A putative bioactive conformation for the altered peptide ligand of myelin basic protein and inhibitor of experimental autoimmune encephalomyelitis [Arg91, Ala96] MBP87–99

[Arg(91), Ala(96)] MBP(87-99) is an altered peptide ligand (APL) of myelin basic protein (MBP), shown to actively inhibit experimental autoimmune encephalomyelitis (EAE), which is studied as a model of multiple sclerosis (MS). The APL has been rationally designed by substituting two of the critical residues for recognition by the T-cell receptor. A conformational analysis of the APL has been sought using a combination of 2D NOESY nuclear magnetic resonance (NMR) experiments and detailed molecular dynamics (MD) calculations, in order to comprehend the stereoelectronic requirements for antagonistic activity, and to propose a putative bioactive conformation based on spatial proximities of the native peptide in the crystal structure. The proposed structure presents backbone similarity with the native peptide especially at the N-terminus, which is important for major histocompatibility complex (MHC) binding. Primary (Val(87), Phe(90)) and secondary (Asn(92), Ile(93), Thr(95)) MHC anchors occupy the same region in space, whereas T-cell receptor (TCR) contacts (His(88), Phe(89)) have different orientation between the two structures. A possible explanation, thus, of the antagonistic activity of the APL is that it binds to MHC, preventing the binding of myelin epitopes, but it fails to activate the TCR and hence to trigger the immunologic response. NMR experiments coupled with theoretical calculations are found to be in agreement with X-ray crystallography data and open an avenue for the design and synthesis of novel peptide restricted analogues as well as peptide mimetics that rises as an ultimate goal.

Conformation and bioactivity. Design and discovery of novel antihypertensive drugs

Peptidomimitism is applied to the medicinal chemistry in order to synthesize drugs that devoid of the disadvantages of peptides. AT1 antagonists constitute a new generation of drugs for the treatment of hypertension designed and synthesized to mimic the C-terminal segment of Angiotensin II and to block its binding action on AT1 receptor. An effort was made to understand the molecular basis of hypertension by studying the conformational analysis of Ang II and its derivatives as well as the AT1 antagonists belonging to SARTANs class of molecules. Such studies offer the possibility to reveal the stereoelectronic factors responsible for bioactivity of AT1 antagonists and to design and synthesize new analogs. An example will be given which proves that drugs with better pharmacological and financial profiles may arise based on this rational design.

Conformational and biological studies for a pair of novel synthetic AT1 antagonists: stereoelectronic requirements for antihypertensive efficacy

One of the major systems which interferes with the disease of hypertension, is the Renin Angiotensin Aldosterone System (RAS). The octapeptide hormone angiotensin II is the active product of RAS which causes vasoconstriction when binds to the AT(1) receptor. In the last years, there has been a development of drugs which block the Angiotensin II from binding the AT(1) receptor and are called AT(1) antagonists. In an effort to comprehend their stereoelectronic features, a study has been initiated to compare the conformational properties of drugs already marketed for the treatment of hypertension and others which are designed and synthesized in our laboratory possessing structural characteristics necessary for antihypertensive activity. In this study, two synthetic non-peptide AT(1) antagonists, are structurally elucidated and their conformational properties and bioactivity are compared to the prototype and first approved drug of this category in the market; losartan (trade name: COZAAR).

Influence of chirality of the preceding acyl moiety on the cis/trans ratio of the proline peptide bond

We report that the cis/trans ratio of the proline peptide bond can be strongly influenced by the chirality of the acyl residue preceding proline. Acyl moieties derived from (2S)-2,6-dimethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazine-2-carboxylic acid (8) and (2R)-3-methoxy-2-methyl-2-(4-methyl-2-nitrophenoxy)-3-oxopropanoic acid (5) in acyl-Pro molecules influence isomerization of the proline peptide bond constraining the omega dihedral angle to the trans orientation. Structures of benzyl (2S)-1-([(2S)-2,6-dimethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl]carbonyl)-2-pyrrolidinecarboxylate (3) derived from 2D (1)H NMR conformational analysis and crystallographic data exhibit only the trans conformation of proline peptide bond. On the other hand the diastereomer 4, which contains an (R) acyl moiety, exhibits two sets of signals in (1)H NMR spectra. The signals were assigned to trans (72%) and cis (28%) conformers. Crystallographic analysis of 4 showed that only the cis conformation is present in the crystalline state. The (1)H NMR chemical shift pattern of three sets of signals observed in 2 was observed also in benzyl (2S)-1-[(2R/S)-3-methoxy-2-methyl-2-(4-methyl-2-nitrophenoxy)-3-oxopropanoyl]-2-pyrrolidinecarboxylate. (R)-Carboxylic acid 5, after coupling with (S)-ProOBn, yielded benzyl (2S)-1-[(2R)-3-methoxy-2-methyl-2-(4-methyl-2-nitrophenoxy)-3-oxopropanoyl]-2-pyrrolidinecarboxylate (6), which in DMSO-d(6) exhibited only the trans conformation of the proline peptide bond. These results suggest that in these particular cases acyl-Pro peptide bond isomerization is strongly influenced by the stereochemistry of the acyl residue preceding proline. (2S)-2,6-Dimethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazine-2-carboxylic acid (8) and (2R)-3-methoxy-2-methyl-2-(4-methyl-2-nitrophenoxy)-3-oxopropanoic acid (5) are promising chiral peptidomimetic building blocks that can be used as acyl moieties to force the proline peptide bond into the trans conformation in a variety of acyl-Pro molecules.

Design and structure-activity relationship of thrombin inhibitors with an azaphenylalanine scaffold: potency and selectivity enhancements via P2 optimization

Theoretical and structural studies followed by the directed synthesis and in vitro biological tests lead us to novel noncovalent thrombin pseudopeptide inhibitors. We have incorporated an azapeptide scaffold into the central part of the classical tripeptide D-Phe-Pro-Arg inhibitor structure thus eliminating one stereogenic center from the molecule. A series of compounds has been designed to optimize the occupancy of the S2 pocket of thrombin. Increased hydrophobicity at P2 provides an enhanced fit into this active site S2 pocket. In the present paper, we also report on the structure of these inhibitors in solution and conformational analysis of inhibitors in the active site in order to asses the consequences of the replacement of the central alpha-CH by a nitrogen functionality. In vitro biological testing of the designed inhibitors shows that elimination of R, S stereoisomerism and restriction of conformational freedom influences the binding of inhibitors in a favorable fashion.

Synthesis and study of a cyclic angiotensin II antagonist analogue reveals the role of pi*--pi* interactions in the C-terminal aromatic residue for agonist activity and its structure resemblance with AT(1) non-peptide antagonists

The novel amide linked Angiotensin II (ANG II) cyclic analogue cyclo(3, 5) -[Sar(1)-Lys(3)-Glu(5)-Ile(8)] ANG II (18) has been designed, synthesized and bioassayed in anesthetized rabbits. The constrained cyclic analogue with a lactam amide bridge linking a Lys-Glu pair at positions 3 and 5 and possessing Ile at position 8, was synthesized by solution procedure using the maximum protection strategy. This analogue was found to be inhibitor of Angiotensin II. NMR spectroscopy coupled with computational analysis showed clustering between the side chains of the key aminoacids Tyr(4)-His(6)-Ile(8) similar to that observed with ANG II. The obtained data show that only pi*--pi* interactions observed in ANG II or its superagonist Sar(1) [ANG II] are missing. Therefore, it can be concluded that these interactions are essential for agonist activity. Conformational analysis comparisons between AT(1) antagonists losartan, eprosartan and irbesartan with C-terminal segment of cyclic compound 18 revealed structural similarities.

Structure elucidation and conformational properties of a novel bioactive clerodane diterpene using a combination of high field NMR spectroscopy, computational analysis and X-ray diffraction

The structure of a novel CC clerodane type diterpenoid, namely (+)-19-acetoxy-cis-clerodan-3-ene-15-oic acid 1 was elucidated and its conformational properties were explored using a combination of high field NMR spectroscopy and computational analysis. The structural analysis provided results consistent with those obtained by a single X-ray diffraction study of its dicyclohexylammonium salt. The new clerodane type diterpene isolated in large quantities from Cistus monspeliensis L. leaves was found to exhibit significant antibacterial activity against Staphyloccoci (MIC50 = 0.085 mM) and therefore represents a promising lead compound. Interestingly the deacetylated derivative 2 of compound 1 was inactive.

Vancomycin: conformational consequences of the sugar substituent

High-resolution, three-dimensional structures of vancomycin and aglyco-vancomycin in DMSO were determined by nuclear magnetic resonance, metric matrix distance geometry, and molecular dynamics calculations. Conformational flexibility fast on the NMR time scale was examined by ensemble-based calculations which apply the experimentally derived restraints as an ensemble average. Two families of conformations of vancomycin, differing in the positioning of the vancosamine substituent, were observed. In contrast, the aglyco-vancomycin adopts only one conformation in solution. The conformations of vancomycin and the aglyco-vancomycin differ in the alignment of the amide protons which participate in the hydrogen-bonding network with the cell-wall precursor and orientation of the aromatic rings relative to the backbone. Therefore, the high-resolution structural characterization provides insight into a possible role of glycosylation on the activity of this important family of antibiotics.

Structural characterization of the molecular dimer of the peptide antibiotic vancomycin by distance geometry in four spatial dimensions

The conformation of a dimer of the peptide antibiotic vancomycin is developed from computer simulations based on experimental distance constraints derived from high-resolution NMR measurements. The conformation and topological array of the dimer are determined by a distance geometry based method using the molecules cast into four spatial dimensions. This method was imperative for the refinement of vancomycin given the entwining of the monomers (including hydrogen bonding and interactions between the aromatic ring systems) within the dimer. The development of the high-resolution structure of the monomer and then simple molecular modeling to create the dimer which fulfills all of the experimental observations was not possible. In contrast, the refinement protocol using the dimer cast into four spatial dimensions was able to quickly locate conformations in which both the intra- and intermolecular nuclear Overhauser effects were satisfied. These structures, once converted back to three dimensions, were further refined using standard molecular mechanics energy minimization. The structural characteristics of the dimer with respect to binding to the cell-wall precursor are described.

Glucose transporter of Escherichia coli: NMR characterization of the phosphocysteine form of the IIB(Glc) domain and its binding interface with the IIA(Glc) subunit

The transmembrane subunit of the glucose transporter, IICB(Glc), mediates vectorial transport with concomitant phosphorylation of glucose. Glucose phosphorylation proceeds through a cystein phosphate intermediate of the cytosolic IIB domain of IIC(Glc), which is phosphorylated by the IIA(Glc) subunit of the glucose transporter. Two- and three-dimensional NMR experiments were used to characterize the phosphorylation of the 10 kDa subclonal IIB domain and the complementary binding interfaces of [15N]IIB and [15N]IIA(Glc). The largest chemical shift perturbations and the only NOE differences accompanying IIB phosphorylation are confined to the active site residue Cys35, as well as Ile36, Thr37, Arg38, Leu39, and Arg40, which are all located in the turn between strands beta1 and beta2 and on beta2 itself. The significant increase of the amide cross-peak intensities of Ile36, Thr37, and Arg38 upon phosphorylation suggests that the conformational freedom of these groups becomes restrained, possibly due to hydrogen bonding to the oxygens of the bound phosphate and to interactions between the guanidinium group of Arg38 and the phosphoryl group. The residues of IIB which experience chemical shift perturbations upon binding of IIA are located on a protruding surface formed by residues of strands beta1, beta2, and beta4, the beta4/alpha3 loop, and residues from the first two turns of alpha3. The corresponding binding surface of the IIA(Glc) domain is comprised of residues on five adjacent beta-strands and two short helices surrounding the active site His90. The binding surface of IIA(Glc) for IIB coincides with the binding surface for HPr, the phosphoryl carrier protein by which IIA(Glc) is phosphorylated [Chen, Y., Reizer, J., Saier, M. H., Fairbrother, W. J., & Wright, P. E. (1993) Biochemistry 32, 32-37].

Solution structure of the IIB domain of the glucose transporter of Escherichia coli

The structure of the IIBGlc domain of the Escherichia coli transporter for glucose was determined by multidimensional heteronuclear NMR. The glucose transporter (IICBGlc) belongs to the bacterial phosphotransferase system. It mediates uptake with concomittant phosphorylation of glucose. The N-terminal IICGlc domain spans the membrane, the C-terminal IIBGlc domain (residues 386-477) contains the phosphorylation site, Cys421. The structure of the subclonal IIB domain was determined based on 927 conformational constraints, including 744 NOE derived upper bounds, 43 constraints of ranges of dihedral angles based on measurements of vicinal coupling constants, and 70 upper and lower bound constraints associated with 35 hydrogen bonds. The distance geometry interpretation of the NMR data is based on the previously published sequence-specific 1H, 15N, and 13C resonance assignments [Golic Grdadolnik et al. (1994) Eur. J. Biochem. 219, 945-952]. The sequence of the secondary structure elements of IIB is alpha 1 beta 1 beta 2 alpha 2 beta 3 beta 4 alpha 3. The basic fold consists of a split alpha/beta-sandwich composed of an antiparallel sheet with strand order beta 1 beta 2 beta 4 beta 3 and three alpha-helices superimposed onto one side of the sheet. The hydrophobic helix alpha 1 is packed against helices alpha 2, alpha 3, and the beta-sheet. The phosphorylation site (Cys421) is at the end of beta 1 on the solvent-exposed face of the sheet surrounded by Asp419, Thr423 Arg424, Arg426, and Gln456 which are invariant in 15 homologous IIB domains from other PTS transporters.

Comparison of the conformation of active and nonactive backbone cyclic analogs of substance P as a tool to elucidate features of the bioactive conformation: NMR and molecular dynamics in DMSO and water

The conformations of two backbone-cyclized substance P analogs as derived from 1H NMR and molecular dynamics simulations carried out in DMSO and water are described. The method of floating chiralities is used in the simulations to facilitate the diastereotopic assignment of methylene protons. One of the analogs, cyclo-[-(CH2)3-NH-CO-(CH2)4-Arg-Phe-Phe-N-]-CH2-CO-Leu-Met-NH2, is a highly active, selective agonist for the NK-receptor, while the other, cyclo[-(CH2)2-NH-CO-(CH2)2-Gly-Arg-Phe-Phe-N-]-CH2-CO-Leu-Met-NH2, is inactive. Both analogs contain cyclic ring systems of the same size, varying in only the number of amide linkages. From the conformational analysis, the lack of activity can be attributed to the introduction of too much constraint into the ring system. This has an effect on the topological array of the important residues Arg-Phe-Phe. The results presented here are compared with biologically active analogs previously examined. The differences between conformations of active and inactive compounds are used to develop insight into the conformational requirements for biological activity.

The glucose transporter of Escherichia coli. Assignment of the 1H, 13C and 15N resonances and identification of the secondary structure of the soluble IIB domain

The IICBGlc subunit of the Escherichia coli glucose transporter consists of two domains, the membrane-spanning IIC domain, and the hydrophilic IIB domain which contains the phosphorylation site (Cys421). A functional form of the IIB domain was over-expressed separately and isotopically labelled with 13C and 15N. A variety of 15N-edited and 13C, 15N triple-resonance NMR experiments yielded a nearly complete assignment of the 1H, 13C and 15N resonances. Based on the evaluation of conformationally sensitive parameters including NOE effects, scalar couplings and chemical shifts, the secondary structure of the IIB domain is presented. The protein is comprised of four beta-strands forming an antiparallel beta-sheet, two larger alpha-helices at the N- and C-termini and a smaller helical structure of residues 52-58.