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The JC polyomavirus (JCPyV) infects approximately 50% of the human population. In healthy individuals, the infection remains dormant and asymptomatic, but in immuno-suppressed patients, it can cause progressive multifocal leukoencephalopathy (PML), a potentially fatal demyelinating disease. Currently, there are no drugs against JCPyV infection nor for the treatment of PML. Here, we report the development of small-molecule inhibitors of JCPyV that target the initial interaction between the virus and host cell and thereby block viral entry. Utilizing a combination of computational and NMR-based screening techniques, we target the LSTc tetrasaccharide binding site within the VP1 pentameric coat protein of JCPyV. Four of the compounds from the screen effectively block viral infection in our in vitro assays using SVG-A cells. For the most potent compound, we used saturation transfer difference NMR to determine the mode of binding to purified pentamers of JCPyV VP1. Collectively, these results demonstrate the viability of this class of compounds for eventual development of JCPyV-antiviral therapeutics.

Cell-penetrating peptide (CPP) intracellular delivery of receptor signaling motifs provides an opportunity to regulate specific receptor tyrosine kinase signal transductions. We targeted tyrosine residues Y740 and Y751 of the PDGF receptor β (PDGFRβ) and Y1175 of the VEGF receptor 2 (VEGFR2). The Y740 and Y751 motifs activated ERK and Akt, while the Y1175 motif activated ERK. Targeting either Y740 or Y751 of the PDGFRβ in human pulmonary artery smooth muscle cells (HPASMC) effectively inhibited PDGF activation of ERK or Akt. Interfering with the Y751 region of the PDGFRβ proved more effective than targeting the Y740 region. The phosphorylation of Y751 of the CPP and the length and exact sequence of the mimicking peptide proved crucial. On the other hand, in human pulmonary artery endothelial cell phosphorylation of the VEGFR2 Y1175 CPP was not a determinant in blockage of ERK activation. Likewise, the length of the peptide mimic was not crucial with a very small sequence containing the Y1175 remaining effective. Physiologic proof of concept for the effectiveness of the CPP was confirmed by blockage of HPASMC migration in response to PDGF following culture injury. Thus targeted blockage of tyrosine kinase receptor signaling can be very effective.

We designed and characterized a soluble mimic of the parathyroid hormone (PTH) receptor (PTH1R) that incorporates the N-terminus and third extracellular loop of PTH1R, important for ligand binding. The engineered receptor (PTH1R-NE3) was conceived to enable easy production and the use of standard biochemical and biophysical assays for the screening of competitive antagonists of PTH. We show that PTH1R-NE3 is folded, thermodynamically stable and selectively binds PTH. We also demonstrate the utility of our mimic by identifying a small molecule that competes with PTH in our PTH1R-NE3-based fluorescence polarization assay. Antagonists to PTH1R, a transmembrane protein belonging to the class B G-protein coupled receptor family, may provide new therapeutic options for calcium metabolism diseases like humoral hypercalcemia of malignancy. Proteins 2014; 82:1370–1375. © 2013 Wiley Periodicals, Inc.

The parathyroid hormone, PTH, is responsible for calcium and phosphate ion homeostasis in the body. The first 34 amino acids of the peptide maintain the biological activity of the hormone and is currently marketed for calcium imbalance disorders. Although several methods for the production of recombinant PTH(1-34) have been reported, most involve the use of cleavage conditions that result in a modified peptide or unfavorable side products. Herein, we detail the recombinant production of (15) N-enriched human parathyroid hormone, (15) N PTH(1-34), generated via a plasmid vector that gives reasonable yield, low-cost protease cleavage (leaving the native N-terminal serine in its amino form), and purification by affinity and size exclusion chromatography. We characterize the product by multidimensional, heteronuclear NMR, circular dichroism, and LC/MS.

The dimerization of the G protein-coupled receptors for endothelin-1 (ET-1), endothelin A receptor (ETA) and endolethin B receptor (ETB), is well established. However, the signaling consequences of the homodimerization and heterodimerization of ETA and ETB is not well understood. Here, we demonstrate that peptides derived from the C-termini of these receptors regulate the signaling capacity of ET-1. The C-termini of the ETA and ETB receptors are believed to consist of three α-helices, which may serve as points of interaction between the receptors. The third α-helix in the C-terminus is of particular interest because of its amphipathic nature. In a cell line expressing only the ETA receptor, expression of residues Y430–S442, representing the third helix of the ETB C-terminus, leads to a dramatic increase in the signaling induced by ET-1. In contrast, in a cell line containing only ETB, Y430–S442 has an antagonistic effect, slightly reducing the ET-1 induced signal. Computational docking results suggest that the α-helical ETB-derived peptide binds to the second and third intracellular loops of the ETA receptor consistent with the alteration of its signaling capacity. Our results described here provide important insight into ETA/ETB receptor interactions and possibly a new approach to regulate specific G protein-coupled receptor signal transmission. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.

TAT (a 13-mer derived from the HIV-1 Tat protein)-linked cell-permeable peptides deliver plasma membrane impermeable cargos into the cell. We investigated the effect of a TAT-linked intracellular third loop of the endothelin-1 type B receptor on endothelin-1 activation of ERK. The effect of this peptide on ERK activation was determined in ETB receptor cDNA-transfected Chinese hamster ovary cells and in ETA- and ETB-expressing human pulmonary artery smooth muscle cells obtained from a normal and a bone morphogenetic protein-2 receptor, exon 1-8 deletion subject, with pulmonary hypertension. In the Chinese hamster ovary cells the peptide, at optimum 10 μm concentration, suppressed endothelin-1 activation. In the normal human pulmonary artery smooth muscle cells, the peptide marginally enhanced endothelin-1 activation of ERK. However, it markedly enhanced the endothelin-1 activation of ERK in the bone morphogenetic protein-2 receptor human pulmonary artery smooth muscle cells. While the effective concentration for endothelin-1 activation of ERK remained unchanged in the bone morphogenetic protein-2 receptor human pulmonary artery smooth muscle cells, the number of ETB receptors declined by 2/3. These data point to the intracellular third loop peptide as having variable receptor interactive effects with both signal repressive and enhancing capabilities. Peptides that can alter endothelin-1 signal capabilities are potentially important in the study and treatment of pulmonary hypertension.

Glucagon-like peptide-1 (GLP-1) receptor agonists for the treatment of type 2 diabetes are administered by daily injection because of short plasma half-lives, which result partly from the biochemical instability of these peptides. There is a medical need for GLP-1 analogues that can be administered less frequently for patient convenience.We synthesized a series of human GLP-1 (hGLP-1(7-36)NH(2) ) derivatives containing α-aminoisobutyric acid (Aib) substitutions, analysed their enzymatic stabilities and evaluated their secondary structures using circular dichroism (CD) and nuclear magnetic resonance (NMR).Plasma stability experiments showed that only the analogue containing Aib substitutions in both the N-terminus (position 8) and the C-terminus (position 35), [Aib⁸(,)³⁵]hGLP-1(7-36)NH₂ (BIM-51077), was fully resistant to enzymatic cleavage. Incubation with human plasma kallikrein or plasmin confirmed that the Aib substitution at position 35 prevented protease cleavage around this residue, which contributes to the significantly enhanced plasma stability and increased plasma half-life. CD revealed increased C-terminal α-helicity in Aib³⁵-substituted analogues compared with both hGLP-1(7-36)NH₂ and analogues containing only Aib⁸ substitutions. Based on NMR studies, the secondary structure of BIM-51077 is similar to hGLP-1(7-36)NH₂ with a slight increase in α-helicity in the C-terminus. Compared with hGLP-1(7-36)NH₂, BIM-51077 had similar binding affinity for the human GLP-1 receptor and activated this receptor with similar potency.We have discovered an Aib⁸(,)³⁵-substituted analogue of native hGLP-1(7-36)NH₂ (BIM-51077) that retains the structure of the native peptide, and has similar activity and enhanced stability. A sustained-release formulation of this molecule (taspoglutide) is in phase-3 clinical development.

A cell-penetrating peptide consisting of the second intracellular loop (IC2) of the angiotensin II (AngII) type-I receptor (AT1) linked to the HIV-transactivating regulatory protein (TAT) domain was used to identify the role of this motif In intracellular signal transduction. HEK-293 cells stably transfected with AT1R cDNA and primary cultures of human pulmonary artery smooth muscle cells expressing endogenous AT1 receptor were exposed to the cell-penetrating peptide construct, and the effect on angiotensin II signaling was determined. The AT1 IC2 peptide effectively inhibited AngII-stimulated phosphatidylinositol turnover and calcium influx. It also limited the activation of Akt/PKB as determined by an inhibition of phosphorylation of Akt at Ser473, and completely abolished the AngII-dependent activation of the transcriptional factor NFkappaB. In contrast, the AT1 IC2 peptide had no effect on AngII/AT1 receptor activation of ERK. These results illustrate the potential of using cell-penetrating peptides to both delineate receptor-mediated signal transduction and to selectively regulate G protein-coupled receptor signaling.

Recent research has implicated the C-terminus of G-protein coupled receptors in key events such as receptor activation and subsequent intracellular sorting, yet obtaining structural information of the entire C-tail has proven a formidable task. Here, a peptide corresponding to the full-length C-tail of the human CB1 receptor (residues 400-472) was expressed in E.coli and purified in a soluble form. Circular dichroism (CD) spectroscopy revealed that the peptide adopts an alpha-helical conformation in negatively charged and zwitterionic detergents (48-51% and 36-38%, respectively), whereas it exhibited the CD signature of unordered structure at low concentration in aqueous solution. Interestingly, 27% helicity was displayed at high peptide concentration suggesting that self-association induces helix formation in the absence of a membrane mimetic. NMR spectroscopy of the doubly labeled ((15)N- and (13)C-) C-terminus in dodecylphosphocholine (DPC) identified two amphipathic alpha-helical domains. The first domain, S401-F412, corresponds to the helix 8 common to G protein-coupled receptors while the second domain, A440-M461, is a newly identified structural motif in the distal region of the carboxyl-terminus of the receptor. Molecular modeling of the C-tail in DPC indicates that both helices lie parallel to the plane of the membrane with their hydrophobic and hydrophilic faces poised for critical interactions.

Interaction of ligands with their specific receptors is accompanied by conformational shifts culminating in receptor activation and expression of hormonal activity. Using an engineered disulfide bond formation strategy, we characterized the relative conformational changes taking place within the PTH type 1 receptor (PTHR1) at the interface of transmembrane (TM)5 and TM6 on binding the PTH agonist, PTH(1-34), compared with the antagonist PTH(7-34). Cysteines were singly incorporated into a portion of the extracellular-facing region of TM5 (365–370), while simultaneously a second cysteine was introduced at position 420, 423, or 425 at the extracellular end of TM6, leading to a total of 18 double cysteine-containing PTHR1 mutants. All mutants, except P366C/V423C and P366C/M425C, were expressed in the cell membrane preparations. In the presence of agonist, H420C and M425C in TM6 formed disulfide bonds with all and with most, respectively, of the substituted cysteines incorporated in TM5. In contrast to the conformational shift induced (or stabilized) by agonist in activating the receptor, antagonist binding produced no detectable change from the basal (inactive) conformation of PTHR1. Our studies provide physicochemical evidence that the extracellular-facing ligand binding regions of receptor, TM5 and TM6, are dynamic and move relative to each other on ligand binding. The distinct differences in receptor conformation induced (or stabilized) by agonist PTH(1-34) compared with antagonist PTH(7-34) begin to provide insight into the early events in and mechanism of PTHR1 activation.

Methods to introduce specific secondary structural elements into peptides and proteins are vital for the rational design of peptide and non-peptide drug candidates as well as in the de novo design of proteins. Here the incorporation of a disulfide linkage between cysteine residues spaced three amino acids apart (i, i + 3) as a method to induce helicity is examined. Two dodecamer peptides, A-V-S-E-C-Q-L-C-H-D-K-G-NH2, differing in the chirality of the cysteine at the fifth position (the i position), have been synthesized and conformationally studied both in the linear and cyclized form. This peptide sequence, derived from the N-terminal sequence of parathyroid hormone related protein, does not form helices, even as part of the 1-34 fully active domain of the protein. The four analogs (two cyclic and two linear) were analyzed both in aqueous solution and in the presence of sodium dodecyl sulfate micelles. In aqueous solution the linear peptides display no evidence for secondary structure, while the cyclization induces a turn centered about the cysteine residues. In the presence of micelles the linear form of the peptides adopts bent conformations, containing turns, but results from both NMR and CD provide no evidence of helices. The oxidized L,L-peptide in the micellar solution does not present a well defined conformation, although the presence of one helical turn is evident. The cyclic D,L analog adopts a helical structure (not an alpha-helix) extending from residue 2 to 9, with non-standard phi, psi values caused by the presence of the D-amino acid. These results clearly illustrate that the ability of D-Cys(i), Cys(i + 3) cyclization to initiate helix formation depends greatly on the solvent used. Therefore, any drug-design principle utilizing this modification for helix nucleation must keep the environment in which the peptide is biologically active in mind.

As part of a program to study the structure-activity relationship of peptide opioids we report the synthesis, conformational characterization and biological activity of four analogs related to morphiceptin in which the proline at position two has been substituted with 2-aminocyclopentane carboxylic acid (beta Ae5c). The beta Ac5c residue is a beta amino acid with two chiral centers resulting in four possible configurations; two configurational cis (R,S and S,R) and two configurational trans (R,R and S,S) forms. Utilizing high resolution n.m.r. at 500 MHz and computer simulations with NOE restraints the chirality of the beta Ac5c residues are assigned. The analog containing the R,S-beta Ac5c is active at both the mu and delta-opioid receptors, with a slight preference for the mu-receptor. The (S,R), (S,S), and (R,R) analogs show minimal activity at the mu-receptor and are inactive at the delta-receptor. A comparison of the findings from the conformational analysis and biological assays lends insight into the structure-activity relationship of this important peptide opiate.

As a continuation of our program to study structure-activity relationships of opiate peptides, we report the syntheses and biological activities of a series of 14-membered cyclic dermorphin analogues closely related to enkephalin analogue Tyr-c[D-A2bu-Gly-Phe-Leu] incorporating a phenylalanine at the third position in place of glycine. In addition to two parent dermorphin analogues Tyr-c[D-A2bu-Phe-Phe-(L and D)-Leu], four stereoisomeric retro-inverso modified analogues Tyr-c[D-A2bu-Phe-gPhe-(S and R)-mLeu] with a reversed amide bond between residues four and five, and Tyr-c[D-Glu-Phe-gPhe-(L and D)-rLeu] with two reversed amide bonds between residues four and five, and between residue five and the side chain of residue two have been synthesized. The results from the guinea pig ileum (GPI) and mouse vas deferens (MVD) assays show that all analogues are superactive at either one or both opiate receptors and in general display higher activities as compared to the corresponding enkephalin analogues with a glycine at the third position. Results from the in vitro biological assays and conformational analysis using 1H-NMR spectroscopy (adjoining paper) will provide useful information to understand the role of the Phe3 aromatic side chain in dermorphin, and that of the Phe4 aromatic side chain in enkephalin, on opiate activity since these cyclic dermorphin analogues contain two Phe residues at both the third and fourth positions.

Photoaffinity crosslinking has yielded important insights in the study of G protein-coupled receptors and the mode of ligand binding. The most widely used photolabile moiety is p-benzoylphenylalanine largely because of its reportedly high site specificity, reduced reactivity to water and light, photokinetics, and ease of incorporation into peptide ligands during synthesis. However, in the course of our studies directed at characterizing the binding of parathyroid hormone to its cognate G protein-coupled receptor, we find that inherent properties of p-benzoylphenylalanine, such as its size and conformational flexibility, limit the resulting resolution of the ligand–receptor structure. Here, we examine and define these limits.

Photoaffinity crosslinking has been utilized to probe the nature of the ligand–receptor interface for a number of G protein-coupled receptor systems. Often the photoreactive benzophenone moiety incorporated in the ligand is found to react with a methionine in the receptor. We introduced methionines one-at-a-time into the region 163–176 of the parathyroid hormone receptor, and find that crosslinking occurs to the side-chain of methionine over a range of 11 amino acids. We call this the “Magnet Effect” of methionine. Hence, crosslinking contact points can be significantly shifted by the presence of methionine in a receptor domain.

The Na(+)/H(+) exchanger regulatory factor-1 (NHERF1) is a molecular scaffold important for the signaling of the G-protein coupled receptor for the parathyroid hormone (PTH1R). The two PDZ (PSD-95, Discs-large, ZO1) domains of NHERF1 through association with the C-termini of PTH1R and phospholipase C enhance the signaling pathway associated with PTH. To examine these interactions, we have produced the individual PDZ1 and PDZ2 domains as well as the tandem PDZ1-PDZ2 domains (PDZ12) of NHERF1 and have characterized the binding affinities of the C-terminal motifs of PTH1R and PLCbeta using fluorescence anisotropy. Circular dichroism indicates that the PDZ1 and PDZ2 are properly folded. Based on fluorescence anisotropy we find that the C-terminus of PTH1R, containing ETVM, has similar affinities (approximately 10 microm) for both PDZ1 and PDZ2. The PTH1R displayed reduced binding affinity for the tandem PDZ12 (16 microm) compared with the individual domains or a solution of equal molar concentrations of PDZ1 and PDZ2 (5.8 microm), suggesting negative cooperativity between the PDZ domains or intervening region. The C-termini of PLCbeta (both beta1 and beta2 isozymes were examined, containing DTPL and ESRL, respectively) displayed a diminished affinity for PDZ2 (approximately 30 microm) over that of PDZ1 (approximately 8 microm). Finally, we demonstrate trans PDZ1-PDZ2 association that is enhanced in the presence of the C-terminus of PTH1R or PLCbeta, suggesting oligomerization of NHERF as a mode for enhancing the signaling associated with PTH.

Bradykinin (BK) is a potent short-lived effector belonging to a class of peptides known as kinins. It participates in inflammatory and vascular regulation and processes including angioedema, tissue permeability, vascular dilation, and smooth muscle contraction. BK exerts its biological effects through the activation of the bradykinin B2 receptor (BKB2R) which is G-protein-coupled and is generally constitutively expressed. Upon binding, the receptor is activated and transduces signal cascades which have become paradigms for the actions of the Galphai and Galphaq G-protein subunits. Following activation the receptor is then desensitized, endocytosed, and resensitized. The bradykinin B1 (BKB1R) is a closely related receptor. It is activated by desArg(10)-kallidin or desArg(9)-BK, metabolites of kallidin and BK, respectively. This receptor is induced following tissue injury or after treatment with bacterial endotoxins such as lipopolysacharide or cytokines such as interleukin-1 or tumor necrosis factor-alpha. In this review we will summarize the BKB2R and BKB1R mediated signal transduction pathways. We will then emphasize the relevance of key residues and domains of the intracellular regions of the BKB2R as they relate to modulating its function (signal transduction) and self-maintenance (desensitization, endocytosis, and resensitization). We will examine the features of the BKB1R gene promoter and its mRNA as these operate in the expression and self-maintenance of this inducible receptor. This communication will not cover areas discussed in earlier reviews pertaining to the actions of peptide analogs. For these we refer you to earlier reviews (Regoli and Barabé, 1980, Pharmacol Rev 32:1-46; Regoli et al., 1990, J Cardiovasc Pharmacol 15(Suppl 6):S30-S38; Regoli et al., 1993, Can J Physiol Pharmacol 71:556-557; Marceau, 1995, Immunopharmacology 30:1-26; Regoli et al., 1998, Eur J Pharmacol 348:1-10).

Structurally constraint dipeptidomimetics represent an important class of conformationally rigid dipeptide surrogates and molecular scaffolds, which are frequently employed in peptide-based structure-activity relationships (SAR) and construction of combinatorial libraries. We report on the design of an improved and general synthetic procedure to prepare synthons related to the trisubstituted 1,2,5-hexahydro-3-one-1H-1,4-diazepines [DAP(Xxx)(alpha7)] (DAP: 1,2,5-hexahydro-3-one-1H-1,4-diazepine; DAP(Xxx)(alpha7): the homologous series of DAP in which alpha refers to the location of the chiral carbon in the i(th) amino acid, Xxx represents the three letter notation for the i-1 amino acids, and 7 denotes the number of atoms in the ring) and their higher homologs [DAP(Xxx)(alphaN)] [Xxx = Phe, Asp(beta-OcHex) (cHex: cyclohexyl), and Arg(N(G)-Tos] (Tos: p-toluenesulfonyl); N = 8-10]. These dipetidomimetic structures are generated by reductive alkylation-mediated Calpha(i)-to-N(i-1) bridging between a Calpha (i)-(CH(2))(i-1)(n)-COSEt (n = 1-4) and H(2)N-C(i-1)HR-CO(2)Fm (Fm: 9-fluorenylmethyl) followed by H(2)N(i)-to-C(i-1)-CO(2)H lactam formation. We also describe the preparation of blocked N-Ac-[DAP(Phe)(alphaN)]-CONMe(2) (N = 8-10), which serve as model systems for detailed conformational analysis reported in the accompanying article.

A series of dipeptidomimetics derived from C(alpha)(i)-to-N(i-1) side chain-to-backbone amide cyclization of adjacent amino acids are structurally characterized. The resulting ring systems are either 1,2,5-trisubstituted-3-oxo-1,4-diazepine (DAP) structurally related to benzodiazepines, commonly used in drug candidates and therapeutic agents, or higher homologs of it. Here, we examine the structural consequences of enlarging the ring size from seven members to eight-, nine-, and ten-membered rings. The structural features determined by high-resolution NMR methods, relying largely on homo- and heteronuclear coupling constants, indicate that variation of the ring leads to alternative conformations and topological orientations of the attached chemical moieties or functional groups. Controlling the topological display of the ring substituents required for biological action, using a molecular scaffold made up entirely of functional groups found in peptides, should facilitate the rational, stepwise transformation of peptide lead candidate into a nonpeptidic drug candidate.

The technical difficulties associated with the structure determination of membrane proteins have limited the structural information available for the ligand binding to G-protein coupled receptors (GPCRs). Here, we describe a reductionist approach to GPCR structure determination in which the extracellular domains of the receptor are examined by high-resolution NMR in the presence of a membrane mimetic. The resulting structural features are then incorporated into a molecular model of the receptor, utilizing the x-ray structure of rhodopsin to generate the topological orientation of the transmembrane helices. The results of our study of the neurokinin-1 receptor (NK-1R) and its interactions with substance P (SP) are detailed here. The structure of the N-terminus, NK-1R(1-39), and of the third extracellular loop, NK-1R(264-290), in the presence of dodecylphosphocholine micelles is described. Our findings provide a structural basis for the interpretation of the results from other methods including mutagenesis, fluorescence, and photoaffinity labeling experiments, resulting in an experimentally based, high-resolution model of SP binding to NK-1R.

The conformational features of both free and Ca2+-complexed cyclo[Pro-Phe-Phe-Ala-Xaa]2 (with Xaa=Glu(OtBu), Lys(ClZ), Leu, and Ala) in solution have been determined by NMR spectroscopy and extensive distance–geometry calculations. The decapeptides are conformationally homogeneous in solution and show common structural features in their free and complexed forms. The structures of the free form contain only trans peptide bonds and are topologically similar to the structure of gramicidin-S, folded up in two antiparallel extended structures, stabilized by interstrand hydrogen bonds, and closed at both ends by two β-turns. In contrast, the Ca2+-complexed peptides present two cis peptide bonds and are generally similar to those observed for the metal-complexed forms of antamanide and related analogues, folded into a saddle shape with two β-turns. The Glu(OtBu)-, Leu-, and Lys(ClZ)-containing peptides examined here maintain the biological activity of the cyclolinopeptide A in their ability to competitively inhibit cholate uptake. The natural antamanide and cyclolinopeptide A are both able to inhibit the uptake of bile salts into hepatocytes. They share the same postulated active sequence Pro-Phe-Phe. Based on our structural results, we conclude that the ability to adopt a global conformation, characterized by a clear amphipathic separation of hydrophobic and hydrophilic surfaces, is an important feature for the functioning of this class of peptides.

G-protein-coupled receptors (GPCRs) allow cells to respond to calcium, hormones, and neurotransmitters. Not surprisingly, they currently make up the largest family of validated drug targets. Rational drug design for molecular regulators targeting GPCRs has been limited to theoretical-based computational approaches. X-ray crystallography of intact GPCRs has provided the topological orientation of the seven transmembrane helices, but limited structural information of the extracellular and intracellular loops and protein termini. In this review we detail an NMR-based approach which provides the high-resolution structural features on the extracellular domains of GPCRs and the ligand/receptor complexes formed upon titration of the peptide hormone. The results provide important contact points and a high-resolution description of the ligand/receptor interactions, which may be useful for the rational design of therapeutic agents targeting GPCRs. Recent results from our investigation of the cholecystokinin peptide hormone system are used to highlight this approach.

The conformational features of Pam–Lys0–Arg1–Pro2–Pro3–Gly4–Phe5–Ser6–Pro7–Phe8–Arg9–OH (PKD) and Pam–Gly−1–Lys0–Arg1–Pro2–Pro3–Gly4–Phe5–Ser6–Pro7–Phe8–Arg9–OH (PGKD), the Pam–Lys and Pam–Gly–Lys analogues of bradykinin, have been determined by high-resolution NMR in a zwitterionic lipoid environment. Radical-induced relaxation of the 1H NMR signals was used to probe the topological orientation of the peptides with respect to the zwitterionic lipid interface. The radical-induced relaxation and molecular dynamics (MD) data indicated that the palmitic acid and N-terminal amino acid residues embed into the micelles, while the rest of the polypeptide chain is closely associated with the water-micelle interface. Throughout the entire nuclear Overhauser effect restrained MD simulation, a nonideal type I β-turn was observed in the C-terminus of PKD between residues 6 and 9, and a γ-turn was observed in the C-terminus of PGKD between residues 6 and 7. Therefore, the additional glycine has a dramatic effect on the structural preferences of the biologically important C-terminus, an effect brought about by the interaction with the lipid environment. These structural features are correlated to the biological activity at the bradykinin B2 receptor. © 2001 John Wiley & Sons, Inc. Biopolymers 58: 511–520, 2001

The structural characterization of peptide hormones and their interaction with G-protein (guanine nucleotide-binding regulatory protein) coupled receptors by high-resolution nmr is described. The general approaches utilized can be categorized into three different classes based on their target: the ligand, the receptor, and the ligand/receptor complex. Examples of these different approaches, aimed at facilitating the rational design of peptides and peptidomimetics with improved pharmacological profiles, based on work carried out in our own laboratory, are given. In the ligand-based approach, the high-resolution structures of bradykinin analogues allowing for the development of a structure–activity relationship for activation of the B1 receptor are described. Studies targeting the receptor are to a large extent theoretical, based on computational molecular modeling. However, experimentally based structural features provided by high-resolution nmr can be used to great advantage, providing insight into the mechanism of receptor function, as illustrated here with results from parathyroid hormone. A similar combination of theoretical methods, supplemented by high-resolution structures from nmr has been utilized to probe the formation and stabilization of the ligand/receptor complex both for parathyroid hormone and cholecystokinin. In each of these three approaches, the importance of well-designed peptide mimetics and accurate structural analysis by high-resolution nmr, will be highlighted. © 1999 John Wiley & Sons, Inc. Biopoly 51: 208–220, 1999

The structure and dynamics of the ionophoric antibiotic monensin in the presence of micelles have been determined. The conformation of monensin was derived from 50 nuclear Overhauser enhancement (NOE) derived distance restraints and metric-matrix based distance geometry calculations. The conformation was further refined with extensive NOE restrained molecular dynamics simulations carried out in a biphasic simulation cell. From the addition of doxylstearate and monitoring of the induced relaxation of the nmr signals, the relative topological orientation of the molecule within the micelle was ascertained. The results indicate two dihedral angles that act as hinge regions allowing the molecule to adopt a wide range of conformations. Considering the biological activity of monensin, i.e., the capture and transport of cations across cell membranes, an open and closed form of monensin have been postulated. The identification of these hinge regions, which are only observed in the membrane-like environment of the detergent micelles, provides insight into the mechanism of action and can serve as targets for modification to alter the biological profile of monensin.

The conformation of the natural peptide threonine6 (Thr6)-bradykinin, Arg1-Pro2-Pro3-Gly4-Phe5-Thr6-Pro7-Phe8-Arg9, was investigated in DMSO by nmr spectroscopy and computer simulations. The structural analysis of the Thr6-peptide is made particularly interesting by the fact that despite the high sequence homology with native bradykinin (only one conservative substitution: Ser6/Thr6) there is a marked and significant difference in the biological profiles of the two peptides. The nmr spectra indicate a relatively flexible structure with the presence of an N-terminal turn. Standard distance geometry calculations failed to produce structures in accord with the experimental observations; the resulting structures are indeed too rigid and conformationally restricted for the nmr data. The results of ensemble calculations reveal conformational changes occurring rapidly on the nmr time scale and allow for the establishment of a series of disordered conformations, prevalently extended with a partially populated turn in residues 2–5, which when considered together, as an average, fulfill the experimental restraints. The structural characterization of (Thr6)-bradykinin supports the hypothesis of the significant role of the residue at position 6 on both conformation as well as biological activities and suggests a N-terminal turn as a possible bioactive conformation. © 1997 John Wiley & Sons, Inc. Biopoly 40: 561–569, 1996

The third-cytoplasmic loop of the G-protein coupled receptor responsible for the activity of parathyroid hormone and parathyroid hormone-related protein has been structurally characterized in aqueous solution in the presence of sodium dodecylsulfate and dodecylphosphocholine micelles. The high-resolution conformation of the 29-amino acid peptide containing the sequence of the cytoplasmic loop was obtained by CD and nmr. The structure was refined using a two-step distance geometry based method that first includes the removal of all side chains to quickly locate the globular fold of the peptide. After a simulated annealing protocol, the side chains are added in a random fashion. The resulting conformation was further refined with nuclear Overhauser enhancement restrained molecular dynamics using a two-phase simulation cell consisting of carbon tetrachloride and water as a mimetic of the biphasic, hydrophobic/hydrophilic character of the micelles in which the experimental measurements were carried out. The topological orientation of the cycloplasmic loop within the micelle was determined by addition of 5-doxylstearate and monitoring the decrease of nmr signal intensities from the radical-induced relaxation. The conformation and relative orientation of the peptide provided insight into the mechanism by which the cytoplasmic portion of the receptor activates the heterotrimeric, guanine nucleotide-binding regulatory protein, one of the first steps in signal transduction. © 1997 John Wiley & Sons, Inc. Biopoly 40: 653–666, 1996

Ensemble calculations employing restraints developed from 1H-nmr were used to examine the conformational states of the two microcystins LR and LY. Despite the fast “flip-flop” dynamics about the N-methyl-dehydroalanine residue and adjacent residues, the main conformational characteristics of the cyclic heptapeptides consist of a compact ring formed by five of the seven amino acid residues with expulsion of a dipeptide portion out of the plane and the unnatural C20 β-amino acid (2S. 3S. 8S, 9S)-3-amino-9-methoxy-2, 6, 8-trimethyl-10-phenyldeca-4. 6-dienoic acid pointing upward from the ring. This structure of microcystin LR shows high degrees of similarity with the energy-minimized structure of nodularin, a cyclic pentapeptide of identical inhibitory potency against protein phosphatases 1 and 2A. Comparison of these structures with those of the less toxic LY variant and with the structurally unrelated okadaic acid, known as potent inhibitor of the protein phosphatases 1 and 2A, allowed us to propose a rational binding mode of this structural diverse set of natural inhibitors. © 1995 John Wiley & Sons, Inc.

The conformation of the antibiotic ureido-balhimycin has been investigated by proton nmr and refined with computer simulations. The dimeric structure cj ureido-balhimycin was established by unambiguous identification of 6 nuclear Overhauser effects (NOEs) as intermonomeric, out of the total of 186 NOEs observed. Via distance geometry calculations the antiparallel orientation of the two monomers was demonstrated. Further refinement by molecular dynamics simulations provided the essential hydrogen bonds and aromatic interactions responsible for interfacial stabilization. The computational protocol illustrated here (distance geometry to define the coarse topology and molecular dynamics for refinement) should find general applicability in the study of homodimers. © 1995 John Wiley & Sons, Inc.

Die skalaren Kopplungskonstanten stehen seit ihrer Entdeckung in den fruhen funfziger Jahren im Zentrum des Interesses der NMR-Spektroskopiker. Ihre Bedeutung fur die Strukturaufklarung mit Hilfe der NMR-Spektroskopie beruht auf der Erkenntnis, das die Grose einer Kopplungskonstante mit der Molekulkonformation in einem einfachen Zusammenhang steht. Fur viele Substanzklassen stehen heute parametrisierte Karplus-Gleichungen zur Verfugung, die die Abhangigkeit der vicinalen (d.h. Dreibindungs-) Kopplungskonstanten vom Diederwinkel bezuglich der zentralen Bindung charakterisieren. Neben der Verwendung von Proton-Proton-Abstanden aus NOE-Experimenten ist daher der Einsatz von Kopplungskonstanten in der modernen Konformationsanalyse heute nicht mehr wegzudenken. Mit steigender Molekulgrose der zu untersuchenden Substanzen werden jedoch immer trickreichere Experimente notwendig, um die storenden Einflusse von Uberlagerungen und wachsender Breite der Signale auszuschalten. Eine grose Zahl experimenteller Techniken zur Bestimmung von Kopplungskonstanten wurde bis heute entwickelt, wobei je nach Problemstellung die richtige Methode sorgfaltig ausgewahlt werden mus, damit sich die Kopplungskonstanten moglichst exakt ermitteln lassen und dabei die Meszeit effizient genutzt wird. Auch in der Computer-gestutzten Strukturbestimmung konnen Kopplungskonstanten heute – wie Abstande aus NOE-Daten bereits seit langerem – verwendet werden. Dadurch wird nicht nur die Qualitat der berechneten Strukturen verbessert, sondern es konnen auch Molekuleigenschaften wie die interne Dynamik besser beschrieben werden. Dieser Artikel soll eine Ubersicht uber die heute existierenden Techniken liefern und damit auch dem Nichtexperten als Entscheidungshilfe fur die richtige Wahl des Experiments dienen. Daneben wird das Verwenden von Kopplungskonstanten in Computersimulationen diskutiert.

The cyclic octapeptide cyclo(-Pro-Pro-Tyr-Val-ProLeu-Ile-Ile-) (1), isolated from the Hymeniacidon sponge, was synthesized and examined conformationally using NMR and molecular-dynamics simulations. Most structural parameters of synthetic 1 are in accord with those reported for the isolated material. Our study indicates some small but significant differences in the assignment of the 1H- and 13C-NMR resonances from those of the natural material. The Conformation was determind in both CHCl3 and DMSO using 1H-NMR and molecular-dynamics simulations. Both NOE's and coupling constants were used as experimental restraints during the simulations which utilized explicitly the same solvent as in the NMR study. The differences in the interaction of the solvent with 1 were examined, providing insight into the observed differenced in conformation. The dominant conformation contains a sVIa turn about Ile8-Tyr3 including a Pro1-Pro2cis-peptide bond and a sI or sII turn about Val4-Ile7 in CHCl3 and DMSO, respectively.

The potent immunosuppressant drug FK506 (2) has been examined by 1H- and 13C-NMR spectroscopy and NOE-restrained molecular dynamics to elucidate the conformation in solution. A combination of two- and three-dimensional NMR techniques was used to completely assign the 1H- and 13C-NMR chemical shifts of the two configurational isomers resulting from the cis-trans isomerization about the single amide bond. Hetero- and homonuclear coupling constants were measured to assign the diastereotopic methylene protons at C(16), C(18), and C(23). Intramolecular HH distances were defined from NOESY spectra recorded at −30° in CDCl3 and used as constraints in molecular-dynamics simulations. The conformational preferences of 2 in solution are discussed in light of the constitutional features recently proposed to be necessary for binding and activity.

In this article a few methods or modifications proven to be useful in the conformational examination of peptides and related molecules by molecular dynamics are illustrated. The first is the explicit use of organic solvents in the simulations. For many cases such solvents are appropriate since the nmr measurements (or other experimental observations) were carried out in the same solvent. Here, the use of dimethylsulfoxide and chloroform in molecular dynamics is described, with some advantages of the use of these solvents highlighted. A constant allowing for the scaling of the nonbonded interactions of the force field, an idea previously employed in distance geometry and simulated annealing, has been implemented. The usefulness of this method is that when the nonbonded term is turned to zero, atoms can pass through each other, while the connectivity of the molecule is maintained. It will be shown that such simulations, if a sufficient driving force is present (i.e., nuclear Overhauser effects restraints), can produce the correct stereoconfiguration (i.e., chiral center) as well as configurational isomer (i.e., cis/trans isomers). Lastly, a penalty term for coupling constants directly related to the Karplus curve has been plemented into the potential energy force field. The advantages of this method over the commonly used dihedral angle restraining are discussed. In particular, it is shown that with more than one coupling constant about a dihedral angle a great reduction of the allowed conformational space is obtained. © 1993 John Wiley & Sons, Inc.

The parathyroid hormone (PTH) plays a vital role in the homeostasis of calcium within the blood stream. Given its unique ability to increase bone density, an understanding of the molecular mechanism by which the hormone is recognized and binds to its receptor should provide targets for the development of PTH-based, anabolic agents for the treatment of osteoporosis. Parathyroid hormone related protein (PTHrP), a genetically and structurally distinct hormone which displays similar binding and activation profiles as PTH, has greatly facilitated the effort to establish a structure-biological function relationship by allowing for direct comparisons. In an analogous manner, the presence of two receptors, PTH/PTHrP (PTH1) and PTH2, which differ in their ligand selectivity (PTH2 is activated by PTH, not PTHrP) has provided a unique vehicle for probing the structural motifs of the receptor required for ligand recognition and binding. Recent photo-affinity cross-linking studies of PTH and PTHrP binding to PTH1 have produced direct points of contact between the ligand and receptor. Here, we review each of the components involved in this important hormone system, with particular emphasis on the structural features of each: the ligands (PTH and PTHrP), the receptors (PTH1 and PTH2), and the interaction between ligand and receptor. Although the current understanding of the molecular mechanism of ligand binding and receptor activation does not allow for the rational design of drug candidates, and indeed contains much conjecture, significant strides have been made towards this end.

G-protein-coupled receptors (GPCRs) allow cells to respond to calcium, hormones, and neurotransmitters. Not surprisingly, they currently make up the largest family of validated drug targets. Rational drug design for molecular regulators targeting GPCRs has been limited to theoretical-based computational approaches. X-ray crystallography of intact GPCRs has provided the topological orientation of the seven transmembrane helices, but limited structural information of the extracellular and intracellular loops and protein termini. In this review we detail an NMR-based approach which provides the high-resolution structural features on the extracellular domains of GPCRs and the ligand/receptor complexes formed upon titration of the peptide hormone. The results provide important contact points and a high-resolution description of the ligand/receptor interactions, which may be useful for the rational design of therapeutic agents targeting GPCRs. Recent results from our investigation of the cholecystokinin peptide hormone system are used to highlight this approach.

The conformational features of both free and Ca2+-complexed cyclo[Pro-Phe-Phe-Ala-Xaa]2 (with Xaa=Glu(OtBu), Lys(ClZ), Leu, and Ala) in solution have been determined by NMR spectroscopy and extensive distance–geometry calculations. The decapeptides are conformationally homogeneous in solution and show common structural features in their free and complexed forms. The structures of the free form contain only trans peptide bonds and are topologically similar to the structure of gramicidin-S, folded up in two antiparallel extended structures, stabilized by interstrand hydrogen bonds, and closed at both ends by two β-turns. In contrast, the Ca2+-complexed peptides present two cis peptide bonds and are generally similar to those observed for the metal-complexed forms of antamanide and related analogues, folded into a saddle shape with two β-turns. The Glu(OtBu)-, Leu-, and Lys(ClZ)-containing peptides examined here maintain the biological activity of the cyclolinopeptide A in their ability to competitively inhibit cholate uptake. The natural antamanide and cyclolinopeptide A are both able to inhibit the uptake of bile salts into hepatocytes. They share the same postulated active sequence Pro-Phe-Phe. Based on our structural results, we conclude that the ability to adopt a global conformation, characterized by a clear amphipathic separation of hydrophobic and hydrophilic surfaces, is an important feature for the functioning of this class of peptides.

A penalty function for scalar coupling constants has been applied in molecular dynamics simulations as an experimental constraint. The function is based on the difference between the coupling constant calculated from the dihedral angle and the experimentally measured coupling constant. The method is illustrated on a model cyclic pentapeptide for which 3JHN-H alpha and 3JHN-C beta, both about the phi backbone dihedral angle, have been measured. The function is efficient in producing structures consistent with the scalar couplings, but removed from the conformation observed in solution. This arises from the lack of J restraints for the psi dihedral angle. Simulations with both nuclear Overhauser effect (NOE) and J-coupling restraints illustrates small but significant differences from simulations using only NOEs.

The 36-amino-acid neuropeptide Y (human), which is one of the most potent vasoconstrictors and which exhibits a number of other biological functions, has been synthesized using automated peptide synthesis. The optimized method, using 9-fluorenylmethoxycarbonyl protecting and single-step coupling, yielded the crude product in 90% purity allowing for single-step reversed-phase HPLC purification to greater than 98% purity and a high overall yield (50%). The hormone was characterized by several chromatographic methods, ion-spray mass spectroscopy and Edman degradation. The conformation of human neuropeptide Y was examined by CD, NMR and computer simulations. The CD measurements in trifluoroethanol/water (9:1) show a large percentage of alpha-helix. Variation of concentration, from 0.5 microM increasing up to the 1 mM used for NMR measurements, indicates no evidence for aggregation. In the same solvent system, the NMR line widths were very broad and therefore the resonance assignment was achieved with the exclusive use of two-dimensional NOE spectra. The 248 clearly distinguishable NOEs from the NMR study were used in distance geometry calculations and the resulting structures were refined with restrained molecular dynamics. The results indicate an alpha-helix extending from Arg19 to Gln34. For the N-terminal half of the molecule no regular structure was observed.

The potent immunosuppressant drug FK506 (2) has been examined by 1H- and 13C-NMR spectroscopy and NOE-restrained molecular dynamics to elucidate the conformation in solution. A combination of two- and three-dimensional NMR techniques was used to completely assign the 1H- and 13C-NMR chemical shifts of the two configurational isomers resulting from the cis-trans isomerization about the single amide bond. Hetero- and homonuclear coupling constants were measured to assign the diastereotopic methylene protons at C(16), C(18), and C(23). Intramolecular HH distances were defined from NOESY spectra recorded at −30° in CDCl3 and used as constraints in molecular-dynamics simulations. The conformational preferences of 2 in solution are discussed in light of the constitutional features recently proposed to be necessary for binding and activity.