Modeling an active conformation for linear peptides and design of a competitive inhibitor for HMG-CoA reductase

This study presents an approach that can be used to search for lead peptide candidates, including unconstrained structures in a recognized sequence. This approach was performed using the design of a competitive inhibitor for 3-hydroxy-3-methylglutaryl CoA reductase (HMGR). In a previous design for constrained peptides, a head-to-tail cyclic structure of peptide was used as a model of linear analog in searches for lead peptides with a structure close to an active conformation. Analysis of the conformational space occupied by the peptides suggests that an analogical approach can be applied for finding a lead peptide with an unconstrained structure in a recognized sequence via modeling a cycle using fixed residues of the peptide backbone. Using the space obtained by an analysis of the bioactive conformations of statins, eight cyclic peptides were selected for a peptide library based on the YVAE sequence as a recognized motif. For each cycle, the four models were assessed according to the design criterion ("V" parameter) applied for constrained peptides. Three cyclic peptides (FGYVAE, FPYVAE, and FFYVAE) were selected as lead cycles from the library. The linear FGYVAE peptide (IC(50) = 0.4 microM) showed a 1200-fold increase the inhibitory activity compared to the first isolated LPYP peptide (IC(50) = 484 microM) from soybean. Experimental analysis of the modeled peptide structures confirms the appropriateness of the proposed approach for the modeling of active conformations of peptides.     

Cross-reactive potential of rabbit antibodies raised against a cyclic peptide representing a chimeric V3 loop of HIV-1 gp120 studied by biosensor technique and ELISA

Abstract Rabbit antibodies were induced against a free cyclic peptide representing the chimeric sequence of a consensus V3 loop of HIV-1 gp120. The reactivity of these antibodies was tested in a biosensor system (BIAcore^™, Pharmacia AB, Uppsala, Sweden) and in ELISA with the peptide immunogen in its cyclic and linear forms, as well as with peptides corresponding to the V3 region of different HIV-1 variants. The antibodies reacted with all the peptides tested both in ELISA and in biosensor assays and recognized the cyclic form of the chimeric peptide better than the linear form. Although antibodies raised against the V3 region of particular HIV-1 variants cross-react with other HIV-1 strains, it seems that the use of a chimeric peptide as immunogen improved the cross-reactivity spectrum of recognition of the antibodies. The anti-V3 antibodies were also tested for their ability to neutralize in vitro four HIV-1 laboratory strains. Only the HIV_MN variant was found to be neutralized. Compared to conventional solid phase immunoassays, the BIAcore presents several advantages for measuring the differential reactivity of peptide analogues. In view of their broadly cross-reactive potential, antibodies raised against a consensus sequence should be useful in immunodiagnosis of viral antigenic variants.     

家蝇幼虫抗菌相关蛋白/多肽的诱导及抗菌活性分析

对家蝇Musca domestica 3龄幼虫进行针刺、带菌针刺、热激和超声4种处理,并于处理后不同时间分别收集提取家蝇幼虫体内耐热总蛋白,比浊法测定其抗菌活性,经逐步回归分析确定抗菌相关蛋白/多肽。结果表明,4种处理均能诱导家蝇幼虫产生抗菌物质,其中表观分子量为22 kD的蛋白对藤黄微球菌和大肠杆菌均有抗菌作用,50 kD,13 kD,26 kD,7 kD的蛋白抗菌活性具有专一性。还发现一种37 kD的蛋白对抗菌活性有负作用,推测它可能是促进细胞生长的物质。     

Effect of a modified thymine on the structure and stability of [d(TGGGT)]4 quadruplex

Telomeric guanine-rich sequence can adopt quadruplex structures that are important for their biological role in chromosomal stabilisation. G quartets are characterised by the cyclic hydrogen bonding of four guanine bases in a coplanar arrangement and their stability is ion-dependent. In this work we compare the stability of [d(TGGGT)]₄ and [d(T*GGGT)]₄ quadruplexes. The last one contains a modified thymine, where the hydroxyl group substitutes one hydrogen atom of the methyl group of the thymine in the [d(TGGGT)]₄ sequence. We used a combination of spectroscopic, calorimetric and computational techniques to characterise the G-quadruplex formation. NMR and CD spectra of [d(T*GGGT)]₄ were characteristic of parallel-stranded, tetramolecular quadruplex. CD and DSC melting experiments reveal that [d(T*GGGT)]₄ is less stable that unmodified quadruplex. Molecular models suggest possible explanation for the observed behaviour.     

Flavonoid Deactivation of Ferrylmyoglobin in Relation to Ease of Oxidation as Determined by Cyclic Voltammetry

Fourteen flavonoid aglycones, and the flavonoid glyco-side rutin, with redox potentials ranging from 0.20 (myricetin) to 0.83 V (chrysin) vs. NHE, as determined by cyclic voltammetry at 23°C in aqueous 50 mM phosphate, ionic strength 0.16 (NaCI) with pH = 7.4 and compared with redox potentials determined for four cinnamic acid derivatives, were all found to reduce ferrylmyoglobin, MbFe(IV)=O, to metmyoglo-bin, MbFe(III). Reaction stoichiometry depends strongly on the number of hydroxyl groups in the flavonoid B-ring. All compounds with 3',4'-dihydroxy substitution reduce 2 equivalents of MbFe(IV)=O, whereas naringenin, hesperitin and kaempferol, with one hydroxyl group in the B-ring, reduce with a one-to-one stoichiometry. As studied spectrophotometrically under pseudo-first-order conditions with flavonoids in excess, rutin and apigenin react with MbFe(IV)=O with very similar and moderately high activation enthalpies of ΔH‡₂₉₈ = 69 ± 1kJ mol^-1 and ΔH‡₂₉₈ = 65 ± 3kJ mol-¹, respectively, and with positive activation entropies of ΔH‡₂₉₈ = 23 ± 4Jmol-¹ K^-1 and ΔS‡₂₉₈ = 13 ± 9Jmol^-1K-¹, respectively, in agreement with outer-sphere electron transfer as rate determining. For the fifteen plant polyphenols only qualitative relations exist between redox potential and rate constants rather than a linear free energy relationship (r² = 0.503), and especially the flavone apigenin was found more efficient as reducing agent. For the flava-nones, a linear relation (r² = 0.971) indicate that, in the absence of a 2,3 double bond, removal of the 4-carbonyl group or addition of a 3-hydroxy group only has minor effect on reactivity. The flavonols are the most efficient reducing agents, effectively reducing MbFe(IV)=O to MbFe(III) and establishing a steady state distribution between the flavonol and MbFe(III) and oxymyoglobin, MbFe(II)O₂. Oxidised flavonols reduces MbFe(III) to MbFe(II)0₂ very efficiently and much faster than the parent flavonol.     

Configurationally driven folding of model tetrapeptides containing L- or D-morpholine-3-carboxylic acids as beta-turn nucleators

The conformational analysis by NMR, IR, and molecular modeling of tetrapeptides containing morpholine-3-carboxylic acid (Mor) as a proline surrogate is presented. The relationship between the chirality of the cyclic amino acid at position i+1 and the turn propensity is maintained with respect to the reference proline-containing peptides, although marked differences in the type of folded structures were observed. The conformational profile of morpholine-containing turn peptides as a function of the chirality of the cyclic amino acid indicated that the heterochiral tetrapeptide containing the D-isomer of the cyclic amino acid is more prone to nucleate compact folded structures, although with no resemblance to the beta-turn structures of D-proline-containing peptides. Also, the solvation system proved to influence the organization of folded structures, as in the more interactive CD(3)CN the model peptides showed more compact conformations. The L-Mor-containing peptide displayed two rotamers at the Val-Mor amide bond. The trans isomer did not experience any turn structures, nor any intramolecular hydrogen-bonds, whereas the cis isomer showed a strong preference for a type VI beta-turn structure, thus providing a different conformational asset with respect to the beta-turn structure as reported for the reference L-proline model peptide.     

Cyclic peptides — Small and big and their conformational aspects

Cyclic peptides form an interesting class of compounds for study by conformational analysis, by virtue of their unique conformational features and biological properties. The small cyclic peptides having 3-6 peptide units in their ring, show a variety of conformational characteristics such as occurrence ofcis peptide units, flexibility of peptide dimension and variety in hydrogen bonding. The different possible conformations of cyclic tri- and hexa-peptides are given and certain specific conformational features are discussed for cyclic tetra and pentapeptides. For higher cyclic peptides, the hydrogen bonding requirement for stability of the backbone of the ring, is seen to be kept to a minimum. These various features and their significance are examined and discussed in the light of energy minimization studies and analysis of available experimental data.     

Design of cyclic and other templates for potent and selective peptide alpha-MSH analogues

For over three decades, the design of linear peptide ligands often has incorporated cyclic constraints to improve potency, receptor selectivity, proteolytic stability and biodistribution. Its importance has been so well established that modern day schemes for ligand-based drug design often start with cyclization of linear peptides to rigidify peptide structure, to limit its conformational possibilities, and to find key pharmacophore elements in three-dimensional space. In the past several years, cyclic constraints have been used to develop ligands with improved efficacy, binding affinity, biostability and receptor selectivity for alpha-melanocyte-stimulating hormone (alpha-MSH). Furthermore, potent cyclic alpha-MSH analogues, such as MT-II and SHU-9119, have made structure-activity relationship studies and molecular modeling more useful for creating new three-dimensional, topographical pharmacophore templates.     

Purification and characterization of antimicrobial and vasorelaxant peptides from skin extracts and skin secretions of the North American pig frog Rana grylio

Eight peptides with differential growth–inhibitory activity against the gram-positive bacterium Staphylococcus aureus, the gram-negative bacterium Escherichia coli and the yeast, Candida albicans were isolated from an extract of the skin of the North American pig frog Rana grylio. The primary structures of these antimicrobial peptides were different from previously characterized antimicrobial peptides from Ranid frogs but on the basis of sequence similarities, the peptides may be classified as belonged to four previously characterized peptide families: the ranatuerin-1, ranatuerin-2 and ranalexin families, first identified in the North American bullfrog, Rana catesbeiana, and the temporin family first identified in the European common frog Rana temporaria. Peptides belonging to the brevinin-1, brevinin-2, esculentin-1, and esculentin-2 families, previously isolated from the skins of other species of Ranid frogs, were not identified in the extracts. The ranatuerin-1 and ranalexin peptides showed broadest spectrum of antimicrobial activity whereas the temporins were active only against S. aureus. Synthetic replicates of temporin-1Gb (SILPTIVSFLSKFL.NH₂) and temporin-1Gd (FILPLIASFLSKFL.NH₂) produced concentration-dependent relaxation of preconstricted vascular rings from the rat thoracic aorta (EC₅₀=2.4±0.1 μM for temporin-1Gb and 2.3±0.2 μM for temporin-1Gd). The antimicrobial peptides that were isolated in extracts of the skin R. grylio were present in the same molecular forms in electrically-stimulated skin secretions of the animal demonstrating that the peptides are stored in the granular glands of the skin in their fully processed forms.     

Functional reconstitution of G-protein-coupled receptor-mediated adenylyl cyclase activation by a baculoviral co-display system

Recently, evidence has accumulated in support of the heterologous expression of functional membrane proteins and their complexes on extracellular baculovirus particles (budded virus, BV). In this study, we attempted to apply this BV display system to detect G-protein-coupled receptor (GPCR) signaling. We infected Sf9 cells with a combination of four recombinant baculoviruses individually encoding the dopamine D1 receptor (DR-D1), G-protein -subunit (G_s), G-protein β₁γ₂ subunit dimer (Gβ₁γ₂), and adenylyl cyclase type VI (ACVI). The recovered BV fraction produced cAMP in response to the stimulation with dopamine. Co-expression of all three G-protein subunits in addition to receptor and ACVI led to a maximal response. BV co-expressing DR-D1, G_s, Gβ₁γ₂, and ACVI also responded to dopamine agonists and an antagonist. Furthermore, BV expressing two other G_s-coupled receptors together with G_s, Gβ₁γ₂, and ACVI also produced cAMP in response to their specific ligands. These results indicate the functional coupling of receptor, G_s and ACVI is reconstituted on BV. Since BV is essentially free of endogenous GPCRs, this BV co-display system should prove highly useful for the development of functional assay systems for GPCRs.     

A cyclic peptide analogue of the loop III region of platelet-derived growth factor-BB is a synthetic antigen for the native protein.

We report the synthesis and characterization of a cyclic peptide analogue of the loop III region of platelet-derived growth factor (PDGF) B-chain sequence, cyclo(73Arg-Lys-Ile-Glu-Ile-Val-Arg-Lys-Lys81-Cys), incorporating a C-terminus cysteine residue for the conjugation to a carrier protein. The synthesis involved solid-phase chemistry, utilizing Fmoc-tBu chemistry and acid labile side-chain protecting groups, followed by 'head-to-tail' cyclization using the allyl-protected glutamic acid anchored on its side chain to the solid support with HATU/HOAt as the coupling agent. Conformational differences between the cyclic and its linear counterpart PDGF peptides were determined by circular dichroism measurements in aqueous media. High titre antisera were raised to both cyclic and linear peptide immunogens. Antisera raised to the cyclic peptide cross-reacted with PDGF-BB in both Western blot and ELISA, whereas antisera raised to the linear peptide had no reactivity with PDGF-BB. The cyclic peptide (conformational design analogue) produces an immunogen which is able to antigenically mimic the secondary structure of loop III of PDGF-BB and forms a basis from which further small molecular mimetics of PDGF may be designed for use as both immunogens and also potential agonists/antagonists of PDGF. Similarly constructed immunogens may also be useful in the design of vaccines which direct responses to loop regions in other target proteins.     

Structural basis for the enhanced activity of cyclic antimicrobial peptides: the case of BPC194

We report the molecular basis for the differences in activity of cyclic and linear antimicrobial peptides. We iteratively performed atomistic molecular dynamics simulations and biophysical measurements to probe the interaction of a cyclic antimicrobial peptide and its inactive linear analogue with model membranes. We establish that, relative to the linear peptide, the cyclic one binds stronger to negatively charged membranes. We show that only the cyclic peptide folds at the membrane interface and adopts a β-sheet structure characterised by two turns. Subsequently, the cyclic peptide penetrates deeper into the bilayer while the linear peptide remains essentially at the surface. Finally, based on our comparative study, we propose a model characterising the mode of action of cyclic antimicrobial peptides. The results provide a chemical rationale for enhanced activity in certain cyclic antimicrobial peptides and can be used as a guideline for design of novel antimicrobial peptides.     

Treatment of experimental allergic encephalomyelitis (EAE) by a rationally designed cyclic analogue of myelin basic protein (MBP) epitope 72-85

In this report the rational design, synthesis and pharmacological properties of an amide-linked cyclic antagonist analogue of the guinea pig myelin basic protein epitope MBP_72–85 are described. Design of the potent cyclic analogue was based on 2D NOESY nuclear magnetic resonance and molecular dynamics studies carried out in the linear antagonist Ala⁸¹MBP_72–85. The cyclic antagonist completely prevented the induction of experimental allergic/autoimmune encephalomyelitis when coinjected with linear and cyclic agonist analogues MBP_72–85 and cyclo(2–9)MBP_72–85.     

The cellular and molecular regulation of 1,25(OH)2D3 production.

The synthesis of 1,25(OH)₂D₃ is a critical control point in the regulation of calcium metabolism, and possibly in the growth and differentiation of a number of cell types. This paper reviews our current understanding of the regulation of this process at the cellular and molecular levels, with the emphasis on the mechanisms of feedback control 1,25(OH)₂D₃ itself, control of parathyroid hormone, the roles of cyclic AMP dependent protein kinase and protein kinase C, and the interaction between the various intracellular regulators of 1,25(OH)₂D₃ production.     

Structure of C-terminal fragment of merozoite surface protein-1 from Plasmodium vivax determined by homology modeling and molecular dynamics refinement

One current vaccine candidate against Plasmodium vivax targeting asexual blood stage is the major merozoite surface protein-1 of P. vivax (PvMSP-1). Vaccine trials with PvMSP-1₁₉ and PvMSP-1₃₃ have succeeded in protecting monkeys and a large proportion of individuals, naturally exposed to P. vivax transmission, develop specific antibodies to PvMSP-1₁₉. This study presents a model for the three-dimensional structure of the C-terminal 19 kDa fragment of P. vivax MSP-1 determined by means of homology modeling and molecular dynamics refinement. The structure proved to be consistent with MSP-1₁₉ of known crystal or solution structures. The presence of a main binding pocket, well suited for protein–protein interactions, was determined by CASTp. Corrections reported to the sequence of PvMSP-1₁₉ Belem strain were also inspected. Our model is currently used as a basis to understand antibody interactions with PvMSP-1₁₉.     

Structural determinations, magnetic and EPR studies of complexes involving the Cr(OH)2Cr unit

Five heterometallic compounds with formulae [Ba(H₂O)₄Cr₂(μ-OH)₂(nta)₂] · 3H₂O (I), [M(bpy)₂(H₂O)₂] [Cr₂(OH)₂(nta)₂] · 7H₂O, where M²⁺ = Zn, (II); Ni, (III); Co, (IV) and [Mn(H₂O)₃(bpy)Cr₂(OH)₂(nta)₂] · (bpy) · 5H₂O (V); bpy = 2,2′-bipyridine, (nta = nitrilotriacetate ion) have been prepared by reaction of I with the corresponding M^II-sulfates in the presence of 2,2′-bipyridine. Substances I–V have been characterized by magnetic susceptibility measurements, EPR and X-ray determinations. I represents a 2D coordination polymer formed by coordination of centrosymmetrical dimeric chromium(III) units and Barium cations. The 10-coordinate Ba polyhedron is completed by four water molecules. Compounds II–IV are isostructural and consist of non-centrosymmetric dimeric anions [Cr₂(μ-OH)₂(nta)₂]²⁻, complex cations [M^II(bpy)₂(H₂O)₂]²⁺ and solvate water molecules. The octahedral coordination of chromium atoms implies four donor atoms of the nta³⁻ ligands and two bridging OH groups. Multiple hydrogen bonds of coordinated and solvate water molecules link anions and cations in a 3D network. A similar [Cr₂(μ-OH)₂(nta)₂]²⁻ unit is found in V. The bridging function is performed by a carboxylate oxygen atom of the nta ligand that leads to the formation of a trinuclear complex [Mn(bpy)(H₂O)₂Cr₂(μ-OH)₂(nta)₂]. Experimental and calculated frequency and temperature dependences of EPR spectra of these compounds are presented. The fine structure appearing on the EPR spectra of compound V is analyzed in detail at different temperatures. It is established that the main part of the EPR signals is due to the transitions in the spin states of a spin multiplet with S = 2. Analyses of experimental and calculated spectra confirm the absence of interaction between metal ions (M^II) and Cr-dimers in complexes III and IV and the presence of weak Mn–Cr interactions in V. The temperature dependence of magnetic susceptibilities for I–V was fitted on the basis of the expression derived from isotropic Hamiltonian including a bi-quadratic exchange term.     

Hydroformylation of alkenes and alkynes using a heterobinuclear Rh---W catalyst

Hydroformylation reactions of a series of alkenes and alkynes have been carried out using the heteronuclear Rh---W catalyst, (CO)₄ hH(CO)(PPh₃) (1). The results of these reactions have been compared with corresponding reactions using [Rh(OAc)₂]₂ as catalyst. Catalysis of a reaction of styrene using 1 gave a very high yield of the branched chain aldehyde containing only a trace of the straight chain isomer. Reactions of the phosphinoalkene, Ph₂P(CH₂)₃CH=CH₂ (7) and the corresponding alkyne, Ph₂P(CH₂)₃CCH (11) gave similar products using either catalyst system with the alkryne reaction being significantly slower. Reaction of the alkenyl dithiane, H---CH₂CH=CH₂ (2), using the Rh---W catalyst (1) gave a higher ratio of linear to branched aldehydes (47 linear:53 branched) than the corresponding reaction using [Rh(OAc)₂]₂ (25 linear:75 branched). Reactions of vinyl acetate using 1 as catalyst gave a significant amount of linear aldehyde in contrast to reactions using [Rh(OAc)₂]₂ but reactions of allyl acetate gave similar products for both catalyst systems.     

Solution structure of regioselectively addressable functionalized templates: An NMR and restrained molecular dynamics investigation

Three cyclic peptides that are Regioselectively Addressable Functionalized Templates (RAFT) for use in protein de novo design have been investigated using a combination of nmr, restrained molecular dynamics, and CD spectroscopy. These peptides contain up to four selectively addressable sites (orthogonally protected lysine side chains) or have selectively addressable faces. The results show a common stable conformation for templates of this kind based on two type II β-turns and an associated β-sheet structure. A preferential orientation for the side chains is also demonstrated. The significance of these findings is discussed in the context of applications of RAFT that rely on their conformational rigidity and ability to present functionalities in a defined spatial arrangement. © 1996 John Wiley & Sons, Inc.     

Structural characterization of cyclic kallidin analogues in DMSO by nuclear magnetic resonance and molecular dynamics.

The conformational properties in DMSO of two head-to-tail cyclic analogues of kallidin ([Lys(0)]-bradykinin, KL) as well as those of the corresponding linear peptides were studied by NMR and molecular dynamics (MD) simulations. The modifications in the sequence were introduced at position 6, resulting in the four peptides, [Tyr(6)]-KL (YKL), [Trp(6)]-KL (WKL), cyclo-([Tyr(6)]-KL) (YCKL) and cyclo-([Trp(6)]-KL) (WCKL).The linear WKL analogue was significantly more potent than kallidin on rat duodenum preparations, whereas YKL was significantly less potent. Both cyclic peptides, YCKL and WCKL displayed similar activity, lower than that of the linear analogues and also of cyclo-KL.The two linear analogues display high conformational flexibility in DMSO. In the predominant conformer, for both peptides, all three X-Pro bonds adopt a trans configuration. Three out of four conformers present in YCKL and WCKL were completely assigned. The configurations at the X-Pro bonds are the same for the two analogues. All cyclic conformers show a cis configuration in at least one X-Pro bond and always opposite configuration for the two consecutive X-Pro bonds.The NOE-restrained MD calculations resulted in the detection of several elements of secondary structure in each of the conformers. Such elements are described and their possible relevance to biological activity is discussed.     

Molecular structure of the carbon-bound phosphorus ylide complex trans-dichlorobis(benzoyltri-n-butylphosphorane)palladium(II)

The molecular structure of trans-[Pd(PhC(O)CHP(n-C₄H₉)₃)₂Cl₂] has been determined via a single crystal X-ray diffraction study: triclinic,P1,a = 8.876(2),b = 10.908(3),c = 11.938(4)Å, = 97.06(2)°, β = 102.79(2)°, γ = 100.51(2)°,V= 1092.1(5)ų,Z = 1 and R(F) = 4.61%. The phosphorus ylide molecules are bound to the palladium atom through their methine carbon atoms, the overall coordination geometry about the palladium being square planar. The protons in the ortho-positions of the two phenyl group are poised above and below the palladium atom, suggesting that the complex is a precursor of the ortho-metalated complex [Pd(μ-Cl)(C₆H₄C(O)CHP(n-C₄H₉)₃)]₂ synthesized earlier in our laboratory.