Reaction of the antitumor antibiotic CC-1065 with DNA: structure of a DNA adduct with DNA sequence specificity.

Sequence-dependent variations in DNA revealed by x-ray crystallographic studies have suggested that certain DNA-reactive drugs may react preferentially with defined sequences in DNA. Drugs that wind around the helix and reside within one of the grooves of DNA have perhaps the greatest chance of recognizing sequence-dependent features of DNA. The antitumor antibiotic CC-1065 covalently binds through N-3 of adenine and resides within the minor groove of DNA. This drug overlaps with five base pairs for which a high sequence specificity exists.

Solution structures of stromelysin complexed to thiadiazole inhibitors.

Unregulated or overexpressed matrix metalloproteinases (MMPs), including stromelysin, collagenase, and gelatinase. have been implicated in several pathological conditions including arthritis and cancer. Small-molecule MMP inhibitors may have therapeutic value in the treatment of these diseases. In this regard, the solution structures of two stromelysin/ inhibitor complexes have been investigated using 1H, 13C, and 15N NMR spectroscopy. Both-inhibitors are members of a novel class of matrix metalloproteinase inhibitor that contain a thiadiazole group and that interact with stromelysin in a manner distinct from other classes of inhibitors. The inhibitors coordinate the catalytic zinc atom through their exocyclic sulfur atom, with the remainder of the ligand extending into the S1-S3 side of the active site. The binding of inhibitor containing a protonated or fluorinated aromatic ring was investigated using 1H and 19F NMR spectroscopy. The fluorinated ring was found to have a reduced ring-flip rate compared to the protonated version. A strong, coplanar interaction between the fluorinated ring of the inhibitor and the aromatic ring of Tyr155 is proposed to account for the reduced ring-flip rate and for the increase in binding affinity observed for the fluorinated inhibitor compared to the protonated inhibitor. Binding interactions observed for the thiadiazole class of ligands have implications for the design of matrix metalloproteinase inhibitors.

Solution structure of human interleukin-1 receptor antagonist protein.

Interleukin-1 receptor antagonist protein (IRAP) is a naturally occurring inhibitor of the interleukin-1 receptor. In contrast to IL-1 beta, IRAP binds to the IL-1 receptor but does not elicit a physiological response. We have determined the solution structure of IRAP using NMR spectroscopy. While the overall topology of the two 153-residue proteins is quite similar, functionally critical differences exist concerning the residues of the linear amino acid sequence that constitute structurally homologous regions in the two proteins. Structurally homologous residues important for IL-1 receptor binding are conserved between IRAP and IL-1 beta. By contrast, structurally homologous residues critical for receptor activation are not conserved between the two proteins.

Purification and structural characterization of the CD11b/CD18 integrin alpha subunit I domain reveals a folded conformation in solution.

The alpha subunits of the leukocyte CD11/CD18 integrins contain an approximately 200 amino acid 'inserted' or I domain. The I domain of the cell-surface Mac-1 (CD11b/CD18) integrin has been shown to be the major recognition site for several adhesion ligands, including iC3b, fibrinogen, factor X, and ICAM-1. The I domain from the Mac-1 alpha subunit has been expressed in Escherichia coli as a soluble GST-fusion protein containing a factor Xa sensitive cleavage site. Analytical characterization of the purified I domain reveals that it is obtained in very high quality at high yields. CD and NMR spectra indicate that I domain adopts a predominantly folded structure in solution, independent of the remainder of the alpha subunit. Addition of Ca2+ and Mg2+ did not significantly perturb the structural conformation.

Synthesis and renin inhibitory activity of angiotensinogen analogues having dehydrostatine, Leu psi [CH2S]Val, or Leu psi [CH2SO]Val at the P1-P1' cleavage site.

The synthesis and in vitro renin inhibitory potencies of angiotensinogen (ANG) analogues having amide (CONH) bond replacements at P1-P1', the Leu-Val cleavage site, corresponding to Leu psi[CH2SO]Val, and the trans olefinic analogue of statine (Sta), 4(S)-amino-6-methyl-2(E)-heptenoic acid (dehydrostatine, Dhs), are reported. These are compared to P1-P1' Leu psi[CH2NH]Val-, Sta-, or Phe-Phe-substituted analogues of the same template. The Dhs pseudodipeptide was found to be an adequate mimic of a trans CONH bond and gave a peptide, H-Pro-His-Pro-Phe-His-Dhs-Ile-His-D-Lys-OH, approximately equal in potency to a Phe-Phe-containing inhibitor, but 200-fold less potent than its Sta-substituted congener. That the enhanced potency of the Sta-containing peptide most likely depends on hydrogen bonding as well as tetrahedral geometry is indicated by the 50-100-fold lower potency of the tetrahedral Leu psi[CH2S]Val and Leu psi[CH2SO]Val analogues as compared to the Leu psi[CH2NH]Val-containing congener.

Naphtho and benzo analogues of the kappa opioid agonist trans-(+/-)-3,4-dichloro-N-methyl-N-[2-(1-pyrrolidinyl)cyclohexyl] benzeneacetamide.

Further elaboration on the structure-activity relationships in our U-50,488 series has revealed that benzologation of this cyclohexane-1,2-diamine derivative provides compounds which either maintain the interaction with the kappa receptor (e.g. compounds 3a and 5a in the phenylacetamido series) or eliminate the mu receptor mediated analgesia (e.g. compounds 3-6 in the benzamido series). Naphthologation also caused the elimination of mu receptor mediated analgesia (e.g. compounds 17a and 17b).

Kinetics and equilibrium of the reversible alprazolam ring-opening reaction.

Alprazolam underwent a facile 1,4-benzodiazepine ring-opening reaction in an acidic aqueous solution to form a benzophenone compound. The reaction was demonstrated by means of UV, IR, and 1H- and 13C-NMR spectroscopy. Its reverse cyclization reaction to alprazolam occurred when an acidic solution was neutralized. Both the ring-opening and the cyclization rate constants were obtained from the overall rate constant measured at 25 degrees over a pH range of 0.5--8.0; the latter was measured by monitoring the UV spectral change of the reaction. Although the equilibrium was favored for the benzophenone compound in acidic solutions, it was possible to directly measure the cyclization rate at three acidic pH values by providing a sink condition for the product, alprazolam, using a biphasic reaction system. The bell-shaped cyclization rate pH profile was interpreted in terms of a change in the rate-determining step. The pH profile of the ring-opening rate showed an inflection point indicating a different reactivity of mono- and dicationic alprazolam. The apparent equilibrium between alprazolam and the benzophenone compound at a given pH was estimated from the rate constants for the ring-opening and cyclization reactions. The results agree with the apparent pKa measured by a conventional UV spectrophotometry and a titration technique. The pKa of monocationic alprazolam, the reactive species for the covalent hydration, was determined from the pH dependence of the initial absorbance when an alprazolam solution is acidified.

Secondary structure of a human growth hormone-releasing factor fragment (Leu27-hGRF(15-32)NH2) in aqueous/SDS micelle environments.

The secondary structure of a human growth hormone-releasing factor (hGRF) fragment (Leu27-hGRF(15-32)NH2) has been studied by 1H NMR at 500 MHz in aqueous solutions containing varying concentrations of d25-sodium dodecyl sulfate (SDS). Chemical shifts, coupling constants and NOESY data show that the secondary structure of the peptide is random in aqueous solution in the absence of SDS. At relatively low molar ratios of SDS to peptide (1.3:1 to 3.3:1 SDS:peptide) the 1D 1H spectrum of the peptide changes as the peptide resonances are broadened significantly. NOESY patterns consistent with helical structure are present in the region of residues 22-29 when the SDS:peptide molar ratio is 1.3:1 and the SDS concentration is slightly below the critical micelle concentration (CMC). At higher molar ratios of SDS to peptide (16:1 to 72:1), where the SDS concentration is significantly above the CMC, the lineshape of the peptide's 1H NMR spectrum is sharpened. In these environments an alpha-helical conformation is induced in residues 19-32 of the hGRF fragment, as shown both by NOESY and by chemical shift data. Thus, the well-known tendency of this region of the GRF peptide to form alpha-helix in isotropic mixed-solvent systems (e.g., methanol/water, trifluoroethanol (TFE)/water) is seen also in SDS/aqueous systems.

Heteronuclear three-dimensional NMR spectroscopy of a partially denatured protein: the A-state of human ubiquitin.

Human ubiquitin is a 76-residue protein that serves as a protein degradation signal when conjugated to another protein. Ubiquitin has been shown to exist in at least three states: native (N-state), unfolded (U-state), and, when dissolved in 60% methanol:40% water at pH 2.0, partially folded (A-state). If the A-state represents an intermediate in the folding pathway of ubiquitin, comparison of the known structure of the N-state with that of the A-state may lead to an understanding of the folding pathway. Insights into the structural basis for ubiquitin's role in protein degradation may also be obtained. To this end we determined the secondary structure of the A-state using heteronuclear three-dimensional NMR spectroscopy of uniformly 15N-enriched ubiquitin. Sequence-specific 1H and 15N resonance assignments were made for more than 90% of the residues in the A-state. The assignments were made by concerted analysis of three-dimensional 1H-15N NOESY-HMQC and TOCSY-HMQC data sets. Because of 1H chemical shift degeneracies, the increased resolution provided by the 15N dimension was critical. Analysis of short- and long-range NOEs indicated that only the first two strands of beta-sheet, comprising residues 2-17, remain in the A-state, compared to five strands in the N-state. NOEs indicative of an alpha-helix, comprising residues 25-33, were also identified. These residues were also helical in the N-state. In the N-state, residues in this helix were in contact with residues from the first two strands of beta-sheet. It is likely, therefore, that residues 1-33 comprise a folded domain in the A-state of ubiquitin. On the basis of 1H alpha chemical shifts and weak short-range NOEs, residues 34-76 do not adopt a rigid secondary structure but favor a helical conformation. This observation may be related to the helix-inducing effects of the methanol present. The secondary structure presented here differs from and is more thorough than that determined previously by two-dimensional 1H methods [Harding et al. (1991) Biochemistry, 30, 3120-3128].

1H and 15N resonance assignments and solution secondary structure of oxidized Desulfovibrio vulgaris flavodoxin determined by heteronuclear three-dimensional NMR spectroscopy.

Sequence-specific 1H and 15N resonance assignments have been made for all 145 non-prolyl residues and for the flavin cofactor in oxidized Desulfovibrio vulgaris flavodoxin. Assignments were obtained by recording and analyzing 1H-15N heteronuclear three-dimensional NMR experiments on uniformly 15N-enriched protein, pH 6.5, at 300 K. Many of the side-chain resonances have also been assigned. Observed medium-and long-range NOEs, in combination with 3JNH alpha coupling constants and 1HN exchange data, indicate that the secondary structure consists of a five-stranded parallel beta-sheet and four alpha-helices, with a topology identical to that determined previously by X-ray crystallographic methods. One helix, which is distorted in the X-ray structure, is non-regular in solution as well. Several protein-flavin NOEs, which serve to dock the flavin ligand to its binding site, have also been identified. Based on fast-exchange into 2H2O, the 1HN3 proton of the isoalloxazine ring is solvent accessible and not strongly hydrogen-bonded in the flavin binding site, in contrast to what has been observed in several other flavodoxins. The resonance assignments presented here can form the basis for assigning single-site mutant flavodoxins and for correlating structural differences between wild-type and mutant flavodoxins with altered redox potentials.

1H NMR analysis and in vitro bioactivity of Leu27-bGRF(1-29)NH2 and its D-Ala2 and des-(Tyr1-Ala2)-analogs.

Relative growth hormone-releasing potencies of bovine growth hormone-releasing factor (bGRF) analogs bGRF(1-44)NH2 (I), Leu27-bGRF(1-29)NH2 (II) and D-Ala2, Leu27-bGRF(1-29)NH2 (III) in in vitro bovine anterior pituitary cell cultures were determined to be 100%, 48% and 77%, respectively. The potencies of II and III, although numerically different, were not statistically different. Leu27-bGRF(3-29)NH2 (IV) was approximately 10,000 times less potent than 1. 1H NMR studies of peptides II, III and IV in 35% d3-2,2,2-trifluorethanol (TFE)/65% phosphate buffer at pH 4 revealed very similar, highly helical secondary structures in the 8-29 region, with only subtle differences at the N-termini. This lack of correlation between secondary structure in solution and in vitro bioactivity suggests that either 1) the biological conformations induced at the GRF receptor for II and III vs. IV are different from those generated in TFE/buffer, 2) similar secondary structures may be necessary but not sufficient for the observed bioactivity or 3) residues 1 and 2 of analogs II and III are important contact residues crucial for effective GRF-receptor interaction.

Proton, carbon, and nitrogen chemical shifts accurately delineate differences and similarities in secondary structure between the homologous proteins IRAP and IL-1 beta.

1H alpha, 13C alpha, and 15N alpha secondary shifts, defined as the difference between the observed value and the random coil value, have been calculated for interleukin-1 receptor antagonist protein and interleukin-1 beta. Averaging of the secondary chemical shifts with those of adjacent residues was used to smooth out local effects and to obtain a correlation dependent on secondary structure. Differences and similarities in the placement of secondary structure elements in the primary sequences of these structurally homologous proteins are manifested in the smoothed secondary chemical shifts of all three types of nuclei. The close correlation observed between the secondary chemical shifts and the previously defined locations of secondary structure, as defined by traditional methods, exemplifies the advantage of chemical shifts to delineate regions of secondary structure.

Isolation, identification and synthesis of a metabolite of tazadolene succinate.

Metabolism of tazadolene (1), a novel non-opioid analgesic with antidepressant properties, affords the 4-hydroxy and 3-methoxy-4-hydroxy derivatives (phenyl ring) of the drug, and N-[2-(phenylmethylene)cyclohexyl]-beta-alanine (4). The isolation, identification and synthesis of the latter metabolite is described.

Secondary structure and topology of interleukin-1 receptor antagonist protein determined by heteronuclear three-dimensional NMR spectroscopy.

Interleukin-1 (IL-1) proteins, such as IL-1 beta, play a key role in immune and inflammatory responses. Interaction of these cytokines with the IL-1 receptor induces a variety of biological changes in neurologic, metabolic, hematologic, and endocrinologic systems. Interleukin-1 receptor antagonist protein (IRAP) is a naturally occurring inhibitor of the interleukin-1 receptor. The 153-residue protein binds to the receptor with an affinity similar to that of IL-1 beta but does not elicit any physiological responses. As a first step toward understanding IRAP's mode of action, we have used multidimensional, heteronuclear NMR spectroscopy to determine the antagonist's solution secondary structure and global fold. Using a combination of 3D 1H-15N NOESY-HMQC and TOCSY-HMQC and 3D 1H-15N-13C HNCA and HN(CO)CA experiments on uniformly 15N- or doubly 13C/15N-enriched IRAP, we have made resonance assignments for more than 90% of the main-chain atoms. Analysis of short- and long-range NOE's indicates that IRAP is predominantly beta-sheet, with the same overall topology as IL-1 beta but with different regions of the primary sequence comprising the beta-strands. Two short helical segments also were identified. The 14% sequence identity between IL-1 beta and IRAP increases to 25% when differences in the locations of secondary structure elements in the primary sequences are taken into account. Still, numerous differences in side chains, which ultimately play a major role in receptor interaction, exist.(ABSTRACT TRUNCATED AT 250 WORDS)

An NMR study of the covalent and noncovalent interactions of CC-1065 and DNA.

The binding of the antitumor drug CC-1065 has been studied with nuclear magnetic resonance (NMR) spectroscopy. This study involves two parts, the elucidation of the covalent binding site of the drug to DNA and a detailed investigation of the noncovalent interactions of CC-1065 with a DNA fragment through analysis of 2D NOE (NOESY) experiments. A CC-1065-DNA adduct was prepared, and an adenine adduct was released upon heating. NMR (1H and 13C) analysis of the adduct shows that the drug binds to N3 of adenine by reaction of its cyclopropyl group. The reaction pathway and product formed were determined by analysis of the 13C DEPT spectra. An octamer duplex, d(CGATTAGC.GCTAATCG), was synthesized and used in the interaction study of CC-1065 and the oligomer. The duplex and the drug-octamer complex were both analyzed by 2D spectroscopy (COSY, NOESY). The relative intensity of the NOEs observed between the drug (CC-1065) and the octamer duplex shows conclusively that the drug is located in the minor groove, covalently attached to N3 of adenine 6 and positioned from the 3'----5' end in relation to strand A [d(CGATTA6GC)]. A mechanism for drug binding and stabilization can be inferred from the NOE data and model-building studies.

An NMR study of conformations of substituted dipeptides in dodecylphosphocholine micelles: implications for drug transport.

Efficient transport of intact drug (solute) across the intestinal epithelium is typically a requirement for good oral activity. In general, the membrane permeability of a solute is a complex function of its size, lipophilicity, hydrogen bond potential, charge, and conformation. In conjunction with theoretical/computational and in vitro drug transport studies, seven dipeptide (R(1)-D-Xaa-D-Phe-NHMe) homologues were each dissolved in a micellar d(38)-dodecylphosphocholine solvent system. In this homologous dipeptide series, factors such as size, lipophilicity, hydrogen-bond potential, and charge were either tightly controlled or well-characterized by other methods in order to investigate by nmr how conformational factors relate to transport. Nuclear Overhauser effect spectroscopy experiments and amide-NH-H(2)O chemical exchange rates showed that the five more lipophilic dipeptides were predominately associated with micelle, whereas the two less lipophilic analogues were not. Rotating frame nuclear Overhauser effect spectroscopy derived interproton distance restraints for each analogue, along with (3)J(HH)-derived dihedral restraints, were used in molecular dynamics/simulated annealing computations. Our results suggest that-other factors being equal-flexible dipeptides having a propensity to fold together nonpolar N- and C-terminal moieties allow greater segregation of polar and nonpolar domains and may possess enhanced transport characteristics. Dipeptides that were less flexible or that retained a less amphiphilic conformation did not have comparably enhanced transport characteristics. We suggest that these conformational/transport correlations may hold true for small, highly functionalized solutes (drugs) in general.