Dynamical search for bis-penicillamine enkephalin conformations

Small molecule peptidomimetic trypsin inhibitors: validation of an EKO binding mode, but with a twist

Examination of a series of naturally-occurring trypsin inhibitor proteins, led to identification of a set of three residues (which we call the "interface triplet") to be determinant of trypsin binding affinity, hence excellent templates for small molecule mimicry. Consequently, we attempted to use the Exploring Key Orientation (EKO) strategy developed in our lab to evaluate small molecules that mimic the interface triplet regions of natural trypsin inhibitors, and hence potentially might bind and inhibit the catalytic activity of trypsin. A bis-triazole scaffold ("TT-mer") was the most promising of the molecules evaluated in silico. Twelve such compounds were synthesized and assayed against trypsin, among which the best showed a K_d of 2.1 μM. X-ray crystallography revealed a high degree of matching between an illustrative TT-mer's actual binding mode and that of the mimics that overlaid the interface triplet in the crystal structure. Deviation of the third side chain from the PPI structure seems to be due to alleviation of an unfavorable dipole-dipole interaction in the small molecule's actual bound conformation.

Design criteria for minimalist mimics of protein-protein interface segments

Small molecules that can interrupt or inhibit protein-protein interactions (PPIs) are valuable as probes in chemical biology and medicinal chemistry, but they are also notoriously difficult to develop. Design of non-peptidic small molecules that mimic amino acid side-chain interactions in PPIs ("minimalist mimics") is seen as a way to fast track discovery of PPI inhibitors. However, there has been little comment on general design criteria for minimalist mimics, even though such guidelines could steer construction of libraries to screen against multiple PPI targets. We hypothesized insight into general design criteria for minimalist mimics could be gained by comparing preferred conformations of typical minimalist mimic designs against side-chain orientations on a huge number of PPI interfaces. That thought led to this work which features nine minimalist mimic designs: one from the literature, and eight new "hypothetical" ones conceived by us. Simulated preferred conformers of these were systematically aligned with >240 000 PPI interfaces from the Protein Data Bank. Conclusions from those analyses did indeed reveal various design considerations that are discussed here. Surprisingly, this study also showed one of the minimalist mimic designs aligned on PPI interface segments more than 15 times more frequently than any other in the series (according to uniform standards described herein); reasons for this are also discussed.

Interplay Of Stereochemistry, Conformational Rigidity, And Ease Of Synthesis For 13-Membered Cyclic Peptidomimetics Containing APC Residues

As part of a program to design small molecules that bind proteins, we require cyclic peptides (or peptidomimetics) that are severely constrained such that they adopt one predominant conformation in solution. This paper describes syntheses of the 13-membered cyclic tetrapeptides 1 containing aminopyrrolidine carboxyl (APC) residues. A linear precursor was prepared and used to determine optimal conditions for cyclization of that substrate. A special linker was prepared to enable cyclization of similar linear peptidomimetics on a solid phase, and the solution-phase cyclization conditions were shown to be appropriate for this too. Stereochemical variations were then used to determine the ideal APC configuration for cyclization of the linear precursors (on a solid phase, using the conditions identified previously). Consequently, a series of compounds were prepared that are representative of compounds 1. Conformational studies of representative compounds in DMSO solution were performed primarily using (i) NOE studies, (ii) quenched molecular dynamics simulations using no constraints from experiment, and (iii) MacroModel calculations with NMR constraints. All three strategies converged to the same conclusion: the backbone of molecules based on 1 tends to adopt one preferential conformation in solution and that conformation can be predicted from the stereochemistries of the α-amino acids involved.

Anthranilic acid-containing cyclic tetrapeptides: at the crossroads of conformational rigidity and synthetic accessibility

Each amino acid in a peptide contributes three atom units to main-chains, hence natural cyclic peptides can be 9, 12, 15, …. i.e. 3n membered-rings, where n is the number of amino acids. Cyclic peptides that are 9 or 12-membered ring compounds tend to be hard to prepare because of strain, while their one amino acid homologs (15-membered cyclic pentapeptides) are not conformationally homogeneous unless constrained by strategically placed proline or d-amino acid residues. We hypothesized that replacing one genetically encoded amino acid in a cyclic tetrapeptide with a rigid β-amino acid would render peptidomimetic designs that rest at a useful crossroads between synthetic accessibility and conformational rigidity. Thus this research explored non-proline containing 13-membered ring peptides 1 featuring one anthranilic acid (Anth) residue. Twelve cyclic peptides of this type were prepared, and in doing so the viability of both solution- and solid-phase methods was demonstrated. The library produced contained a complete set of four diastereoisomers of the sequence 1aaf (i.e. cyclo-AlaAlaPheAnth). Without exception, these four diastereoisomers each adopted one predominant conformation in solution; basically these conformations feature amide N-H vectors puckering above and below the equatorial plane, and approximately oriented their N-H[combining low line] atoms towards the polar axis. Moreover, the shapes of these conformers varied in a logical and predictable way (NOE, temperature coefficient, D/H exchange, circular dichroism). Comparisons were made of the side-chain orientations presented by compounds 1aaa in solution with ideal secondary structures and protein-protein interaction interfaces. Various 1aaa stereoisomers in solution present side-chains in similar orientations to regular and inverse γ-turns, and to the most common β-turns (types I and II). Consistent with this, compounds 1aaa have a tendency to mimic various turns and bends at protein-protein interfaces. Finally, proteolytic- and hydrolytic stabilities of the compounds at different pHs indicate they are robust relative to related linear peptides, and rates of permeability through an artificial membrane indicate their structures are conducive to cell permeability.

Bioactive conformations of two seminal delta opioid receptor penta-peptides inferred from free-energy profiles

Delta-opioid (DOP) receptors are members of the G protein-coupled receptor (GPCR) sub-family of opioid receptors, and are evolutionarily related, with homology exceeding 70%, to cognate mu-opioid (MOP), kappa-opioid (KOP), and nociceptin opioid (NOP) receptors. DOP receptors are considered attractive drug targets for pain management because agonists at these receptors are reported to exhibit strong antinociceptive activity with relatively few side effects. Among the most potent analgesics targeting the DOP receptor are the linear and cyclic enkephalin analogs known as DADLE (Tyr-D-Ala-Gly-Phe-D-Leu) and DPDPE (Tyr-D-Pen-Gly-Phe-D-Pen), respectively. Several computational and experimental studies have been carried out over the years to characterize the conformational profile of these penta-peptides with the ultimate goal of designing potent peptidomimetic agonists for the DOP receptor. The computational studies published to date, however, have investigated only a limited range of timescales and used over-simplified representations of the solvent environment. We provide here a thorough exploration of the conformational space of DADLE and DPDPE in an explicit solvent, using microsecond-scale molecular dynamics and bias-exchange metadynamics simulations. Free-energy profiles derived from these simulations point to a small number of DADLE and DPDPE conformational minima in solution, which are separated by relatively small energy barriers. Candidate bioactive forms of these peptides are selected from identified common spatial arrangements of key pharmacophoric points within all sampled conformations.

Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS)

Peptide mimics that display amino acid side-chains on semi-rigid scaffolds (not peptide polyamides) can be referred to as minimalist mimics. Accessible conformations of these scaffolds may overlay with secondary structures giving, for example, "minimalist helical mimics". It is difficult for researchers who want to apply minimalist mimics to decide which one to use because there is no widely accepted protocol for calibrating how closely these compounds mimic secondary structures. Moreover, it is also difficult for potential practitioners to evaluate which ideal minimalist helical mimics are preferred for a particular set of side-chains. For instance, what mimic presents i, i + 4, i + 7 side-chains in orientations that best resemble an ideal α-helix, and is a different mimic required for a i, i + 3, i + 7 helical combination? This article describes a protocol for fitting each member of an array of accessible scaffold conformations on secondary structures. The protocol involves: (i) use quenched molecular dynamics (QMD) to generate an ensemble consisting of hundreds of accessible, low energy conformers of the mimics; (ii) representation of each of these as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; (iii) similar representation of each combination of three side-chains in each ideal secondary structure as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; and, (iv) overlay Cα and Cβ coordinates of all the conformers on all the sets of side-chain "triads" in the ideal secondary structures and express the goodness of fit in terms of root mean squared deviation (RMSD, Å) for each overlay. We refer to this process as Exploring Key Orientations on Secondary structures (EKOS). Application of this procedure reveals the relative bias of a scaffold to overlay on different secondary structures, the "side-chain correspondences" (e.g. i, i + 4, i + 7 or i, i + 3, i + 4) of those overlays, and the energy of this state relative to the minimum located. This protocol was tested on some of the most widely cited minimalist α-helical mimics (1-8 in the text). The data obtained indicates several of these compounds preferentially exist in conformations that resemble other secondary structures as well as α-helices, and many of the α-helical conformations have unexpected side-chain correspondences. These observations imply the featured minimalist mimics have more scope for disrupting PPI interfaces than previously anticipated. Finally, the same simulation method was used to match preferred conformations of minimalist mimics with actual protein/peptide structures at interfaces providing quantitative comparisons of predicted fits of the test mimics at protein-protein interaction sites.

Pyrrolinone-pyrrolidine oligomers as universal peptidomimetics

Peptidomimetics 1-3 were prepared from amino acid-derived tetramic acids 7 as the key starting materials. Calculations show that preferred conformations of 1 can align their side-chain vectors with amino acids in common secondary structures more effectively than conformations of 3. A good fit was found for a preferred conformation of 2 (an extended derivative of 1) with a sheet/β-turn/sheet motif.

Minimalist and universal peptidomimetics

Many "new generation" peptidomimetics are designed to present amino acid side chains only; they do not have structural features that resemble peptide main chains. These types of molecules have frequently been presented in the literature as mimics of specific secondary structures. However, many "side-chain only" peptidomimetics do not rest in single conformational states, but exist in a limited number of freely interconverting forms. These different conformations may resemble different secondary structures, so referring to them as, for instance, turn- or helical-mimics understates the ways they could adapt to various binding situations. Sets of scaffolds that can be used to mimic aspects of nearly every secondary structure, i.e. universal peptidomimetics, can be constructed. These may assume a privileged place in library design, particularly in high throughput screening for pharmacological probes for which binding conformations, or even the target itself, is unknown at the time the library is designed (critical review, 101 references).

Universal peptidomimetics

This paper concerns peptidomimetic scaffolds that can present side chains in conformations resembling those of amino acids in secondary structures without incurring excessive entropic or enthalpic penalties. Compounds of this type are referred to here as minimalist mimics. The core hypothesis of this paper is that small sets of such scaffolds can be designed to analogue local pairs of amino acids (including noncontiguous ones) in any secondary structure; i.e., they are universal peptidomimetics. To illustrate this concept, we designed a set of four peptidomimetic scaffolds. Libraries based on them were made bearing side chains corresponding to many of the protein-derived amino acids. Modeling experiments were performed to give an indication of kinetic and thermodynamic accessibilities of conformations that can mimic secondary structures. Together, peptidomimetics based on these four scaffolds can adopt conformations that resemble almost any combination of local amino acid side chains in any secondary structure. Universal peptidomimetics of this kind are likely to be most useful in the design of libraries for high-throughput screening against diverse targets. Consequently, data arising from submission of these molecules to the NIH Molecular Libraries Small Molecule Repository (MLSMR) are outlined.

Cyclic semipeptoids: peptoid-organic hybrid macrocycles

[structure: see text] Cyclic semipeptoids 1 and 2 represent constrained, secondary structure mimics where the R(1) and R(2) side chains correspond to those of amino acids. Solid-phase syntheses and conformational analyses of these compounds are described.

Ring Closure to β-Turn Mimics via Copper-Catalyzed Azide/Alkyne Cycloadditions

[Structure: see text]. Copper-catalyzed azide alkyne cycloadditions of the linear substrates 1 were used to form the cyclic derivatives 2. Computational, NMR, and CD analyses of these compounds indicate that their most favorable conformational states include type I and type II beta-turn conformations. Selectivity for the dimeric products 6 in these cyclization reactions is discussed.

A Quenched Molecular Dynamics−Rotating Frame Overhauser Spectroscopy Study of a Series of Semibiosynthetically Monoacylated Anthocyanins

Quenched molecular dynamics (QMD), in conjunction with NMR (ROESY) studies, was used to investigate the conformational behavior of some semibiosynthetic anthocyanins of the type 6-O-acyl-beta-D-Glcp-(166)-beta-D-Galp-(1-->O(3))-cyanidin, with and without a beta-D-Xylp branch at the 2-O-Gal position. These compounds, which are produced by the addition of selected carboxylic acids to growing tissue cultures of Daucus carota (wild carrot), are of interest as color-stabilized anthocyanins, some of which have potential as useful colorants in the nutraceutical and pharmaceutical industries. The QMD-ROESY studies, performed for the first time on anthocyanins, have led to the identification of families of conformers of these flexible molecules that are of interest in work toward determining the mechanism for stabilization of color among these compounds in solution.

Syntheses of second generation, 14-membered ring beta-turn mimics

Efficient solid phase syntheses of the constrained beta-turn peptidomimetics 1-3 were devised, and the conformational properties of three representative compounds in DMSO were determined.

Simulation of the bis-(penicillamine) enkephalin in ammonium chloride solution: a comparison with sodium chloride

In order to quantify specific ion effects, a simulation study of bis(penicllamine) enkephalin, also known as DPDPE, has been performed in aqueous ammonium chloride solution and has been compared to a previous simulation of DPDPE in aqueous sodium chloride solution. Global thermodynamics have been calculated for a model system and the solution environment around DPDPE has been characterized. Associations of ions with DPDPE have been investigated. The observed differences between sodium chloride solution and ammonium chloride solution suggest that individual cations affect the solvation and peptide binding properties of a given anion.

Design, synthesis, and evaluation of opioid analogues with non-peptidic beta-turn scaffold: enkephalin and endomorphin mimetics

We have identified a mu-selective opioid receptor agonist without a cationic amino group in the molecule from libraries of bicyclic beta-turn peptidomimetics. The biologically active conformation of the lead is proposed to mimic an endomorphin type III 4 --> 1 beta-turn conformation.

Simulations of the bis-penicillamine enkephalin in sodium chloride solution: a parameter study

A simulation study of DPDPE in sodium chloride solution has been performed and compared with previous simulations using a different interaction potential for the ions. Both global thermodynamics as well as a characterization of association to DPDPE have been calculated. We show that the parameters used for the ions have a profound effect on the association to the peptide in 1M NaCl. The observed differences suggest that individual associations in these and previous simulations are sensitive to parameters.

Structural basis for the activity of pp60(c-src) protein tyrosine kinase inhibitors

Conformational searches on three closely related pp60(c-src) protein tyrosine kinase inhibitors of varying potencies were performed to determine a structural basis for their activity. The first was a linear peptide (PDNEYAFFQf), the second its 10-membered cyclic analogue, and the third a cyclic analogue with a para carboxyphenylalanine in place of one the F residues. A common backbone conformation with an antiparallel beta-sheet-like geometry capped by similar beta-turns was found for all three peptides, which may be a binding conformation and gives a candidate pharmacophore for further testing. The interaction between some polar side chains and between some of the aromatic rings may be important for maintaining the correct conformation. The differences in potencies of these inhibitors may be attributed to certain thermodynamic and chemical reasons.

Conformation-activity relationships of opioid peptides with selective activities at opioid receptors

The discovery of endogenous opioid peptides 25 years ago opened up a new chapter in efforts to understand the origins and control of pain, its relationships to other biological functions, including inflammatory and other immune responses, and the relationships of opioid peptides and their receptors to a variety of undesirable or toxic side effects often associated with the nonpeptide opiates such as morphine including addiction, constipation, a variety of neural toxicities, tolerance, and respiratory depression. For these investigations the need for potent and highly receptor selective agonists and antagonists has been crucial since they in principle allow one to distinguish unequivocally the roles of the different opioid receptors (mu, delta, and kappa) in the various biological and pathological roles of the opioid peptides and their receptors. Conformational and topographical constraint of the linear natural endogenous opioid peptides has played a major role in developing peptide ligands with high selectivity for mu, delta, and kappa receptors, and in understanding the conformational, topographical, and stereoelectronic structural requirements of the opioid peptides for their interactions with opioid receptors. In turn, this had led to insights into the three-dimensional pharmacophore for opioid receptors. In this article we review and discuss some of the developments that have led to potent, selective, and stable peptide and peptidomimetic ligands that are highly potent and selective, and that have delta agonist, mu antagonist, and kappa agonist biological activities (other authors in this issue will discuss the development of other types of activities and selectivities). These have led to ligands that provide unique insight into opioid pharmacophores and the critical roles opioid ligands and receptor scan play in pain, addiction, and other human maladies.

Complementarity of delta opioid ligand pharmacophore and receptor models

The elaboration of a pharmacophore model for the delta opioid receptor selective ligand JOM-13 (Tyr-c[D-Cys-Phe-D-Pen]OH) and the parallel, independent development of a structural model of the delta receptor are summarized. Although the backbone conformation of JOM-13's tripeptide cycle is well defined, considerable conformational lability is evident in the Tyr(1) residue and in the Phe(3) side chain, key pharmacophore elements of the ligand. Replacement of these flexible features of the ligand by more conformationally restricted analogues and subsequent correlation of receptor binding and conformational properties allowed the number of possible binding conformations of JOM-13 to be reduced to two. Of these, one was chosen as more likely, based on its better superposition with other conformationally constrained delta receptor ligands. Our model of the delta opioid receptor, constructed using a general approach that we have developed for all rhodopsin-like G protein-coupled receptors, contains a large cavity within the transmembrane domain that displays excellent complementarity in both shape and polarity to JOM-13 and other delta ligands. This binding pocket, however, cannot accommodate the conformer of JOM-13 preferred from analysis of ligands, alone. Rather, only the "alternate" allowed conformer, identified from analysis of the ligands but "disfavored" because it does not permit simultaneous superposition of all pharmacophore elements of JOM-13 with other delta ligands, fits the binding site. These results argue against a simple view of a single, common fit to a receptor binding site and suggest, instead, that at least some binding site interactions of different ligands may differ.

A three-dimensional model of the delta-opioid pharmacophore: comparative molecular modeling of peptide and nonpeptide ligands

A comparative molecular modeling study of delta-opioid ligands was performed under the assumption that potent peptide and nonpeptide agonists may have common three-dimensional (3D) arrangement of pharmacophore groups upon binding to the delta-receptor. Low-energy conformations of the agonists 7-spiroindanyloxymorphone (SIOM) and 2-methyl-4a-alpha-(3-hydroxyphenyl)-1,2,3,4,4a,5,12, 12a-alpha-octahydro-quinolino[2,3,3-g]isoquinoline (TAN-67), and a partial agonist oxomorphindole (OMI) were determined by high-temperature molecular dynamics (MD). A good spatial overlap was found for the pharmacophore groups of SIOM, TAN-67, and OMI, including the basic nitrogen, phenol hydroxyl, and two aromatic ring. Based on this overlap we proposed a 3D pharmacophore model for nonpeptide delta-opioid agonists with a distance of 7.0 +/- 1.3 A between the two aromatic rings and of 8.2 +/- 1.0 A between the nitrogen and phenyl ring. The potent and highly delta-opioid receptor selective agonist [(2S,3R)-TMT(1)]DPDPE, which shares global backbone constraints of the 14-membered disulfide cycle and a strong preference for the trans rotamer of the TMT(1) side chain, was chosen as a peptide template of the delta-opioid pharmacophore. Extensive MD simulations at 300 K with the AMBER force field were performed for [(2S,3R)-TMT(1)]DPDPE and the less potent [(2S, 3S)-TMT(1)]DPDPE analogue. Multiple MD trajectories were collected for each peptide starting from the x-ray structures of DPDPE and [L-Ala(3)]DPDPE and from models proposed in the literature. Low-energy MD conformations were filtered by the nonpeptide pharmacophore query and then directly superimposed with SIOM, OMI, and TAN-67. Two conformers of [(2S,3R)-TMT(1)]DPDPE that showed the best overlap with the nonpeptide pharmacophore (rms deviation </= 1. 0 A for N,O atoms and centroids of two aromatic rings) were selected as possible delta-receptor binding conformations. These conformations have similar backbone structures, and trans rotamers of the TMT(1) side-chain group. They are reasonably close to the crystal structure of [L-Ala(3)]DPDPE, and differ significantly from the crystal structure of DPDPE. The conformer with a gauche(-) rotamer of Phe(4) is most consistent with structure-activity relationships of delta-opioid peptides. The proposed 3D models were used for rational design of new nonpeptide delta-receptor ligands.

Thrombin receptor-activating peptides (TRAPs): investigation of bioactive conformations via structure-activity, spectroscopic, and computational studies

The thrombin receptor (PAR-1) is an unusual transmembrane G-protein coupled receptor in that it is activated by serine protease cleavage of its extracellular N-terminus to expose an agonist peptide ligand, which is tethered to the receptor itself. Synthetic peptides containing the agonist motif, such as SFLLRN for human PAR-1, are capable of causing full receptor activation. We have probed the possible bioactive conformations of thrombin receptor-activating peptides (TRAPs) by systematic introduction of certain conformational perturbations, involving alpha-methyl, ester psi(COO), and reduced-amide psi(CH2N) scans, into the minimum-essential agonist sequence (SFLLR) to probe the importance of the backbone conformation and amide NH hydrogen bonding. We performed extensive conformational searches of representative pentapeptides to derive families of putative bioactive structures. In addition, we employed 1H NMR and circular dichroism (CD) to characterize the conformational disposition of certain pentapeptide analogues experimentally. Activation of platelet aggregation by our pentapeptide analogues afforded a structure-function correlation for PAR-1 agonist activity. This correlation was assisted by PAR-1 receptor binding data, which gauged the affinity of peptide ligands for the thrombin receptor independent of a functional cellular response derived from receptor activation (i.e. a pure molecular recognition event). Series of alanine-, proline-, and N-methyl-scan peptides were also evaluated for comparison. Along with the known structural features for PAR-1 agonist peptides, our work adds to the understanding of peptide topography relative to platelet functional activity and PAR-1 binding. The absolute requirement of a positively charged N-terminus for strong agonist activity was contradicted by the N-terminal hydroxyl peptide psi(HO)S-FLLR-NH2. The amide nitrogen between residues 1 and 2 was found to be a determinant of receptor recognition and the carbonyl groups along the backbone may be involved in hydrogen bonding with the receptor. Position 3 (P3) of TRAP-5 is known to tolerate a wide variety of side chains, but we also found that the amide nitrogen at this position can be substituted by an oxygen, as in SF-psi(COO)-LLR-NH2, without diminishing activity. However, this peptide bond is sensitive to conformational changes in that SFPLR-NH2 was active, whereas SF-NMeL-LR-NH2 was not. Additionally, we found that position 3 does not tolerate rigid spacers, such as 3-aminocyclohexane-1-carboxylic acid and 2-aminocycloalkane-1-carboxylic acid, as analogues 1A, 1B, 2A, 2B, 3, 4, 5A and 5B lack agonist activity. On the basis of our results, we suggest that an extended structure of the agonist peptide is principally responsible for receptor recognition (i.e. binding) and that hydrophobic contact may occur between the side chains of the second (Phe) and fourth (Leu) residues (i.e. P2-P4 interaction).

Modeling of alpha-MSH conformations with implicit solvent

A conformational search for the most probable structures of the hormone alpha-MSH in aqueous solution was performed in order to help determine the structural features necessary for biological activity. The free-energy surface was modeled using methods from integral equation theory, and high-temperature molecular dynamics was used to enhance conformational sampling. Families of low free-energy structures have been found. The minimum energy structure shows a stable beta-turn conformation in the putative message region that is stabilized by a salt bridge between Glu5 and Lys11. The orientation of the side chains reflects the amphiphilic nature of the peptide, and a close interaction between the side chains of the His6, Phe7 and Trp9 was observed. Several structural features observed in the minimum energy structure agree well with experimental results. The conformational features led to a hypothesis of a receptor-hormone interaction model in which the hydrophobic side chains of Phe7 and Trp9 interact with the transmembrane portion of the human melanocortin (MC1) receptor. Also, the positively charged side chain of Arg8 and the imidazole side chain of His6 may interact with the negatively charged portions of the receptor which may even be on the receptor's extracellular loops.

Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation

The dielectrically consistent reference interaction site model (DRISM) integral equation theory is applied to determine the potential of mean force (PMF) for an alanine tetramer. A stochastic dynamics simulation of the alanine tetramer using this PMF is then compared with an explicit water molecular dynamics simulation. In addition, comparison is also done with simulations using other solvent models like the extended reference interaction site model (XRISM) theory, constant dielectric and linear distance-dependent dielectric models. The results show that the DRISM method offers a fairly accurate and computationally inexpensive alternative to explicit water simulations for studies on small peptides.

Comparisons of the conformational biases imposed by trans-2,3-methanomethionine and alpha-methylmethionine

A comparative study of four peptidomimetics of the sequence Phe-Met-Arg-Phe-amide (FMRFa) was performed to compare the conformational bias caused by trans-2,3-methanomethionine and alpha-methylmethionine stereoisomers. The specific compounds studied were {(2S,3S)-cyclo-M} RFa, F{(2R,3R)-cyclo-M} RFa, F{(S)-alpha-Mem} RFa, and F{(R)-alpha-MeM} RFa. Molecular simulations based on CHARMm 22 indicate that gamma-turn, inverse gamma-turn, and alpha-helical conformations about the cyclo-M residue are accessible to the two F{cyclo-M} RFa stereoisomers. Similar calculations for F{(S)-alpha-MeM} RFa, and F{(R)-alpha-MeM}RFa indicate that the alpha-methylamino acids tend to favor alpha-helical conformations. The nmr data is presented for the four peptidomimetics. Most informative were the rotating frame nuclear Overhauser effect cross peaks between the NH protons proximal to the methionine surrogates, and the C beta hydrogens. Overall, these nmr data indicate F{(2S,3S)-cyclo-M} RFa and F{(2R,3R)-cyclo-M} RFa preferentially adopt inverse gamma-turn and gamma-turn conformations, respectively, whereas F{(S)-alpha-MeM} RFa and F{(R)-alpha-MeM} RFa tend to form partial left- and right-handed helical structures (although energy differences between the two turn structures, and between the two helical structures are likely to be small). It is suggested that the wider NH-C alpha-CO angle of cyclopropane amino acids and their more severe steric requirements around the C beta carbons force the peptidomimetic N- and C-termini into the same region of conformational space. This favors C7 turns in the cyclopropane amino acid series relative to the less constrained alpha-methyl derivatives.

Conformations of cis- and trans-2,3-methanomethionine stereoisomers in the tripeptide mimic system Ac[cyclo-M]NHiPr

Quenched molecular dynamics (QMD) was used to simulate low-energy conformers of the tripeptide mimics Ac¿cyclo-Met¿NHiPr, where the 2.3-methanomethionine is the cis-derivative (2R,3S)-cyclo-Met and the trans-derivative (2R,3R)-cyclo-Met. Variations of the favored omicron, upsilon values. and differences between the simulated preferred conformations for the two structures, were rationalized and discussed. Physical data for the cis-derivative (NMR, CD and FT-IR) gave no conclusive evidence for any preferred conformation. However for the trans-derivative, Ac¿(2R,3R)-cyclo-Met¿NHiPr, the physical data suggests that a conformer with partial helical structure is favored. This work provides details of how the rigidly constrained side chain and cyclopropane of 2,3-methanoamino acids can be used to manipulate phi, psi values in a logical fashion.

Synthesis and solution conformation of cyclo[RGDRGD]: a cyclic peptide with selectivity for the alpha V beta 3 receptor

Three peptides, cyclo[RGDRGD], cyclo[RGDRGd] (d = D-Asp), and the linear sequence RGDRGD, were prepared via solid phase syntheses. These were tested in binding assays based upon the alpha IIb/beta 3-fibrinogen and the alpha V beta 3-vitronectin interactions and found to be selective for the alpha V beta 3 integrin. The alpha V beta 3-vitronectin is important in bone regeneration, hence the compounds were also tested in an osteoclast regeneration assay; all three compounds, cyclo-[RGDRGD], cyclo[RGDRGd], and RGDRGD, showed modest activities. Molecular modeling, NMR, and CD studies were undertaken to elucidate the conformational preferences of cyclo-[RGDRGD], in aqueous solutions. Results from these studies strongly suggest that the molecule tends to adopt a type I beta-turn conformation with a relatively short distance between the Asp and Arg side chains. These observations are in harmony with the first correlations made between alpha V beta 3 selectivity and solution conformation for a peptide ligand (Pfaff, M.; et al. J. Biol. Chem. 1994, 269, 20233).

Comparison of cyclic delta-opioid peptides with non-peptide delta-agonist spiroindanyloxymorphone (SIOM) using the message-address concept: a molecular modeling study

Based upon the message-address concept, this molecular modeling study used the delta-selective agonist spiroindanyloxymorphone (SIOM) as a molecular template for a conformational search and analysis of delta-selective opioid peptides. It was assumed that the tyramine moiety plays the same role for delta-opioid receptor recognition in both peptide and non-peptide ligands. Using 20 reported low-energy conformations of Tyr-cyclo[D-Cys-D-Pen]-OH (JOM-13) for comparison, the geometrical relationship of the two aromatic rings present in SIOM was used for the identification of potential active conformations of JOM-13, from which two delta-receptor-binding models (I and II) were constructed. Models I and II differ from each other in the arrangement of the peptide backbones. To evaluate the two models, a conformational search of two other known delta-selective ligands, [D-Pen2,D-Pen5]enkephalin (DPDPE) and [D-Pen2,L-Pen5]enkephalin (DPLPE) was performed, using the geometrical relationship of the two aromatic rings defined in the two receptor-binding models as a molecular template. Among the conformations generated from the molecular simulation, low-energy conformers of DPDPE and DPLPE conforming to models I and II were identified. Unlike model I, conformers of DPDPE and DPLPE that fit model II contain a cis amide bond in the Gly3 residue.

Conformational analysis of beta-methyl-para-nitrophenylalanine stereoisomers of cyclo[D-Pen2, D-Pen5]enkephalin by NMR spectroscopy and conformational energy calculations

Solution conformations of beta-methyl-para-nitrophenylalanine4 analogues of the potent delta-opioid peptide cyclo[D-Pen2, D-Pen5]enkephalin (DPDPE) were studied by combined use of nmr and conformational energy calculations. Nuclear Overhauser effect connectivities and 3JHNC alpha H coupling constants measured for the (2S, 3S)-, (2S, 3R)-, and (2R, 3R)-stereoisomers of [beta-Me-p-NO2Phe4]DPDPE in DMSO were compared with low energy conformers obtained by energy minimization in the Empirical Conformational Energy Program for Peptides (ECEPP/2) force field. The conformers that satisfied all available nmr data were selected as probable solution conformations of these peptides. Side-chain rotamer populations, established using homonuclear (3JH alpha H beta) and heteronuclear (3JH alpha C gamma) coupling constants and 13C chemical shifts, show that the beta-methyl substituent eliminates one of the three staggered rotamers of the torsion angle chi 1 for each stereoisomer of the beta-Me-p-NO2Phe4. Similar solution conformations were suggested for the L-Phe4-containing (2S, 3S)- and (2S, 3R)-stereoisomers. Despite some local differences, solution conformations of L- and D-Phe4-containing analogues have a common shape of the peptide backbone and allow similar orientations of the main delta-opioid pharmacophores. This type of structure differs from several models of the solution conformations of DPDPE, and from the model of biologically active conformations of DPDPE suggested earlier. The latter model is allowed for the potent (2S, 3S)- and (2S, 3R)-stereoisomers of [beta-Me-p-NO2Phe4]DPDPE, but it is forbidden for the less active (2R, 3R)- and (2R, 3S)-stereoisomers. It was concluded that the biologically active stereoisomers of [beta-Me-p-NO2Phe4]DPDPE in the delta-receptor-bound state may assume a conformation different from their favorable conformations in DMSO.

Conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus group A by Metropolis Monte Carlo simulations

Metropolis Monte Carlo simulations have been performed on four substructures from the cell-wall polysaccharide antigen of Streptococcus group A to explore the conformational behaviour of these compounds. The compounds examined are the trisaccharide, propyl 3-O-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-2-O-(alpha-L-rhamnopyranosyl)- alpha-L-rhamnopyranoside, 1, the tetrasaccharide, propyl 3-O-(3-O-(2-acetamido-2-deoxy-beta-D- glucopyranosyl)-2-O-(alpha-L-rhamnopyranosyl)-alpha-L-rhamnopyranosyl)-alpha-L- rhamnopyranoside, 2, the hexasaccharide, propyl 3-O-(2-O-(3-O-(3-O-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-alpha-L- rhamnopyranosyl)-alpha-L-rhamnopyranosyl)-3-O-(2-acetamido-2-deoxy-beta-D- glucopyranosyl)-alpha-L-rhamnopyranosyl)-alpha-L-rhamnopyranoside, 3, and the hexasaccharide, propyl 3-O-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-2-O-(3-O-(3-O-(2-acetamido-2- deoxy-beta-D-glucopyranosyl)-2-O-(alpha-L-rhamnopyranosyl)-alpha-L- rhamnopyranosyl)-alpha-L-rhamnopyranosyl)-alpha-L-rhamnopyranoside, 4. In general, the conformational flexibility of similar glycosidic linkages in different compounds is comparable. However, in a few cases, small differences in the conformations available to these linkages in different structural environments could be detected. Interestingly, a second conformation found for the beta-D-GlcNAc-(1-->3)-alpha-L-Rha linkage in three of the compounds was not populated in the hexasaccharide 4. Furthermore, a conformational locale of the alpha-L-Rha-(1-->3)-alpha-L-Rha linkage found to be populated in the trisaccharide 1, tetrasaccharide 2, and hexasaccharide 4 is negligibly populated in the hexasaccharide 3. Ensemble averaged proton-proton distances compare favourably with experimental average distances obtained from NMR spectroscopy. The trisaccharide branch point in the hexasaccharides is shown to be a highly defined conformational feature. The same unit has been found to be one of the crucial elements recognized by anti-Group A Streptococcus antibodies, a result that has implications for the design of improved immunodiagnostics and vaccines.

Delta opioid receptor selective ligands; DPLPE-deltorphin chimeric peptide analogues

Further efforts to correlate the topography of the bioactive structures of DPDPE and the deltorphins, two delta-opioid receptor active peptide families, are reported. A number of DPLPE-deltorphin chimeric peptides have been synthesized in which the C-terminal dipeptide delta-address of the deltorphins (-Val-GlyNH2, -Nle-GlyNH2) have been linked to the highly delta-opioid selective cyclic peptides DPDPE or DPLPE. These studies demonstrate that a major structural feature determining high potency of hybrid analogues is the chirality of the amino acid residue in position 5. The radioligand binding assays have revealed a decrease in potency (compared to DPDPE) at delta-receptors when the C-terminal dipeptides were added to DPDPE. On the other hand, chimeric peptides of DPLPE with these same C-terminal dipeptides retained high delta-selectivity and affinity. Similar results were obtained using the mouse vas deferens (MVD) and guinea pig ileum (GPI) bioassays. The importance of the hydrophilicity of amino acids in positions 2 and 5 for delta-selectivity is consistent with the previous finding for DPLPE and DPDPE. On the other hand, the replacement of phenylalanine-4 with p-chlorophenylalanine-4 did not increase delta-selectivity as in DPDPE. These findings suggest that the delta-receptor interacts with hybridized enkephalins and deltorphins somewhat differently than with DPDPE.

Conformational analysis of arachidonic and related fatty acids using molecular dynamics simulations

Arachidonic acid has recently gained attention as a result of current evidence indicating that it may play the role of a 'second messenger' in signal transduction processes. In order to gain insight into the mechanism behind its action, quenched molecular dynamics simulations were performed on arachidonic (20:4) and related fatty acids: linoleic (18:2), oleic (18:1), arachidic (20:0), and stearic (18:0). The angle-iron structure, representative of arachidonic acid in the crystal or very-low-temperature state, readily gave way at higher temperature to a dominant hairpin structure whereby the COOH end of arachidonic acid comes into close proximity with the C14-15 pi-bond resulting in a packed pi-bond-rich loop. The lowest energy conformer for arachidonic acid was found to be 10.65 kcal/mol below that of the energy-minimized crystal structure. In the case of saturated fatty acids, the crystal all-trans conformation remained the lowest energy form. Analysis of conformational energy contours for carbon-carbon torsion angles representative of fatty acids suggest that the flexibility of arachidonic acid is, in part, a result of the relative torsional freedom of C-C (single) bonds located between or adjacent to C = C (double) bonds. It is hypothesized that the ability of arachidonic acid to form packed structures with curved regions containing pi-bonds may allow for hydrophobic interactions with proteins, and/or hydrogen bonding between the pi-bonds of arachidonic acid and polar groups of the protein structures.

Molecular dynamics simulations of opioid peptide analogs containing multiple conformational restrictions

Molecular dynamics simulations were performed on the potent and slightly mu-receptor selective cyclic dermorphin analog H-Tyr-D-Orn-Phe-Glu-NH2 as well as on analogs containing a conformationally restricted phenylalanine derivative in place of Phe in the 3 position of the peptide sequence. Peptides studied included the potent and highly mu-selective analogs H-Tyr-D-Orn-Aic-Glu-NH2 (Aic = 2-aminoindan-2-carboxylic acid), H-Tyr-D-Orn-Atc-Glu-NH2 (Atc = 2-aminotetralin-2-carboxylic acid) and H-Tyr-D-Orn-D-Atc-Glu-NH2, and the weakly active analog H-Tyr-D-Orn-Tic-Glu-NH2 (Tic = tetrahydroisoquinoline-3-carboxylic acid). Four different starting conformations were chosen for each peptide, and after equilibration each simulation was allowed to proceed for 100 picoseconds at 600 degrees K. The 14-membered ring structures in the Phe-, Aic-, L- and D-Atc-containing analogs showed moderate structural flexibility, while the peptide ring in the Tic-containing analog was more rigid. As theoretically predicted, the phi 3 and psi 3 angles of the Aic-, L- and D-Atc-containing analogs were limited to values of either about +50 degrees or -50 degrees during almost the entire period of the simulations. In the Tic-containing analog the phi 3 and psi 3 angles were 0 degrees and 90 degrees, respectively, and did not change for the entire duration of the simulation. The side chains of the constrained amino acids showed limited movement, but transitions between the allowed conformations did occur on the time scale of the simulations.(ABSTRACT TRUNCATED AT 250 WORDS)