Side-chain OH Research Articles

Interplay of intra‐ and intermolecular H‐bonds for the addition of a water molecule to the neutral and N‐protonated forms of noradrenaline

AbstractThe conformational flexibility of noradrenaline in its N‐protonated and neutral forms was considered at the Hartree–Fock (HF)/6‐31G* level, taking into account the orientation of the two hydroxy groups located on the catechol ring and the interconversion pathways between their stable arrangements. The difference in stability among the various forms of N‐protonated noradrenaline was maintained including either more diffuse functions on the heteroatoms or Møller–Plesset second order (MP2) correlation corrections. The embedding in aqueous solution, in the polarizable continuum model framework, of the conformers kept rigid at their in vacuo geometries favored the T conformers with respect to the G ones at the HF level (for neutral noradrenaline at the MP2 level as well). The addition of a single water molecule to noradrenaline (either N‐protonated or not) caused the intramolecular H‐bond within the side chain to weaken until formation of one or two intermolecular H‐bonds with water. This fact, coupled to the intramolecular H‐bond strain relaxation, further stabilized the G1 and T conformers. Continuum solvation of the hydrated clusters of neutral noradrenaline favored significantly the Twater adducts at the HF level, but only slightly at the MP2 level, because of their large energy gap in vacuo with respect to G1water, even enhanced by MP2 geometry optimizations. The dependence of the potential energy profile for the NH2 group rotation on the catechol ring and side chain OH group orientation was examined in noradrenaline and compared to the trend shown by dopamine. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Dimethyl propionate ester heme-containing cytochrome b5: structure and stability.

A derivative of rat microsomal cytochrome b5, obtained by substitution of the native heme moiety with protoporphyrin IX dimethyl ester, has been characterized by 1H and 15N NMR spectroscopy. Besides the two usual A and B forms, which depend on the orientation of the heme in the prostethic group cavity, two other minor forms have been detected which presumably indicate different conformations of the vinyl side chains. The shifts of the heme methyls, as well as the directions of the rhombic axes of the magnetic susceptibility tensor, indicate a small difference in the orientation of the imidazole planes of the histidine axial ligands. The solution structure was determined by using 1,303 meaningful NOEs and 241 pseudocontact shifts, the latter being derived from the native reduced protein. A family of 40 energy-minimized conformers was obtained with average RMSD of 0.56+/-0.09 A and 1.04+/-0.12 A for backbone and heavy atoms, respectively, and distance and pseudocontact shift penalty functions of 0.50+/-0.07 A2 and 0.51+/-0.02 ppm2. The structure shows some changes around the cavity and in particular a movement of the 60-70 backbone segment owing to the absence of two hydrogen bonds between the Ser64 backbone NH and side-chain OH and the carboxylate oxygen of propionate-7, present in the native protein. The analysis of the NMR spectra in the presence of unfolding agents indicates that this protein is less stable than the native form. The decrease in stability may be the result of the loss of the two hydrogen bonds connecting propionate-7 to Ser64 in the native protein. The available data on the reduction potential and the electron transfer rates are discussed on the basis of the present structural data.

Structural effects on the OH-promoted fragmentation of methoxy-substituted 1-arylalkanol radical cations in aqueous solution: the role of oxygen acidity.

A kinetic and product study of the OH- -induced decay in H2O of the radical cations generated from some di-and tri-methoxy-substituted 1-arylalkanols (ArCH(OH)R*+) and 2- and 3-(3,4-dimethoxyphenyl)alkanols has been carried out by using pulse- and gamma-radiolysis techniques. In the 1-arylalkanol system, the radical cation 3,4-(MeO)2C6H3CH2-OH*+ decay at a rate more than two orders of magnitude higher than that of its methyl ether; this indicates the key role of the side-chain OH group in the decay process (oxygen acidity). However, quite a large deuterium kinetic isotope effect (3.7) is present for this radical cation compared with its a-dideuterated counterpart. A mechanism is suggested in which a fast OH deprotonation leads to a radical zwitterion which then undergoes a rate-determining 1,2-H shift, coupled to a side-chain-to-ring intramolecular electron transfer (ET) step. This concept also attributes an important role to the energy barrier for this ET, which should depend on the stability of the positive charge in the ring and, hence, on the number and position of methoxy groups. On a similar experimental basis, the same mechanism is suggested for 2,5-(MeO)2C6H3CH2OH*+ as for 3,4-(MeO)2C6H3CH2OH*+, in which some contribution from direct C-H deprotonation (carbon acidity) is possible. In fact, the latter process dominates the decay of the trimethoxylated system 2,4,5-(MeO)3C6H2CH2-OH*+, which, accordingly, reacts with OH- at the same rate as that of its methyl ether. Thus, a shift from oxygen to carbon acidity is observed as the positive charge is increasingly stabilized in the ring; this is attributed to a corresponding increase in the energy barrier for the intramolecular ET. When R=tBu, the OH- -promoted decay of the radical cation ArCH(OH)R*+ leads to products of C-C bond cleavage. With both Ar = 3,4- and 2,5-dimethoxyphenyl the reactivity is three orders of magnitude higher than that of the corresponding cumyl alcohol radical cations; this suggests a mechanism in which a key role is played by the oxygen acidity as well as by the strength of the scissile C-C bond: a radical zwitterion is formed which undergoes a rate-determining C-C bond cleavage, coupled with the intramolecular ET. Finally, oxygen acidity also determines the reactivity of the radical cations of 2-(3,4-dimethoxyphenyl)ethanol and 3-(3,4-dimethoxyphenyl)propanol. In the former the decay involves C-C bond cleavage, in the latter it leads to 3-(3,4-dimethoxyphenyl)propanal. In both cases no products of C-H deprotonation were observed. Possible mechanisms, again involving the initial formation of a radical zwitterion, are discussed.

Fluorocholesterols, in contrast to hydroxycholesterols, exhibit interfacial properties similar to cholesterol

We used an automated Langmuir-Pockels surface balance to characterize the air–water interfacial properties of cholesterol (CH) and its derivatives with hydrophilic OH and F substitutions at isologous sites on the sterol body or side chain. We studied 6-fluorocholesterol, 25-fluorocholesterol, 25,26,26,26,27,27,27-heptafluorocholesterol, 7α-hydroxycholesterol, 7β-hydroxycholesterol, 25-hydroxycholesterol and 27-hydroxycholesterol, alone and in mixtures with 1-palmitoyl-2-oleoyl-sn-3-glycero-phosphocholine (POPC). Pressure–area isotherms of the fluorocholesterols were essentially indistinguishable from CH and all condensed POPC monomolecular layers (monolayers) to variable degrees. Both nucleus-substituted hydroxycholesterols formed expanded monolayers, with lift-offs from baseline 22–26 Å2/molecule larger than CH, suggesting interfacial tilting; furthermore, in binary mixtures, they condensed POPC monolayers less than CH. In contrast, the side chain hydroxylated CHs were oriented horizontally in the interface at large molecular areas, and became vertical below 140 Å2/molecule with the side chain-OH rather than 3-OH group anchored in the subphase, as evidenced by low collapse pressures and smaller molecular areas than CH. Both side chain hydroxycholesterols expanded POPC monolayers at molar ratios <30%, but induced condensation with higher ratios, suggesting that OH-acyl chain (POPC) repulsion is superceded at higher mole fractions by lateral phase separation and intersteroidal H-bonding.These studies predict that fluorocholesterols should exhibit intramembrane spatial occupancy nearly identical to CH, whereas nucleus and especially side chain hydroxycholesterols will perturb membrane lipid packing notably.

Breaking and making of the S–S linkage via nucleophilic substitution.: An ab initio study

The energetics of nucleophilic opening and closing of protonated disulphide bridges has been studied for the case of two sulphur-containing (H 2S and CH 3SH) nucleophiles. The energetics of this reaction was compared to that of the nucleophilic opening and closing of disulphide bridges with thiolate ions: In the former case a not so good nucleophile is combined with an excellent leaving group, and in the latter case a superior nucleophile is combined with a relatively poor leaving group. The barrier heights for these S N2-type reactions were found to be comparable as calculated by ab initio MO methods. In addition, two oxygen-containing nucleophiles (H 2O, HCONH–CH[CH 2OH]–CONH 2) have also been studied in the following reaction: The water molecule is not nucleophilic enough to open the disulphide bridge. However, in a serine residue, in which the oxygen of the side-chain OH group is activated through backbone/side-chain hydrogen bonding, the hydroxy group is sufficiently nucleophilic to open the disulphide bridge, just like the sulphur-containing nucleophiles mentioned above.

The Crystal Structure of the N-terminal SH3 Domain of Grb2

The 3-D structure of the N-terminal SH3 domain of the regulatory protein Grb2 has been determined by X-ray analysis at 2.8 Å resolution and refined to a crystallographicRfactor of 21.5%. The structure, which is very similar to those of other SH3 domains, consists of two orthogonal, antiparallel up-down β-sheets, with three variable loops and a 310helix. Docking of the proline-rich peptide, 3BP1 on Grb2-N SH3, shows that the polyproline type II helix can bind the SH3 domain forming conserved hydrogen bonds between the main-chain carbonyl oxygens of Met4 and Pro7 of the proline-rich peptide and the reoriented side-chains of Trp36 and Asn51, respectively, and a hydrogen bond between the main-chain carbonyl of Leu8 of the proline rich peptide with the side-chain OH of Tyr52 of the Grb2-N SH3. The peptide side-chain binding occurs on the surface of SH3 domain at three major sites involving the side-chains of the residues in the hydrophobic patch (Tyr7, Phe9, Trp36, Phe47, Pro49 and Tyr52) and the RT-Src and n-Src loops of the SH3 domain. The proline-rich peptides could bind the Grb2-N SH3 in either orientation and maintain the key hydrogen bonds because of the pseudo-symmetry of the polyproline type II helix. However, for the mSos1 peptide a salt bridge can be formed between the arginine of the proline-rich peptide and the protein at Asp15, Glu16 and Glu31 only in one direction; this orientation seems to be strongly preferred. The conservatively varied RGD sequence motif (sometimes KGE or KGD) in SH3 domains might be involved in interactions at the cell membrane.

Molecular and absolute crystal structure of pindolol-1-(1H-indol-4-yloxy)-3-[(1-methylethyl)amino]-2-propanol: A specific beta-adrenoreceptor antagonist with partial agonist activity

The crystal and molecular structure of pindolol, 1-(1H indol-4-yloxy)-3-[(1-methylethyl)amino]-2-propanol, has been determined by direct methods. Crystals are tetragonal,\(P\bar 42_1 c\),a=b=15.809(4),c=11.246(2) A,Z=8,Dc=1.174 mg m−3. The finalR-factor for 2271 reflections withI>2σ(I) is 0.038. Refinement by full-matrix least-squares on F2 also enabled the absolute configuration of the structure to be established. The molecule is essentially planar, including much of the side-chain which is stabilized by the existence of two intramolecular H-bonds, between the ethyl oxygen and OH group, and between the OH and side-chain amide groups, respectively. The crystal structure is formed by three intermolecular hydrogen bonds including two side-chain-side-chain interactions, between ethyl oxygen to amide and OH to amide, and an interaction between the side-chain OH to indole NH.

The tyrosine corner: A feature of most greek key β‐barrel proteins

The Tyr corner is a conformation in which a tyrosine (residue "Y") near the beginning or end of an antiparallel beta-strand makes an H bond from its side-chain OH group to the backbone NH and/or CO of residue Y - 3, Y - 4, or Y - 5 in the nearby connection. The most common "classic" case is a delta 4 Tyr corner (more than 40 examples listed), in which the H bond is to residue Y - 4 and the Tyr chi 1 is near -60 degrees. Y - 2 is almost always a glycine, whose left-handed beta or very extended beta conformation helps the backbone curve around the Tyr ring. Residue Y - 3 is in polyproline II conformation (often Pro), and residue Y - 5 is usually a hydrophobic (often Leu) that packs next to the Tyr ring. The consensus sequence, then, is LxPGxY, where the first x (the H-bonding position) is hydrophilic. Residues Y and Y - 2 both form narrow pairs of beta-sheet H-bonds with the neighboring strand. delta 5 Tyr corners have a 1-residue insertion between the Gly and Tyr, forming a beta-bulge. One protein family has a delta 4 corner formed by a His rather than a Tyr, and several examples use Trp in place of Tyr. For almost all these cases, the protein or domain is a Greek key beta-barrel structure, the Tyr corner ends a Greek key connection, and it is well-conserved in related proteins. Most low-twist Greek key beta-barrels have 1 Tyr corner. "Reverse" delta 4 Tyr corners (H bonded to Y + 4) and other variants are described, all less common and less conserved. It seems likely that the more classic Tyr corners (delta 4, delta 5, and delta 3 Tyr, Trp, or His) contribute to the stability of a Greek key connection over a hairpin connection, and also that they may aid in the process of folding up Greek key structures.

Potential antitumor agents. 62. Structure-activity relationships for tricyclic compounds related to the colon tumor active drug 9-oxo-9H-xanthene-4-acetic acid

A series of tricyclic analogues of 9-oxo-9H-xanthene-4-acetic acid have been prepared and evaluated for their ability to cause hemorrhagic necrosis in subcutaneously implanted colon 38 tumors in mice, in an effort to extend the structure-activity relationships for this series. As was found previously with analogues of flavone-8-acetic acid (FAA) (Atwell et al. Anti-Cancer Drug Des. 1989, 4, 161), all electronic modifications of the XAA nucleus led to severe decreases or complete abolition of activity, suggesting narrow structure-activity relationships. Dipole moments for many of the compounds were computed, and the degree to which the molecular dipole moment lay out of the plane of the aromatic part of these molecules was found to be determined largely by the contributions from the acetic acid moiety relative to that from the tricyclic ring system. There did not appear to be any general relationship between the magnitude of the dipole moment and activity. However, for compounds containing the 9-carbonyl functionality, the orientation of the dipole vector may be of significance. In all compounds possessing an ether group peri to the acetic acid side chain, there was a close approach (ca. 2.4 A) between this and the side chain OH.

Orally potent human renin inhibitors derived from angiotensinogen transition state: design, synthesis, and mode of interaction

A three-dimensional structure of the complex of human renin and the scissile site P4 Pro to P1' Val of angiotensinogen was deduced in order to design potent human renin inhibitors rationally. On the basis of this structure, an orally potent human renin inhibitor (1a) was designed from the angiotensinogen transition state and synthesized. The inhibitor 1a contains a (2R)-3-(morpholinocarbonyl)-2-(1-naphthylmethyl)propionyl residue (P4-P3) with a retro-inverso amide bond, L-histidine, and a novel amino acid, (2R,3S)-3-amino-4-cyclohexyl-2-hydroxybutyric acid, named cyclohexylnorstatine (2a). The optically pure cyclohexylnorstatine was efficiently prepared from Boc-L-cyclohexylalaninol (3), and the stereochemistry of 1a was established by X-ray crystal analysis. The analyses of interaction between 1a and human renin using modeling techniques indicated that (1) the cyclohexyl group of P1 and the naphthyl group of P3 were accommodated in large hydrophobic subsites S1 and S3, respectively; (2) the imidazole of P2 His was hydrogen bonded to the side chain OH of Ser-233 to contribute to the selectivity of renin inhibition; (3) cyclohexylnorstatine isopropyl ester residue was accommodated in S1-S1'. The importance of the stereochemistry in the potent and specific inhibitor was clearly shown. Oral administration to monkeys of this inhibitor resulted in a drop of 10-20 mmHg in mean blood pressure and a reduction of plasma renin activity for a 5-h period.

Methylphosphinyl (Dmp): A new protecting group of tyrosine suitable for peptide synthesis by use of boc-amino acids

Use of dimethylphosphinyl (Dmp) group as a side-chain phenolic OH protecting group of tyrosine in peptide synthesis was studied. The Dmp group is resistant to trifluoroacetic acid and hydrogenolysis and removed by fluoride ion or liquid HF.

Design of anticancer drugs using modeling techniques.

Flexibility of intercalation site geometries within a B-DNA helix was investigated in the twist-shift plane using energy minimization methods. The parameters optimized included sugar conformation, the glycosidic angles and phosphodiester torsion angles. Our calculations show several regions of energetically favorable intercalation geometries in the twist-shift plane. Modeling studies using interactive computer graphics and electrostatic potential surface compatibility provided initial hypotheses for the structures of the drug-DNA complexes. These hypotheses were supported and extended by energy minimizations of these complexes. Binding positions, conformational features and relative minimum binding energies of two anticancer drugs, mitoxantrone and bisantrene, were computed for intercalation complexes with DNA in the theoretically defined intercalation sites. Mitoxantrone intercalates DNA from the minor groove and the side chain OH or NH groups are involved in hydrogen bonds with the main chain phosphate groups of DNA, thereby cross-linking the complementary strands. The hydroxyl groups of mitoxantrone can also participate in hydrogen bonding with phosphate oxygens of another chain, thereby cross-linking DNA helices. Bisantrene intercalates DNA favorably from the major groove and the NH group of the dihydroimidazole ring can participate in hydrogen bonding with the phosphate oxygens of the backbone. These models are consistent with the physicochemical and electron microscopic studies of the interaction of mitoxantrone and bisantrene with DNA. Our results are now being used to guide the design of novel anticancer drugs that should interact with DNA in a manner similar to that proposed for our representative drugs.

Spectroscopic and potentiometric studies on coordination abilities of tetrapeptides containing proline and tyrosine or phenylalanine

The insertion of proline residues, a ‘break-point’ [1–3] in the second position of a tetrapeptide divides the ligand molecule into two fragments which are potentially able to interact with metal ions independently, i.e. the N-terminal aminoacid ( e.g. via NH 2, CO) and two C-terminal aminoacid residues ( via e.g. 2N −, COO −). The introduction of tyrosine to such a peptide sequence complicates solution equilibria distinctly [1, 3]. Phenylalanine, which is not able to use its side-chain for the direct metal ion binding, is a good analogue for tyrosine and both residues were used for the synthesis and the study of the coordination abilities of tetrapeptides. The spectroscopic and thermodynamic studies of cupric complexes with tetrapeptides: GlyProGlyTyr, GlyProTyrGly, TyrProGlyGly, GlyProPheGly, GlyProDPheGly and PheProGlyGly have shown that the metal peptide interaction always starts at the N-terminal (NH 2, CO donors). The tyrosine residue may involve its side-chain OH in the metal ion binding with formation of monomeric or dimeric species. The complex equilibria strongly depend on the position of tyrosine residue in the peptide sequence. The lack of the direct involvement of phenylalanine side-chain in the direct metal ion coordination leads to much simpler equilibria. The presence of proline residue in the ligand molecule causes very unusual coordination modes in the formal complex species with formation of unusually large chelate rings. The combination of spectroscopic and potentiometric approaches led to the satisfactory description of very complicated systems which may be used as reasonable spectroscopic and structural models for biosystems.

The structure of bovine liver rhodanese: II. The active site in the sulfur-substituted and the sulfur-free enzyme

X-ray studies at 2.5 Å resolution show that the active site of bovine liver rhodanese is a depression between the two domains. In sulfur-substituted rhodanese the density of the essential Cys247 corresponds with that of a persulfide. Both sulfur atoms are interacting via hydrogen bonds with several peptide NH and side-chain OH groups. One side of the active site pocket contains mainly hydrophylic, the other side mainly hydrophobic residues. None of these hydrophylic or hydrophobic groups appears to interact strongly with the persulfide. Crystals of the sulfur-substituted enzyme were treated with cyanide, a sulfur acceptor. Subsequent difference Fourier studies show that the extra sulfur atom has been removed. Only minor conformational differences appear to exist between the two rhodanese species studied. These are a movement of the Sγ atom of Cys247 and some rearrangement of solvent molecules near the active site. The combination of these observations with the results of experiments performed by other investigators suggest a mechanism for sulfur transfer by rhodanese in which the thiol group of Cys247 is the essential nucleophile, whereas the positive charges on Arg186 and Lys249 act in various ways as “electrophilic assistants”. The transition state and the persulfide in the sulfur-substituted enzyme are stabilized by several hydrogen bonds.

Proton NMR, EPR and absorption spectra studies of palladium(II) and copper(II) complexes with L-alanyl-L-serine

The conformation of L-alanyl—L-serine has been established by proton NMR spectra for various pH ranges. A hydrogen bond between the hydroxyl and the carboxyl group was assumed in order to explain the particular stability of the serine residue rotamers, in which both groups are gauche to each other. A structure for the Pd(II) and Cu(II) complexes with Ala—Ser in various pH solutions has been proposed from the NMR, EPR and absorption spectra. The coordination ability of the hydroxyl group of the serine residue was found at higher pH region. The serine side-chain OH group interaction with the Pd(II) ion was suggested to be responsible for the unusual stability of the gauche rotamer of the serine residue, in the 1:1 complex at pH 3–10.