Conformational interpretation of intramolecular electron transfer in Met5-enkephalins between Tyr and Met(S:.Br) radical.

Mean distances between C beta atoms of redox centers and mean values of the exponentially distance dependent rate constants for intramolecular electron transfer, (k), in aqueous solution were calculated for Met5-enkephalin and its D-Ala2 analogue using the molecular mechanics and Monte Carlo techniques. The ratio of (k) values thus obtained proved similar to that determined experimentally for intramolecular electron transfer accompanying Met(S:.Br)----TyrO.radical transformation in these two peptides. This agreement indicates that the almost 2-fold difference observed between experimental k values for Met5-enkephalin and its D-Ala2 analogue can be attributed to the effect of Gly2 for D-Ala2 replacement on the average separation of the redox centers.

Dynamic space structure of the Leu-enkephalin molecule in DMSO solution.

The dynamical space structure of the Leu-enkephalin molecule in DMSO solution was described combining the ROE measurements and Monte Carlo energy calculations. The statistical weights for possible Leu-enkephalin conformers were estimated by comparing the NMR-experimental parameters and the same parameters average over statistical samples of molecular structures obtained by Monte Carlo techniques for every low-energy conformer. The statistical weight estimations reveal that the Leu-enkephalin molecule in DMSO solution is apparently represented by a mixture of at least two peptide backbone conformers with the mean statistical weight values of 70% and 30%. Both conformers possess significant local conformational fluctuations. Each of them represents a folded backbone structure with the folding at the Gly2-Gly3 and Gly3-Phe4 fragments occurring simultaneously in solution.

A model for the delta-receptor-bound conformation of enkephalin.

Sets of low-energy structures were determined by energy calculations for two cyclic analogues of enkephalin (Ek), [D-Pen2, D-Pen5]-Ek and [D-Pen2, L-Pen5]-Ek, possessing the highest specificity towards delta-opioid receptors. Comparison of mutual spatial orientations of the alpha-amino group and aromatic moieties of the Tyr and Phe residues permitted one to suggest a model for the delta-receptor-bound conformation of enkephalin-related peptides. The model involves a pronounced gamma-like turn of the peptide backbone centred on the Gly3 residue.

Equilibrium of conformers in solution: spin-labelled angiotensin.

The number of structural parameters were determined for spin-labelled angiotensin in aqueous solution with the use of fluorescence spectroscopy and 1H NMR relaxation induced by the spin label. At the same time all measured parameters were estimated theoretically by means of energy calculations and Monte-Carlo techniques. The matching procedure for experimental and computational data allows one to suggest a dynamic equilibrium between conformers of the molecule in aqueous solution and to estimate the values of their weights.

Possible bioactive conformations of alpha-melanotropin.

By comparing the results of energy calculation for alpha-MSH and its semirigid analogues Ac-[ Cys4 , Cys10 ]-alpha- MSH4 -10-NH2, Ac-[ Cys4 , Cys10 ]-alpha- MSH4 -13-NH2, and [ Cys4 - Cys10 ]-alpha-MSH, a detailed description of two possible bioactive conformations for the 'specific' central site of alpha- MSH6 -9 is proposed representing variants of chain-reversal structure. A possible explanation of the rise in melanotropic activity of the latter two semirigid analogues is presented.

Ac-[3- and 4-alkylthioproline31]-CCK4 analogs: synthesis and implications for the CCK-B receptor-bound conformation.

It has been reported that substitution of the Met31 residue in Boc-CCK4 (Boc-Trp30-Met31-Asp32-Phe33-NH2, CCK33 numbering) by trans-3-propyl-L-proline yields a highly potent and selective CCK-B agonist. To further explore the structural requirements of the Met31 side chain in the receptor-bound conformation of CCK4, we have synthesized several Ac-CCK4 analogs containing substitution of Met31 by 3- and 4-(alkylthio)-substituted proline derivatives. To this end we have developed novel synthetic routes to enantiomerically pure N-Boc-4-cis- and -trans-(methylthio)prolines and racemic N-Boc-3-cis and -trans-[(4-methylbenzyl)thio]prolines. The protected mercaptoprolines were incorporated into Ac-CCK4 analogs using SPPS and were alkylated using various electrophiles following cleavage from the solid support. Binding assays reveal that 3-(alkylthio)prolines analogs have higher affinities at the CCK-B receptor than the corresponding 4-(alkylthio)proline analogs, and that trans-3-(alkylthio)proline analogs had higher affinities than corresponding cis-3-(alkylthio)proline analogs. Within both the cis- and trans-3-(alkylthio)proline series, the order of potency was found to be Me < Et < n-Pr. The trans-3-(n-propylthio)-L-proline analog demonstrates a higher affinity than that reported for Boc-CCK4[trans-3-propyl-L-Pro31]. Comparison of the low-energy structures calculated for several high-affinity Ac-CCK4 analogs reveal a common geometry which we propose to be the CCK-B receptor-bound conformation. This model shows grouping of the hydrophobic side chains of Trp, Met, and Phe at one side of the molecule and the hydrophilic side chain of Asp and the C-terminal carboxamide at the other side.

Novel cyclic analogs of angiotensin II with cyclization between positions 5 and 7: conformational and biological implications.

To study the conformational features of molecular recognition of angiotensin II (Asp1-Arg2-Val3-Tyr4-Val/IIe5-His6-Pro7-Phe8, AII), the synthesis and biological testing of several cyclic analogs of AII cyclized between positions 5 and 7 have been performed. The synthesized analogs were Sar1-Arg2-Val3-Tyr4-cyclo(Cys5-His6-Pen7)-Phe8 (3), Sar1-Arg2-Val3-Tyr4-cyclo(Asp5-His6-Apt7)-Phe8 (4), Sar1-Arg2-Val3-Tyr4-cyclo(Glu5-His6-Apt7)-Phe8 (5), Sar1-Arg2-Val3-Tyr4-cyclo-(Cys5-His6-Mpt7)-Phe8 (6), Sar1-Arg2-Val3-Tyr4-cyclo(Cys5-His6-Mpc7)-Phe8 (7), Sar1-Arg2-Val3-Tyr4-cyclo(Hcy5-His6-Mpt7)-Phe8 (8), and Sar1-Arg2-Val3-Tyr4-cyclo(Hcy5-His6-Mpc7)-Phe8 (9), where Apt stands for 4-amino-trans-proline, and Mpt and Mpc for 4-mercapto-trans- and -cis-prolines, respectively. Compound (9) showed good affinity at AT-1 receptors, namely a KD = 20 nM. In functional assays, it showed the characteristics of a weak partial agonist with a relative affinity of 0.26% of that for AII and an intrinsic efficacy, alpha E, of 0.42. Molecular modeling suggested a possible explanation for this finding: the relatively strong binding and the weak partial agonistic activity of compound 9 are due to interaction with AT-1 receptor of only two functionally important groups, namely, the side chains of the His6 and Phe8 residues.

Design, synthesis, biology, and conformations of bicyclic alpha-melanotropin analogues.

Seven side chain-constrained bicyclic alpha-melanotropin (alpha-MSH) analogues were designed and synthesized, their conformations analyzed, and their biological properties examined in the frog skin and lizard skin bioassays. The structure of these analogues is based on the central sequence Ac-Cys4-Xaa5-His6-DPhe7-Arg8-Trp9-Cys10-Lys11 -NH2 (Xaa5 = Asp or Glu) and has been extended on the N-terminal with the amino acids Ser1-Tyr2-Ser3 and on the C-terminal with Pro12-Val13 to more closely resemble the native hormone alpha-MSH. The analogue Ac-Cys4-Asp5-His6-DPhe7-Arg8-Trp9-Lys10-Cys11 -NH2 also was synthesized, and its conformational and biological properties were examined. Design of these analogues was based upon the previously identified superpotent monocyclic peptides [Cys4,DPhe7,Cys10]alpha-MSH(4-10)-NH2 and [Nle4,Asp5,DPhe7,Lys10]alpha-MSH(4-10)-NH2 with the rationale of increasing conformational constraints to restrict the available backbone conformations as a means to identify the conformations that facilitate biological activity. Computer-assisted conformational analysis of the central tetrapeptide residues 6-9 identified beta-turns which varied with respect to the residue in the i + 1 position. Each highly constrained peptide contains D-Phe7 and a 23-membered ring which has previously been identified as crucial to produce prolonged acting peptides with superagonistic activities. The bicyclic peptides reported in this study are full agonists and are 25-400-fold less potent than alpha-MSH in the frog and lizard skin bioassays.

The use of topographical constraints in receptor mapping: investigation of the topographical requirements of the tryptophan 30 residue for receptor binding of Asp-Tyr-D-Phe-Gly-Trp-(N-Me)Nle-Asp-Phe-NH2 (SNF 9007), a cholecystokinin (26-33) analogue that binds to both CCK-B and delta-opioid receptors.

The cholecystokinin (26-33) [CCK (26-33)] octapeptide analog Asp-Tyr-D-Phe-Gly-Trp(N-Me)-Nle-Asp-Phe-NH2 (SNF 9007) is a potent and selective ligand for both the CCK-B and delta-opioid receptors. Pharmacological studies of SNF 9007 suggest a relationship between the ligand requirements of CCK-B and delta-opioid receptors, which further implies a possible structural relationship between these receptors. We have utilized topographical constrainment of the important Trp30 residue to investigate structural features of SNF 9007 that would distinguish between binding requirements in this region for the CCK-B and delta-opioid receptors. Thus, the four optically pure isomers of beta-MeTrp were substituted for L-Trp30 of SNF 9007. Receptor binding results suggest that the preferred topography of the Trp30 residue for CCK-B receptor binding may be the 2S,3S (erythro-L) configuration whereas for the delta-opioid receptor it may be the 2S,3R (threo-L) configuration. Molecular modeling studies of these ligands further support the recently revised receptor-bound model for CCK-B octapeptide ligands (Kolodziej et al. J. Med. Chem. 1995, 38, 137-149) and are in good agreement with the DPDPE-delta opioid receptor "template" model (Nikiforovich et al. Biopolymers 1991, 31, 941-955).

Novel approach to computer modeling of seven-helical transmembrane proteins: current progress in the test case of bacteriorhodopsin.

G-protein coupled receptors (GPCRs) are thought to be proteins with 7-membered transmembrane helical bundles (7TM proteins). Recently, the X-ray structures have been solved for two such proteins, namely for bacteriorhodopsin (BR) and rhodopsin (Rh), the latter being a GPCR. Despite similarities, the structures are different enough to suggest that 3D models for different GPCRs cannot be obtained directly employing 3D structures of BR or Rh as a unique template. The approach to computer modeling of 7TM proteins developed in this work was capable of reproducing the experimental X-ray structure of BR with great accuracy. A combination of helical packing and low-energy conformers for loops most close to the X-ray structure possesses the r.m.s.d. value of 3.13 A. Such a level of accuracy for the 3D-structure prediction for a 216-residue protein has not been achieved, so far, by any available ab initio procedure of protein folding. The approach may produce also other energetically consistent combinations of helical bundles and loop conformers, creating a variety of possible templates for 3D structures of 7TM proteins, including GPCRs. These templates may provide experimentalists with various plausible options for 3D structure of a given GPCR; in our view, only experiments will determine the final choice of the most reasonable 3D template.

Combined use of spectroscopic and energy calculation methods for the determination of peptide conformation in solution.

This paper describes the combined use of energy calculations and spectroscopic data for the determination of peptide conformations in solution. The approach involves (i) experimental measurements of spectroscopic parameters for a molecule, (ii) calculation of these parameters for low-energy conformers previously determined with regard to local fluctuations in conformation and (iii) a random search for statistically weighted combinations of conformers which provide a good agreement between the calculated and experimental data. The above approach was used to study the conformation of a spin-labelled angiotensin molecule (SL-AT). It appears that the C-terminal hexapeptide of SL-AT possesses two geometrically different spatial forms of the backbone in aqueous solution, with mean values for the statistical weight of 0.78 and 0.22, respectively. In contrast, the N-terminal part of the molecule is conformationally labile. The data obtained can be used to describe the conformation of angiotensin in solution.

Determination of cyclopeptide conformations in solution using NMR data and conformational energy calculations.

The three-dimensional structure of the cyclic analogs of bradykinin and substance P C-terminal hexapeptide was studied using conformational energy calculations. Initial conformations for energy minimization were selected with the aid of the measured intensities of local nuclear Overhauser effects (NOEs) and other 1H-NMR data. Expected values of the 1H-NMR parameters for low-energy conformations of the cyclopeptides were calculated and compared with those observed experimentally using semiquantitative gradation of NOE intensities. Several low-energy structures of the cyclic bradykinin analog, possessing similar backbone conformations stabilized by two beta-turns, are in agreement with experimental data. None of the low-energy conformations of the substance P cyclic hexapeptide were in satisfactory agreement with the experimental set of NOEs. The agreement was achieved only by averaging of the calculated 1H-NMR parameters over several combinations of the low-energy conformations.

The space structure of a conformationally labile oligopeptide in solution: angiotensin.

The paper describes a new approach to the problem of space structure description for conformationally labile molecules existing in solution as a set of different conformers in dynamic equilibrium. In such a case the "average" model derived exclusively from physico-chemical data represents a virtual structure devoid of physical sense. The proposed approach involves the selection of statistical weights wi for molecular conformers in solution by combined use of spectroscopic data and energy calculations (including the Monte-Carlo technique). Consequently, it appears possible to confine the entire region of all wi values only by those points (wi) that provide a reasonable agreement between the results of calculations and the experimental data. The approach was put to trial by using the linear octapeptide angiotensin, a well-known bioregulator with a wide spectrum of action. The 1H NMR and fluorescence spectroscopy were used as a source of experimental evidence concerning the space structure of the peptide in aqueous solution. The spin-lattice relaxation rates induced by the spin label allowed to estimate simultaneously several parameters characterizing the distance between the spin label and different functional groups in the angiotensin molecule. At least 5 types of angiotensin conformers were shown to be "indispensable" to achieve a good agreement between the results of energy calculations and 1H NMR spectroscopy data obtained in solution. The statistical weight estimates for angiotensin conformers permit to predict, with a high degree of accuracy, the value of singlet-singlet energy transfer between the Phe and Tyr aromatic chromophores of the molecule in aqueous solution. The proposed approach to the description of conformationally labile molecules can be actually regarded as stepwise refinement of statistical weight limits for sets of low-energy conformers in solution upon accumulation of new experimental evidence. The same appears to apply to conformationally labile molecules of non-peptide nature.

[Statistical weights of conformers of thyroliberin molecule and the averaging of its calculated structural characteristics]. / Statisticheskie vesa konformerov molekuly tiroliberina i usrednenie ee raschetnykh strukturnykh kharakteristik.

A statistical ensemble of thyroliberin conformations has been generated using Monte-Carlo techniques. The averaged vicinal coupling constants for the peptide backbone and His side chain, percentage of prolyl cis-isomers and characteristics of possible intramolecular hydrogen bonds have been calculated. The obtained mean values are in good agreement with the experimental results. This fact indicates that the generated statistical ensemble is similar to the true one and evidences against the existence in solution of a single unique structure of thyroliberin.

[Comparison of conformation characteristics of bradykinin and igercin molecules]. / Sopostavlenie konformatsionnykh vozmozhnostei molekul bradikinina i igertsina.

A certain resemblance of three-dimensional molecular organizations of the known peptide bioregulator bradykinin (Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg) and the tentative cytophilic centre of the human IgE igercin (Arg-Ala-Val-Ser-Val-Asn-Pro-Gly-Lys) existing along with their pronounced structural similarity was shown by means of energy calculations. This is, however, not the case with the "biologically active" bradykinin conformations suggested earlier.

[Conformational-functional relationships of tetragastrin analogs]. / Konformatsionno-funktsional'nye otnosheniia analogov tetragastrina.

Sets of low-energy backbone conformations of the active tetragastrin analogue Boc-Trp-Leu-Asp-Phe-NH2 and two competitive antagonists Boc-Trp-Leu psi (CH2NH)-Asp-Phe-NH2 and Boc-Trp-Leu-Asp-O-CH2-CH2-C6H5 were obtained using theoretical conformational analysis methods. Groups of the conformations were selected for the three analogues, allowing a spatial matching of Trp, Asp and Phe residues responsible for the gastrin receptor binding. Three conformations possessing the lowest energies among the geometrically similar structures of these three peptides are suggested as a model for the "receptor-bound" conformations of these analogues. Backbone spatial folding resembling an alpha-helix turn is characteristic of these conformations. The correspondence of the proposed model to the available data on structure--activity relationships for tetragastrin analogues is discussed. Orientations of the putative receptor-bound conformations in a "water--lypophylic medium" two-phase system were investigated.

[Synthesis, biological activity and conformation of enkephalin analogs structurally related to kyotorphin]. / Sintez, biologicheskaia aktivnost' i konformatsionnye issledovaniia analogov énkefalina, strukturno rodstvennykh kiotrofinu.

[D-Arg2,Leu5]Enkephalin and two series of its N-terminal short-chain analogues with a free and modified C-terminal carboxylic group, viz. amides and ethyl esters of tri- and tetrapeptides, were synthesized in solution and by solid-phase method. Their analgesic activity, assayed by the "tail pinch" method following intracisternal and intravenous administration to mice, was compared with activity of enkephalins and morphine. To study the space structure of the synthesized compounds, conformational calculations and fluorescence spectroscopy were applied to measure distance between aromatic nuclei of tyrosine and phenylalanine residues in the two tetrapeptides. Ethyl esters of the tri- and tetrapeptides exceed in analgesic activity the corresponding carboxylic acids and amides. In contrast to the pentapeptide, the tetrapeptide analogues were active upon intravenous administration. Conformational aspects of this series of analogues are discussed in detail; the abrupt increase in activity upon transition from tri- to tetrapeptides does not appear to be related to conformational changes.

[Conformational aspects of the molecular mechanism of action of bradykinin. II. Conformation and selectivity of action of bradykinin cycloanalogs]. / Konformatsionnye aspekty molekuliarnogo mekhanizma deistviia bradikinina. II. Conformatsiia i selektivnost' deistviia tsikloanalogov bradikinina.

Conformation energy calculations performed for cyclo[(epsilon-lysine1, glycine6)]bradykinin and cyclo-epsilon-kallidin indicate the absence of spatially equivalent low-energy structures for bradykinin and cyclobradykinin molecules, whereas cyclokallidin has conformations similar to the "biologically active" ones for bradykinin that are implicated in binding to both B1 and B2 type receptors.

[Synthesis and biological activity of a lysine-containing cyclic analog of [Leu5]enkephalin]. / Sintez i biologicheskaia aktivnost' lizinsoderzhashchego tsikloanaloga [Leu5]énkefalina.

The cyclic analogue of [Leu5]enkephalin--cyclo (Lys-Tyr-Gly-Gly-Phe-Leu) and two corresponding linear hexapeptides with lysine residue attached to the N- or C-terminus of the molecule have been synthesized by classical methods of peptide chemistry. The addition of lysine residue to the N-terminus of cyclization of the molecule reduce the interaction of these analogues with both central and peripheral opiate receptors. The addition of lysine residue to the C-terminus of the molecule through the epsilon-amino group does not affect the interaction of the analogue with mu-receptors but reduces approximately tenfold its affinity for delta-receptors. All three analogues have analgesic potency similar to that of [Leu5]enkephalin as assayed after intracisternal administration to mice.

[Conformation of the enkephalin cycloanalog Lys-Tyr-Gly-Gly-Phe-Leu-]. / Prostranstvennaia struktura molekuly tsikloanaloga énkefalina Lys-Tyr-Gly-Gly-Phe-Leu-.

The spatial structure of an enkephaline cycloanalogue Lys-Tyr-Gly-Gly-Phe-Leu--has been investigated by means of energy calculations, fluorescence and CD-spectroscopy. Despite the high conformational mobility of the cycloanalogue, little resemblance exists between its and parent peptide's low-energy structures. Conformational factors for possible mechanisms of interaction between specific enkephalin receptors and cycloanalogue are discussed.