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The 10-membered cyclotripeptide cyclo(-MeβAla-Phe-Pro) 3 and its diastereoisomer cyclo(-MeβAla-Phe-dPro-) 4 have been synthesized under mild cyclization conditions starting from linear precursors containing C-terminal proline. The crystal and molecular structure of the two models has been determined by X-ray crystallography. Analysis of the NMR spectra supported by NOE data clearly indicates that the conformations found in the crystals are retained in solution. Both cyclotripeptides exhibit a cis-cis-trans backbone conformation. The two tertiary peptide bonds, at the proline and MeβAla nitrogen atoms, adopt a cis conformation whereas the CO—NH junctions are trans in both the models. The deviations from planarity of the peptide units vary from Δω values of ca. 18° for the Pro-MeβAla and dPro-MeβAla bonds to ca. 7° for Phe-Pro and Phe-dPro bonds. Relevant conformational details of 3 and 4, as revealed by X-ray and NMR analysis, are reported. Crystals of 3 are monoclinic: P21, a= 5.317(2), b= 17.059(6), c= 9.514(3)A, β= 99.18(3), Z = 2. The final R and Rw are 0.054 and 0.071 respectively. Crystals of 4 are orthorhombic: P212121, a= 8.797(2), b= 19.440(9), c= 21.605(10)A, Z = 8. The final R and Rw are 0.069 and 0.104 respectively.

In order to investigate the relative formation tendency of different tautomeric ring systems (cyclols, cyclodepsipeptides and corresponding N-acyl-diketopiperazines), two linear peptide precursors containing proline as C-terminal residue, have been synthesized and subjected to cyclizing conditions. Boc-Ser-Phe-Pro-ONp (I) gave three isomeric cyclic compounds: Boc-Ser-Phe-Pro- (IV), N-(Boc-Ser)-cyclo-(Phe-D-Pro) (III) and the corresponding aza-cyclol (II). Starting from Hyb-Phe-Pro-ONp (V) two epimeric N(3-hydroxybutyryl)diketopiperazines (VI) and (VII) and the corresponding 10-membered cyclodepsipeptide (VIII) could be isolated. Crystal and molecular structure of VIII is reported. Crystals of VIII are orthorhombic, P212121 with a = 9.684, b = 22.985, c = 7.841, z = 4. The two peptidic bonds are cis with omega values of 6.6 degrees and - 18.1 degrees, whereas the lactonic bond is of transoid type. The pyrrolidine ring has C2-C gamma-exo conformation.

The tripeptide N-formyl-L-Met-L-Leu-L-Phe-OMe (FMLP-OMe) crystallizes in the orthorhombic system, space group P 2(1)2(1)2(1), with the following unit-cell parameters: a = 21.727, b = 21.836, c = 5.133 A, Z = 4. The structure has been solved and refined to a final R of 0.068 for 1838 independent reflexions with I greater than 2 omega (I). The peptide backbone is folded at the Leu residue (phi L = -67.7, psi L = -49.1 degrees) without intramolecular hydrogen bonds. Considering each peptide plane, the Leu side-chain is oriented on the same side of that of the Phe residue and on the opposite side of that of the Met residue, respectively. The crystal conformation differs from all the other conformations proposed for FMLP-OMe and the anionic form of N-formyl-L-Met-L-Leu-L-Phe-OH (FMLP) in solution accounts for the amphiphilic character of the peptide, giving rise, through intermolecular hydrogen bonds, to a stacking of molecules which could be maintained in the aggregation states experimentally observed in solvents of low polarity. Intramolecular potential energy calculations have been carried out in order to compare the energies of the various backbone conformers.

The solid-state self-assembly properties of distal dimethoxy-p-H-calix[4]dihydroquinone, 3, are described. Three different crystalline forms were obtained under different crystallization conditions. The cone conformation is maintained in all three crystalline forms, being favored by lower rim hydrogen bond formation. The first crystal, 3A, is constituted by mutual-inclusion calixarene trimers connected to each other by water molecules. The second and third ones (3B and 3C) are formed by alternate layers of crystallographically independent calixarene molecules.

The epoxidation of quinone rings of calixquinones represents a valid route for the introduction of oxygenated functionalities into the de-tert-butylated calixarene walls originating cis-diepoxy-p-dione moieties. Carbonyl reduction of these systems leads to hybrid calixarenes containing dianhydroinositol moieties (calixinositols) belonging to the calixcyclitols family. The regio- and stereochemistry of these derivatives was determined by 2D NMR studies, in conjunction with MM3 calculations and X-ray crystallography.

One of the molecular factors contributing to Leishmania sp. virulence and pathogenesis is the major surface metalloprotease GP63, alternatively called leishmanolysin, MSP, and PSP (EC 3.4.24.36). Here, the molecular dynamics simulation of Leishmania major GP63 in water at pH 7 is reported. Upon solvation, GP63 undergoes a sharp structural relaxation with respect to the crystal structure. The fluctuation pattern occurs essentially in solvent-exposed nonstructured regions. By contrast, the active site turns out to be rigid. Essential dynamics and dynamic-domain analyses, both carried out on the equilibrated portion of GP63, show that the fingerprint fluctuations of GP63 are practically characterized by the motion of a large part of the N-terminal domain. These results appear to be in line with substrate recognition and (pro)enzyme activation played by the N-terminal domain of GP63. A systematic analysis among a series of 10 homologs of GP63 also shows that the residues involved in the interdomain bending result highly conserved. This finding also suggests possible relationship between the maintainance of proteolytic activity and the similarity of the dynamical properties of the related enzymes.

TIBO- and TBO-like sulfone derivatives 1 and 2 were designed, synthesized, and tested for their ability to block the replication cycle of HIV-1 in infected cells. The anti-HIV-1 activities of sulfones 3, which were intermediates in the syntheses of 1 and 2, were also evaluated. Surprisingly, the sulfone analogues of TIBO R82913 (compounds 1) were inactive, whereas interesting results were obtained for truncated derivatives 2. Compound 2 w was the most potent among this series in cell-based assays (EC50=0.07 microM, CC50>200 microM, SI>2857). It was twofold less potent than R82913, but more selective. An X-ray crystallographic analysis was carried out to establish the absolute configuration of 2 w and its enantiomer 2 x, which were obtained by semipreparative HPLC of 2 v, one of the most potent racemates. Compounds 1-3 were proven to target HIV-1 RT. In fact, representative derivatives inhibited recombinant HIV-1 RT in vitro at concentrations similar to those active in cell-based assays. 3D QSAR studies and docking simulations were developed on TIBO- and TBO-like sulfone derivatives to rationalize their anti-HIV-1 potencies and to predict the activity of novel untested sulfone derivatives. Predictive 3D QSAR models were obtained with a receptor-based alignment by docking of TIBO- and TBO-like derivatives into the NNBS of RT.

[structure: see text] The first example of two discrete calix[8]arene conformational isomers, 2 and 2a, has been obtained by exhaustive benzylation of 1,5-tetramethylene-bridged calix[8]arene 1. It is demonstrated, with the aid of X-ray crystallography, that these atropisomers have two 3/4-cone halves oriented syn or anti with respect to the bridge/bridgeheads moiety. VT NMR studies indicate that the tert-butyl-through-the-annulus inversion is inhibited in 1, while groups larger than n-hexyl or benzyl are required for curtailing the O-through-the-annulus route.

Human neutrophil collagenase (HNC, MMP-8) is one of the target enzymes for drug treatment of pathologic extracellular matrix degradation. Peptidomimetic inhibitors bind in the S'-side of the enzyme active site occupying the S-1(') primary specificity pocket by their large hydrophobic side-chains. The crystal structure of the complex between the catalytic domain of MMP-8 and Pro-Leu-l-Trp(P)(OH)(2) (PLTP) showed that this phosphonate inhibitor binds in the S side of the active site. This finding was unexpected since it represents the first example of accommodation of the bulky Trp indolyl chain in the S-1 rather than in the S-1(') subsite. Dynamical and structural factors favouring this uncommon mode of binding were therefore investigated. MD simulations performed on the uncomplexed enzyme show that its structure in aqueous solution is only slightly different from the crystal structure found in the complex with PLTP. ED analysis of the MD simulations, performed on PLTP alternatively interacting with the S- or S'-side of the active site, shows that the enzyme fluctuation increases in both cases. The main contribution to the overall enzyme fluctuation is given by the loop 164-173. The fluctuation of this loop is spread over more degrees of freedom when PLTP interacts with the S-side. This dynamical factor can enhance the preference of PLTP for the S subsites of MMP-8. MD simulations also show that ligation of PLTP in the S subsites is further favoured by better zinc chelation, a cation-pi interaction at the S-3 subsite and unstrained binding conformations. The role of the S-3, S-3(') and S-1(') subsites in determining the inhibitor binding is discussed.

The effect of a series of physostigmine analogs on acetylcholinesterase activity was investigated. The second-order rate constant kon of the enzyme–inhibitor complex correlates with the conformational positioning of aromatic residues, especially Trp84, in the transition state complex. The van der Waals interactions are an important structural element of this conformational change. A transient mobility of the cysteine loop (Cys67–Cys94) was confined only to the presence of a significant steric effect. Even with this limitation, however, the steric effect seems to be an appropriate model for future tests on the “back door” hypothesis involving facilitated opening for faster product clearance. © 2002 Wiley Periodicals, Inc. J Biochem Mol Toxicol 16:64–69, 2002; Published online in Wiley Interscience (www.interscience.wiley.com). DOI 10.1002/jbt.10026

The synthesis, solution NMR investigation and solid-state structural characterization of a new difunctionalized β-cyclodextrin (β-CD) are reported. 6I,6II-Dideoxy-6I,6II-bis[2-(2-pyridyl)ethylamino]-β-cyclomaltoheptaose is synthesized for the first time using a regioselective synthetic procedure. On the basis of an aqueous solution NMR investigation, the intramolecular interaction of the two pyridine rings with the upper rim of the cavity is proposed. 6I,6II-Dideoxy-6I,6II-bis[2-(2-pyridyl)ethylamino]-β-cyclomaltoheptaose, C56H86N4O33, crystallizes in the monoclinic P21 space group with cell dimension a = 26.303(5), b = 15.670(5), c = 8.276(2) A and β = 103.60(2)°, and 5.5 molecules of water for each independent β-cyclodextrin molecule. The structure refines to R = 0.103 for 2270 observed reflections [I ≥ 3σ(I)] and represents the first example of a complete structural characterization of a branched difunctionalized β-cyclodextrin. In the solid state, the macrocycle structure maintains an approximate seven-fold symmetry with only small changes occurring in the cyclic carbohydrate conformation where two consecutive primary hydroxy groups are substituted with bulky moieties. The two aminoethylpyridine groups linked to contiguous glucosidic units show different behaviour, with one group extending away from the cavity of the β-CD, the other remaining in the proximity of the ‘mouth’ of the cavity. However, in the crystal the aminoethylpyridine group extending away from the cavity of the β-CD is deeply inserted into the cavity of the adjacent β-CD molecule translated along the c axis, giving rise to long rows of β-CD molecules stabilized by these host–guest interactions. The resulting polymeric arrangement has already been observed in crystal structures of other monosubstituted β-CDs.

The crystallographic investigation of the retro-inverso peptide Bz-S-gAla-R-mAla-NHPh reveals an extended backbone conformation where the NH groups of the gem-diamino alkyl moiety and the CO groups of the malonyl residue face side by side. This extended conformation, presenting all carbonyls on opposite sides of the NH groups, is stabilized by interstrand H-bonds running in a single direction of the parallel beta-sheets that characterize the crystal packing. These sheets differ from the beta-sheets formed by native amino acids only. (1)H-NMR nuclear Overhauser effect spectroscopy (NOESY) experiments suggest that a conformation similar to that found in the crystal also prevails in dimethylsulfoxide solution. Previous potential energy calculations of gem-diamino alkyl (g) and malonyl (m) Ala residues predicted that extended forms were less stable than the helical ones because of strong electrostatic repulsions between the parallel polar groups. Similar arguments were invoked to give more weight to helical forms of the retro-peptide units in the proposal of packing models of some nylons in their crystalline polar regions. The present findings show that both g and m Ala residues can experience the extended conformation in the beta-sheet aggregation. The energy increase occurring in one strand, due to the parallel orientation of consecutive peptide dipoles, is more than compensated by favorable cooperative interactions among head-to-tail aligned peptide dipoles of facing strands, resulting in the formation of two C==O...H==N H-bonds per residue.

5,5′-Bicalix[4]arene 1 , a ditopic host possessing two divergent cavities, crystallizes from CH 2 Cl 2 and p -xylene to give an iterative assembly of a three-component zigzag array. This array is formed by CH-π inclusion of a linear CH 2 Cl 2 · p -xylene connector within the facing cavities of two molecules of 1 . Each zigzag array is perpendicularly interconnected to the lateral one through hydrophilic interactions of calixarene-OH groups.

The new pseudodipeptide Boc-azaTic-Leu-OMe (1), incorporating the conformationally and topographically constrained 3,4-dihydro-2(1H)-phthalazinecarboxylic acid (azaTic) residue, has been synthesized together with the three related models Boc-azaTic-NHMe (3), MeCO-azaTic-Gly-OMe (4), and azaTic-Leu-OMe (6). Both the epimers of 1, generated by opposite absolute configuration at an azaTic nitrogen stereogenic centre, have been found in the asymmetric unit of the crystal. The conformational perturbations, deriving by the introduction of the azaTic residue into a peptide backbone, are described and the nature of the NH…N interaction, which gives rise to a typical backbone folding closing a 5-membered ring, has been studied.

Phosphonate analogues of the peptidomimetic N -(Furan-2-yl)carbonyl-Leu-Trp-OH were prepared with the goal of evaluating the effect of phosphonate for carboxylate replacement on binding with snake venom metalloproteinases and MMPs. N -(Furan-2-yl)carbonyl-Leu- l -Trp(P)-(OH) 2 showed a 75-fold increase of the inhibiting activity against adamalysin II, a snake venom metalloproteinase structurally related to MMPs and TACE. Both the phosphonate and carboxylate peptidomimetics fit into the active site adopting a retrobinding mode and provide the structural base for a new class of metalloproteinases inhibitors. ©

Two molecular bowls can be directly linked to give an open-and-shut capsule simply by heating p-H-calix[4]arene in CH3CN at reflux in the presence of FeCl3⋅6 H2O. Double calixarenes of this type could in principle be present as syn or anti conformers (shown schematically on the right). Whereas the anti form was observed in the solid state, there is presumably an equilibrium of the two forms in solution. The globular architecture of the syn conformation suggests the potential for cooperation between two cone binding sites in the endo-calix complexation of suitable guests.

3,4-Dihydro-2(1 H )-phthalazinecarboxylic acid (azaTic) is a new conformationally restricted analogue of phenylalanine which, due to its α-aza-nature, should allow, in addition to the topographical control typical of the Tic residue, a definite local perturbation of the backbone conformation. Two azaTic models, namely azaTic-NH 2 ( 2 ) and MeCO-azaTic-NHMe ( 5 ), have been synthesized and their conformation has been determined and compared to that of the related Tic and azaPro models.

The nature of the interactions between calcium ions and bile salt anions and the effect of the competition between calcium and sodium ions for possible formation of micellar aggregates are investigated. The crystal structures of calcium deoxycholate (CaDC) and glycodeoxycholate (CaGDC) and quasi-elastic light-scattering measurements, carried out on sodium deoxycholate (NaDC) and glycodeoxycholate (NaGDC) aqueous solutions containing CaCl2, are discussed. The calcium ions are coordinated to oxygen atoms of carboxylate groups and water molecules by means of ion−ion and ion−dipole interactions. The hydroxyl groups of the bile salt anions are not involved. The Ca2+-bile salt complexes fulfill both a 1:1 (CaDC) and a 1:2 (CaGDC) stoichiometry. An assembly of wedge-shaped bilayers, cemented with CaDC anions, or an assembly of irregular trimeric units, each one containing three anions, can be recognized in the crystal packing of CaDC. Ca2+ and Cl- ions and water molecules are located in liquid-like regions. The ...

In the context of a research program aimed at synthesizing pseudopeptidic ergopeptines, the incorporation of an α-azaPhe residue into the peptidic moiety of ergotamine has been studied. Acylation of cyclo(-azaPhe-Pro-) 6 with (+)-(S)-2-benzyloxy-2-methylmalonyl monoethyl ester monochloride 5 gives the (E)-isoimide 7 as the predominant reaction product; contrary to expectation the conversion of 7 into the desired imide isomer 8 proceeds with difficulty and is accompanied by decomposition. Hydrogenolysis of 8 leads stereospecifically to the pseudopeptidic oxa-cyclol ethyl ester 9. Subsequent rearrangement of the corresponding oxa-cyclol acyl-azide 11 in the presence of benzyl alcohol fails to give the pseudopeptidic ergotamine oxa-cyclol. The new stable pseudopeptidic aza-cyclol 12 containing the residue of the didehydroalanine has been isolated together with a comparable amount of the imino aza-cyclol derivative 13. The mechanism of the formation of the new products 12 and 13 and the unexpected stability of the (E)-isoimide 7 are discussed.

4-Aminotetrahydrothiopyran-4-carboxylic acid (Thp) is an unusual achiral cyclic α,α-disubstituted amino acid mimicking the natural Met residue. The conformational energy map computed for Ac-Thp-NHMe shows that the γ-turn is the lowest minimum. 1 H-NMR and IR studies performed on For-Thp-Leu-OMe ( 2a ), a short peptide unable to give a 4…>1 H-bond, indicate that the γ-turn is adopted in CDCl 3 solution, whereas is not retained in (CD 3 ) 2 SO. An analogous conformational behaviour in solution has been observed for the strictly related For-Ac 6 c-Leu-OMe ( 2b ), containing 1-aminocyclohexane carboxylic acid (Ac 6 c).

As part of a programme to synthesize pseudopeptidic ergopeptines, the introduction of an α-azaproline residue in place of native proline into an ergotamine-like oxacyclolic system has been investigated. Starting material N-[(R)-2- benzyloxypropionyl]cyclo(-Phe-azaPro-)10 was prepared following two alternative synthetic routes and was subjected to reductive O-debenzylation. N,O-Acyl transfer on the resulting N-[(R)-2-hydroxypropionyl]cyclo(Phe-azaPro-)14 leads, through a new type of four- heteroatom tetrahedral adduct, to (5R)-5-methyl-3-{(1S)-2-phenyl-1-[(pyrazolidin-1-yl)carbonyl]ethyl}oxazolidine-2,4-dione 16, as a unique isolable tautomer. Structural and conformational details of compound 14, as revealed by X-ray analysis, are reported and compared with those of previously studied related models.

In order to study the influence of the conformation on the activity and bioselectivity, the new tetrapeptide ligand of the chemotactic formylpeptide receptors HCO-Met-Leu-Δ Z Phe-Phe-OMe ( 2 ) has been studied. Compound 2 has been designed so as to induce a preferential β-turn conformation with the N -formyl group located outside the backbone loop. The crystallographic analysis reveals that 2 adopts only in part the expected conformation due to the presence of a water molecule isnide the turn. Details on the H-bonding network stabilizing the “open-turn” are given. The tetrapeptide 2 is active towards human neutrophils, stimulating directed migration, superoxide anion generation and lysozyme release. The influence of the backbone conformation on the bioselectivity is discussed.

X-Ray crystallography proves the occurrence in 1,5∶3,7-doubly-bridged calix[8]arenes of a 34-cone geometry which can be transformed, in analogy to calix[4]arenes, to an unprecedented 34-partial-cone arrangement by proper alkylation of the free OH groups.

Two diastereomeric furan-2-carbonylamino-3-oxohexahydroindolizino[8,7-b]indole carboxylates, highly constrained analogues of endogenous pyroglutamyl tripeptide inhibitors of snake venom endopeptidases, have been prepared as potential inhibitors of adamalysin II and matrix metalloproteinases. They proved to be inactive against adamalysin II and weak inhibitors of gelatinase A, gelatinase B, stromelysin 1 and human neutrophyl collagenase. Evaluation of the mode of binding of the (2R,5S,11bR) isomer in the active site of adamalysin II suggests that the decrease of potency may be due to the reorientation of the acylamino chain in three of the heterocyclic nucleus, to a short contact at the entrance of the S′1 hydrophobic cleft and to the loss of flexibility of the tetracyclic nucleus in the P′1, P′2 region of the inhibitor, which prevents optimal arrangement in the S′1 specificity subsite.

Due to their relevant biological functions and specific chemical reactivity 1,2-dithiolanes (five-membered cyclic disulfides) represent an emerging class of heterocyclic compounds. However, despite the extensive research centered on lipoic acid and its analogues, only very few data are at the present available on peptides containing this ring system. We report here synthesis, conformation and bioactivity of a fMLF-OMe analogue, namely For-Met-Adt-Phe-OMe (7), in which the residue of the 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) (4) replaces the central L-leucine. The crystal conformation of the synthetic intermediate Boc-Adt-OMe (5) is also described and compared to that of lipoic acid (R-1,2-dithiolane-3-pentanoic acid) (3) and asparagusic acid (1,2-dithiolane-4-carboxylic acid) (2).

The solid-state assembly of four calix[4]arene derivatives bearing one or two rings oxyfunctionalized with epoxy and hydroxyl functional groups has been structurally studied by X-ray crystallography. In three cases the presence of OH groups pointing towards the exterior of the molecule allows the formation of intermolecular OH⋯epoxy H-bonds, which give rise to columnar structures, with zigzag or parallel oriented molecules, or helical arrangement of quadruplex elements. In one instance, in the absence of intermolecular H-bonds, columnar stacks of molecules are obtained mainly through intermolecular van der Waals interactions.

X-Ray crystallography proves the occurrence in 1,5∶3,7-doubly-bridged calix[8]arenes of a 34-cone geometry which can be transformed, in analogy to calix[4]arenes, to an unprecedented 34-partial-cone arrangement by proper alkylation of the free OH groups.

Boc-Pro-Leu-Ψ(NH-SO 2 )-Gly-NH 2 ( 3 ) has been synthesized as the first example of a pseudopeptide incorporating the NH-SO 2 junction. The crystal structure of 3 indicates that the Ψ(NH-SO 2 ) induces a cisoidal (gauche − ) conformation which induces a backbone folding and prevents the H-bonded β-turn found in the parent peptide.

A number of 1,3-dialkyl-8-(hetero)aryl-9-OH-9-deazaxanthines were prepared and evaluated as ligands of recombinant human adenosine receptors (hARs). Several 1,3-dipropyl derivatives endowed with nanomolar binding affinity at hA(2B) receptors, but poor selectivity over hA(2A), hA(1) and hA(3) AR subtypes were identified. A comparison with the corresponding 7-OH- and 7,9-unsubstituted-deazaxanthines revealed that 9-OH-9-deazaxanthines are more potent hA(2B) ligands with lower partition coefficients and higher water solubility compared to the other two congeneric classes of deazaxanthines. An optimization of the para-substituent of the 8-phenyl ring of 9-OH-9-deazaxanthines led to the discovery of compound 38, which exhibited outstanding hA(2B) affinity (Ki=1.0 nM), good selectivity over hA(2A), hA(1) and hA(3) (selectivity indices=100, 79 and 1290, respectively) and excellent antagonist potency in a functional assay on rat A(2B) (pA(2B)=9.33).

The first molecular structure of a p-hydroxycalix[6]arene 6 has been determined by a single crystal X-ray diffraction study. The calix[6]arene molecule assumes a 1,2,3-alternate conformation with all OH groups at the upper rim engaged in H-bonds with pyridine molecules. The stacking of molecules of p-hydroxycalix[6]arene 6 along the a and c axes gives rise to a solvent pseudo-cylindrical cavity at the centre of the cell.

[structure: see text] The first examples of hybrid calixarene hosts containing cyclitol moieties (calixcyclitols) have been obtained by treatment with LiAlH4 of diepoxydiol and tetraepoxytetrol calix[4]arene derivatives. A 6-oxabicyclo[3:1:1]heptanetriol or a cyclohexanetetrol ring was obtained depending on the stereochemical features of the diepoxydiol moiety. Preliminary binding studies toward anionic guests showed a discrete selectivity of calixcyclitol 9 vs H2PO4-.

The first crystallographic structure of an N-hydroxyurea inhibitor bound into the active site of a matrix metalloproteinase is reported. The ligand and three other analogues were prepared and studied as inhibitors of MMP-2, MMP-3, and MMP-8. The crystal structure of the complex with MMP-8 shows that the N-hydroxyurea, contrary to the analogous hydroxamate, binds the catalytic zinc ion in a monodentate rather than bidentate mode and with high out-of-plane distortion of the amide bonds. (c) 2005 Elsevier Ltd. All rights reserved.

Three novel peptidomimetic phosphinate inhibitors have been synthesized and evaluated as inhibitors of matrix metalloproteinases MMP-2 and MMP-8. Their IC50 values are in the micromolar range, and one of them showed to be the most effective inhibitor of MMP-2. The differences in binding affinities for MMP-2 and MMP-8 of the three phosphinates have been rationalized by means of modelling studies and molecular dynamics simulations.

To study the conformational preferences induced by the insertion of the 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) residue into a peptide backbone, the achiral N-protected dipeptide methylamide Boc-Adt-Adt-NHMe (1) was synthesized and its crystal state and solution conformation studied and compared with that exhibited by its carba-analogue Boc-Ac5c-Ac5c-NHMe containing two residues of 1-aminocyclopentane-1-carboxylic acid (Ac5c). Compound 1 in the crystal adopts a type-III β-turn conformation and an analogous structure is that preferred in chloroform solution as established by 1H-NMR and NOE information. In the crystal packing three different Adt rings form a cavity and the involved sulphur atoms give rise to unusual multiple interactions with one NH group. The chemical nature of these intermolecular and intramolecular main-chain side-chain NH S interactions are discussed in terms of quantum chemical calculations. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd.

[structure: see text] The first examples of epoxy-p-quinol and diepoxy-p-quinol calixarene derivatives have been obtained by base-promoted direct addition of O(2)(oxygenation) to calixarene phenol rings. The regio- and stereochemistry of these derivatives was determined by 2D NMR studies, in conjunction with MM3 calculations, and X-ray crystallography. Both the oxygenation and the subsequent carbonyl reduction occur with a preferential attack to the less hindered exo face of the calixarene rings.

In this study a decreased DPG response by polar bear (Ursus maritimus) hemoglobin was observed, and this response was interpreted as an example of gradual DPG/chloride shifting. This sort of mechanism has been suggested to occur in ruminants and, intuitively, one might guess that for ruminants the DPG/Cl - shifting might have been beneficial and hence selected for at the time of the latest Ice Age. However, sugges- tion that this is purely a temperature effect in polar bears and ruminants conflicts with the existence, in the hot savanna, of mammals that have Hb modulated by chloride. However, acidosis effects caused by routine periods of food shortage, induced in extreme environments may explain the responses of the hemoglobins of animals adapted to extreme habitats. The chloride effect is bound to specific amino acid substi- tutions in key positions. In polar bear Hb, they are specific, additional (with respect to human HbA) O2-linked chloride binding sites located between Lys-76 (b) and Lys-8 (b). The amino acids operate as an additional H + binding site for a chloride anion. Additionally, with respect to human adult HbA, the primary structure of polar bear Hb was characterized by two substitutions in b chains: Pro-5 (A2)→ Gly and Ala-76 (E20)→ Lys. The increased flexibility of the A helix causes the lower DPG effect. We further hypothesize that the resulting widening of the central cavity allows the Lys-82 (b) terminus to be free and constitute an additional, chloride-binding site. © 2004 Elsevier SAS. All rights reserved.

The α/β3-mixed tripeptides R-CO-β3-HMet-Leu-Phe-OMe (1a,b), R-CO-Met-β3-HLeu-Phe-OMe (2a,b) and R-CO-Met-Leu-β3-HPhe-OMe (3a,b) (a, R = tert-butyloxy-; b, R = H−), analogues of the potent chemoattractant For-Met-Leu-Phe-OMe, have been synthesized by classical solution methods and fully characterized. The activities of the new analogues as chemoattractants, superoxide anion producers and lysozyme releasers have been determined on human neutrophils. Whereas all of the three N-formyl derivatives are significantly less active than the parent tripeptide as chemoattractants, compound 1b has been found to be highly active as a superoxide anion producer and 3b as a lysozyme releaser. The results show that the replacement of the native Leu residue at the central position is, in each of the examined cases, the least favourable modification. The three N-Boc derivatives are, as expected, devoid of activity as agonists, but they are all good inhibitors of chemotaxis. Information on the solution conformation has been obtained by examining the involvement of the NH groups in intramolecular H-bonds using 1H NMR. The conformation of the N-Boc analogue 1a has also been determined in the crystal state by x-ray diffraction analysis. The molecule is extended at the β3-HMet residue (φ1 = −87°;θ1 = 172°;ψ1 = 126° ) and no intramolecular H-bond is present. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd.

X-Ray crystallography proves that alkali cations can act as conformational templates for 1,5-bridged calix[8]arenes 1 H 6 – 3 H 6 , folding their skeleton in a ‘tub-shaped’ conformation composed of four 3/4-cone clefts. This templation occurs even for neutral 1 H 6 to give a ( 1 H 6 Cs) + ·Cl − complex, where Cs + was found perfectly fitting inside the eight calix[8]arene oxygens cavity. Conventional ‘electrostatic’ coordination with O atoms occurs whereas cation-π interactions can be excluded.

1,2-dithiolanes (five-membered cyclic disulfides) represent an emerging class of heterocyclic compounds due to their relevant biological functions and specific chemical reactivity. However, despite the extensive research centered on lipoic acid and its analogues, only very few data are at the present available on peptides containing this ring system. Due to an interplay of conformational and electronic effects, connected with the size of the ring, the chemical reactivity of 1,2-dithiolanes is well distinct from that of linear and related cyclic disulfides, and represents the key structural feature on which the activity of relevant biomolecules, such as lipoic acid, is based. In the context of C-alpha tetrasubstituted aminoacids, we have prepared the new 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) residue and we have inserted it into the chemotactic peptide For-Met-Leu-Phe-OMe (fMLP-OMe), obtaining in this way the analog For-Met-Adt-Phe-OMe (fMAP-OMe). The biological activity of the Adt containing tripeptide was determined on human neutrophils and compared with that of the bioactive prototype fMLP-OMe. fMAP-OMe shows a lower potency in inducing directed migration (chemotaxis), but comparable activity in lysozyme release and superoxide anion production.

Two diastereomeric furan-2-carbonylamino-3-oxohexahydroindolizino[8,7-b]indole carboxylates, highly constrained analogues of endogenous pyroglutamyl tripeptide inhibitors of snake venom endopeptidases, have been prepared as potential inhibitors of adamalysin II and matrix metalloproteinases. They proved to be inactive against adamalysin II and weak inhibitors of gelatinase A, gelatinase B, stromelysin 1 and human neutrophyl collagenase. Evaluation of the mode of binding of the (2R,5S,11bR) isomer in the active site of adamalysin II suggests that the decrease of potency may be due to the reorientation of the acylamino chain in three of the heterocyclic nucleus, to a short contact at the entrance of the S′1 hydrophobic cleft and to the loss of flexibility of the tetracyclic nucleus in the P′1, P′2 region of the inhibitor, which prevents optimal arrangement in the S′1 specificity subsite.

Previously, fiber and crystal structural models were proposed for bile acid salt micellar aggregates and verified in aqueous solutions. Electromotive force (emf) measurements on sodium salts versus ionic strength, pH, and bile salt concentration provided micellar aggregate compositions that supported the models. Ionic strength was varied by adding tetramethylammonium chloride (TMACl), although tetramethylammonium (TMA+) and Na+ ions could interfere in the aggregate formation and structure. In this case emf results cannot be used for sodium salts. Tetramethylammonium (TMAGDC) and sodium glycodeoxycholate (NaGDC), which forms helical aggregates constituted by trimers, are studied to clarify this point. TMAGDC crystal structure is solved, and circular dichroism (CD), quasi-elastic light-scattering (QELS), electrolytic conductance, and dielectric measurements on TMAGDC and NaGDC aqueous solutions are compared for determining similarities and dissimilarities in their behavior. TMA+ and Na+ coordinations in TMA...

Two crystal structures of human neutrophil collagenase (HNC, MMP-8), one complexed with a primed- and the other with an unprimed-side inhibitor, were determined using synchrotron radiation at 100 K. Both inhibitors contain non-hydroxamate zinc-binding functions. The Pro-Leu-L-Trp(P)(OH)(2) occupies the unprimed region of the active site, furnishes new structural information regarding interaction between the catalytic zinc ion and the phosphonate group, and is the only example of occupation of the S(1) subsite of MMP-8 by the bulky tryptophan side chain. The (R)-2-(biphenyl-4-ylsulfonyl)-1,2,3, 4-tetrahydroisochinolin-3-carboxylic acid, a conformationally constrained D-Tic derivative, accommodates its biphenyl substituent into the deep primary specificity S(1)' subsite, inducing a widening of the entrance to this pocket; this modification of the protein, mainly consisting in a shift of the segment centered at Pro217, is observed for the first time in MMP-8 complexes. Cation-aromatic interactions can stabilize the formation of both complexes, and the beneficial effect of aromatic substituents in proximity of the catalytic zinc ion is discussed. The phosphonate group bound to either a primed- or unprimed-side inhibitor maintains the same relative position with respect to the catalytic zinc ion, suggesting that this binding function can be exploited for the design of combined inhibitors assembled to interact with both primed and unprimed regions of the active cleft.

The structures of crystals of rubidium glycocholate (monoclinic) and rubidium taurocholate (monoclinic and tetragonal) were solved by X-ray diffraction analysis. These structures, together with those of the sodium salts formerly determined, were used to infer models for the corresponding micellar aggregates in aqueous solutions. The crystal packings of the sodium and rubidium salts were characterized by similar structural units. These were bilayers, 21 helices, distorted 21 helices, and units with a two-fold rotation axis. On the other hand, circular dichroism spectra of the sodium and rubidium salts with bilirubin-IXα in aqueous solution indicated the formation of very similar interaction complexes and micellar aggregates. This hypothesis was supported by quasi-elastic light scattering measurements carried out on aqueous micellar solutions as a function of the ionic strength, concentration, and temperature. Low values of the apparent hydrodynamic radius, corresponding to oligomers of small size, were obt...

The synthesis and X-ray diffraction analysis of two dipeptide taste ligands have been carried out as part of our study of the molecular basis of taste. The compounds L-aspartyl-D-alpha-methylphenylalanine methyl ester [L-Asp-D-(alpha Me)Phe-OMe] and L-aspartyl-D-alanyl-2,2,5, 5-tetramethylcyclopentanyl ester [L-Asp-D-Ala-OTMCP] elicit bitter and sweet taste, respectively. The C-terminal residues of the two analogues adopt distinctly different conformations in the solid state. The aspartyl moiety assumes the same conformation found in other dipeptide taste ligands with the side-chain carboxylate and the amino groups forming a zwitterionic ring with a conformation defined by psi, chi 1 = 157.7 degrees, -61.5 degrees for L-Asp-D-Ala-OTMCP and 151.0 degrees, -68.8 degrees for L-Asp-D-(alpha Me)Phe-OMe. In the second residue, a left-handed helical conformation is observed for the (alpha Me)Phe residue of L-Asp-D-(alpha Me)Phe-OMe with phi 2 = 49.0 degrees and psi 2 = 47.9 degrees, while the Ala residue of L-Asp-D-Ala-OTMCP adopts a semi-extended conformation characterized by dihedral angles phi 2 = 62.8 degrees and psi 2 = -139.9 degrees. The solid-state structure of the bitter L-Asp-D-(alpha Me)Phe-OMe is extended: while the crystal structure of the sweet L-Asp-D-OTMCP roughly adopts the typical L-shaped structure shown by other sweeteners. The data of L-Asp-D-(alpha Me)Phe-OMe are compared with those of its diastereoisomer L-Asp-L-(alpha Me)Phe-OMe. Conformational analysis of the two taste ligands in solution by NMR and computer simulations agrees well with our model for sweet and bitter tastes.

Sodium glycocholate (NaGC) and taurocholate (NaTC) have been studied by means of X-ray and circular dichroism (CD) measurements, using bilirubin-IXα(BR) as probe molecule, together with potential-energy calculations. Helical models for the micellar aggregates of NaGC and NaTC were inferred from crystal structures solved by X-ray analysis. Since it is known that chiral molecules, micellar aggregates and macromolecules select preferentially or exclusively one of the two enantiomeric conformers of BR, CD spectra of BR in submicellar and micellar aqueous solutions of NaGC and NaTC were recorded as a function of pH and BR concentration in order to verify these helical models and the enantioselective ability of the bile salt monomers and micellar aggregates. Potential-energy calculations supported the CD experimental results and provided reasonable bile salt–BR interaction models. The behaviour of NaGC and NaTC is compared with that of sodium deoxycholate (NaDC), previously studied. The CD spectra of the bile salt–BR systems seem to allow characterisation of the typical structure of the bile salt micellar aggregates.

The title Δ z Leu containing N-formyltripeptide 2 , has been synthesized and found active in the superoxide production whereas inactive in the stimulation of human neutrophil migration. The X-ray crystallographic analysis reveals that 2 adopts a β-turn conformation stabilized by an intramolecular H-bond.