide of Providencia alcalifaciens O60

An O-polysaccharide (O-antigen) was isolated by mild acid degradation of the lipopolysaccharide of Providencia alcalifaciens O60 and studied by sugar and methylation analyses as well as ¹H and ¹³C NMR spectroscopy, including 2D ROESY and ¹H,¹³C HMBC experiments in D₂O and a ROESY experiment in a 9:1 H₂O–D₂O mixture to reveal correlations for NH protons. It was found that the polysaccharide is built up of linear pentasaccharide repeating units containing an amide of d-glucuronic acid with l-serine and has the following structure:The O-antigen studied is structurally and serologically closely related to the O-antigen of Proteus vulgaris O44.     

The combined use of selective deuteration and double resonance experiments in assigning the 1H resonances of valine and tyrosine residues of dihydrofolate reductase

Selective deuteration is a general solution to the resolution problem which limits the application of double resonance experiments to the assignment of the ¹H NMR spectra of proteins. Spin-decoupling and NOE experiments have been carried out on Lactobacillus casei dihydrofolate reductase and on selectively deuterated derivatives of the enzyme containing either [γ-²H₆]Val or (α,δ₂,?₁-²H₃]His, [α,δ₁,δ₂,?₁,?₂,ζ-²H₆]Phe, [α,δ₁,?₃,ζ₂,ζ₃,η₂-²H₆]Trp and [α,?₁,?₂-²H₃]Tyr. When combined with ring-current shift calculations based on the crystal structure of the enzyme, these experiments allow us to assign ¹H resonances of Val 61, Val 115, Tyr 46 and Tyr 68.     

A Study and Optimization of Complexation of Cobalt Ions with Dihydroquercetin in Aqueous Solutions

This work continues a series of studies devoted to complex formation of ions of biogenic metals with the flavonoid dihydroquercetin (DHQ). The interaction of Со²⁺ ions with DHQ in aqueous solutions has been investigated. It has been found that, at different pH of a solution, complex compounds (CC) with different stoichiometry are formed; a variation of the pH value of a solution from 6.0 to 7.0 results in the formation of compounds (1)–(3) with the metal : flavonoid ligand ratio (Met : L) from 1 : 2 at рН 6.0 (1), through 2 : 3 at pH 6.4–6.7 (2), to 1 : 1 at рН 6.8–7.0 (3). By using the thermogravimetric method and the data of the elemental analysis, the most probable composition of the compounds with the determination of the amount of bound water has been proposed: [CoL₂(H₂O)₄] for (1), [Co₂L₃(ОН)(H₂O)₄] for (2), and [CoL(ОН)(H₂O)₂] for (3). Conditions for the optimization of product yield in the complexation reaction of Со²⁺ ions with DHQ in an aqueous solution have been determined for compound (2): the рН value of solution 6.7; the reaction time 15 min; the temperature of the reaction solution 90°С; the molar ratio of the initial reagents DHQ : Со²⁺ 1 : 1.5; the initial concentration of DHQ 0.020 mol/L and that of Со²⁺ 0.030 mol/L; and the use of CoSO₄ ? 7H₂O as a source of cobalt ions. The yield of the product is 81.8%.

     

A 1H and 13C NMR Study on the Role of Salt-Bridges in the Formation of a Type I β-Turn in N-Acetyl-L-Asp-L-Glu-L-Lys-L-Ser-NH2

Abstract

The conformation of the tetrapeptide N-Acetyl-Asp⁷-Glu⁸-Lys⁹-Ser¹⁰-NH₂, a fragment of the type I collagen α-1 chain N-telopeptide, has been studied by ¹H and ¹³C NMR and circular dichroism spectroscopy. The spectroscopic evidence, based on two-dimensional, phase-sensitive NMR techniques such as COSY, ROESY, proton-carbon shift correlation and selective COLOC, indicates a strong dependence of the conformation on the experimental conditions. In CD₃OH/H₂O (60/40) at ca. neutral pH the tetrapeptide forms a β-turn, stabilized by a hydrogen bond between NH(S¹⁰) and CO(D⁷) and a strong salt-bridge between COO^?(E⁸) and NH₃ ⁺(K⁹). The β-turn is type I and appears to coexist with a non-hydrogen-bonded structure. The coexistence of these two conformers is proven by proton NMR data such as NH-NH ROEs, reduced NH-H_α(E⁸) coupling constant NH(E⁸) low-field shift and the temperature coefficient of NH(S¹⁰), whereas the conclusion regarding the salt-bridge is based on ¹³C results. In the same solvent, at a pH below the pKa of the carboxyl groups, no evidence for a conformation other than extended can be found. In aqueous solution at approximately neutral pH, evidence for the E⁸-K⁹ charge interaction is observed, but not for a hydrogen bond anywhere in the molecule.     

Human Nucleotide Excision Repair Protein XPA: 1H NMR and CD Solution Studies of a Synthetic Peptide Fragment Corresponding to the Zinc-Binding Domain (101–141)

Abstract

A peptide corresponding to residues 101–141 of the human nucleotide excision repair protein XPA was synthesized with an isoleucine substituted for L138 and its solution structure studied by circular dichroism and homonuclear ¹H NMR spectroscopy. The peptide, (XPA-41), contains a C₄?type zinc-binding motif, C105-(X)₂C108-(X)_l7?C126-(X)₂ C129, which XPA requires for damaged-DNA binding activity. The proton resonances of XPA-41without zinc (apoXPA-41) were assigned using homonuclear TOCSY, NOESY and DQF-COSY data and show the apo-zinc peptide is a random coil. The peptide was folded with the addition of 1.2 equivalents of ZnCl₂ in dilute solution at pH 4.0. Electrospray ionization mass spectroscopy illustrated an increase in the molecular weight of XPA-41 by 65 amu. Circular dichroism spectra of the zinc-folded peptide (zXPA-41) showed the acquisition of elements of secondary structure. Such a conclusion was confirmed with'H NMR data collected at 25°C, pH 6.3. Hα-secondary shifts and NOE patterns indicate that regions V102-C105 and G109-F112 form an anti-parallel β-sheet and residues N128-K137 form a nascent α-helix. Rapid exchange of most amide resonances between S115-C126 prohibited unambiguous assignment of all the proton resonances in this region. However, a 1.19 ppm downfield shift of the H^α resonance of T125 relative to the apo-zinc peptide, together with downfield shifted H^α resonances for the adjacent residues (P124 and L123), suggest a second β-sheet is present in the S115-C126 region. On the basis of structural similarities to GATA-1 (Science 267:438–446), a homology generated structure for zXPA-41 was made, using GATA-1 as the template, which satisfied all the observed NOEs. Using the hybrid homology-NMR based zXPA-41 structure and analogy to GATA-1, models for the role played by the zinc-binding core (101–141) of XPA in DNA damage recognition are proposed.     

Conformational analysis of the nonapeptide leuprorelin using NMR and molecular modeling

The nonapeptide Leuprorelin, one of the LHRH agonists, was studied by means of 2D nuclear magnetic resonance spectroscopy and molecular modeling. NOESY spectra in aqueous/deuterated methanol solution (50%H₂O/CD₃OD) at low temperature (268 K) revealed short-range nOe connectivities (i, i+1), characteristic of flexibility of the molecule. The H^N–H^N sequential connectivities observed provide evidence that the sequence has the propensity to form a bend involving residues 5 and 6 and the N-terminal segment. The -proton chemical shifts compared to random coil and additional data from the amide proton temperature coefficients support this assumption. One long-range nOe cross peak between H₂ –H^NEth is indicative of proximity between C- and N-termini.     

Novel bis(diethylenetriamine)thallium(III) complex. Synthesis and characterization in pyridine solution and in solid

A new complex of thallium(III) with the nitrogen donor ligand diethylenetriamine (dien) has been prepared and characterized by multinuclear NMR (¹H, ¹³C, ²⁰⁵Tl), infrared and Raman spectroscopy, and X-ray diffraction. In solution, the symmetric s-facial isomer of [Tl(dien)₂]³⁺ is formed. This is a fluxional molecule even at low temperature (235 K); therefore, the different rotamers cannot be observed separately. A complete characterization of the complex is given from its non-trivial NMR spectra. The crystal structure of [Tl(dien)₂](ClO₄)₃·H₂O shows u-facial geometry, where the coordination environment around thallium can be described as a distorted trigonal prism.