Nonpolar interactions of thrombin S' subsites with its bivalent inhibitor: methyl scan of the inhibitor linker.

We have designed bivalent thrombin inhibitors, consisting of a nonsubstrate type active site blocking segment, a hirudin-based fibrinogen recognition exosite blocking segment, and a linker connecting these segments. The inhibition provided by the bivalent inhibitors with various linker lengths revealed that a minimum of 15 atoms was required for simultaneous binding of the two blocking segments of the inhibitor to thrombin without significant distortion. The crystal structure of the inhibitors with a 16-atom linker showed some conformational flexibility in the linker portion which still lies deep in the groove joining the active site and the fibrinogen recognition exosite. Since the thrombin S' subsites are not well characterized, we designed a new strategy to search for possible nonpolar interactions between the linker and the thrombin S' subsites. This strategy, the "methyl scan", is based on the incorporation of a methyl side chain at each atom position of the linker by using sarcosine, D,L-alanine, D,L-3-aminoisobutyric acid, or N-methyl-beta-alanine. The methyl groups on the second and the eighth atom positions of the linker, which correspond to the side chains of the P1' and the P3' residues, respectively, improved the affinity of the inhibitors significantly. Further study of the stereospecificity showed that L-Ala at the P1' residue and D-Ala at the P3' residue preferably improved the affinity of the inhibitors 20- and 25-fold, respectively. Molecular modeling calculations using a methyl probe were also carried out to identify favorable nonpolar interacting sites on the thrombin surface. Two sites were identified in the vicinity of the P1' and the P3' residues, supporting the validity of the methyl scan method. Thus, this study has improved our understanding of the interactions taking place in this groove. In particular, we have been able to show that some specific structural features, such as hydrophobic complementarity between the linker and the thrombin S' subsites, could be exploited and make these inhibitors trivalent.

Bioactive peptides: conformational studies of [Tyr4] cyclolinopeptide A.

The solid state conformational analysis of [Tyr4] cyclolinopeptide A has been carried out by x-ray diffraction studies. The crystal structure of the monoclinic form, grown from a dioxane-water mixture [alpha = 9.849 (5) A, b = 20.752 (4) A, c = 16.728 (5) A, beta = 98.83 (3) degrees, space group P21, Z = 2], shows the presence of five intramolecular N-H...O = C hydrogen bonds, with formation of one C17 ring structure, one alpha-turn (C13), one inverse gamma-turn (C7), and two beta-turns (C10, one of type III and one of type I). The Pro1-Pro2 peptide unit is cis (omega = 5 degrees), all others are trans. The structure is almost superimposable with that of cyclolinopeptide A. The rms deviation for the atoms of the backbones is on the average 0.33 A.

Design of potent bivalent thrombin inhibitors based on hirudin sequence: incorporation of nonsubstrate-type active site inhibitors.

Hirudin from medicinal leech is the most potent and specific thrombin inhibitor from medicinal leech with a K(i) value of 2.2 x 10(-14) M. It consists of an active site blocking moiety, hirudin1-48, a fibrinogen-recognition exo-site binding moiety, hirudin55-65, and a linker, hirudin49-54, connecting these inhibitor moieties. Synthetic inhibitors were designed based on the C-terminal portion of hirudin. The bulky active site blocking moiety, hirudin1-48, was replaced by small nonsubstrate-type active site inhibitors of thrombin, e.g., dansyl-Arg-(D-pipecolic acid). The linker moiety was replaced by omega-amino acids of (12-aminododecanoic acid)-(4-aminobutyric acid), and hirudin55-65 was used as a fibrinogen-recognition exo-site binding moiety in most of the inhibitors. The crystal structure of the inhibitor in complex with human alpha-thrombin showed that dansyl, Arg, and D-pipecolic acid of the active site blocking moiety occupy S3, S1, and S2 subsites of thrombin, respectively, and were therefore designated as P3, P1, and P2 residues. The use of dansyl-Arg-(D-pipecolic acid) improved the affinity (K(i)) of the inhibitor 10-100-fold (down to 1.70 x 10(-11) M) compared to that of the similar compounds having D-Phe-Pro-Arg as their substrate-type inhibitor moiety (K(i) = 10(-9)-10(-10) M). The linker connected to P2 residue eliminated the scissile peptide bond. The inhibitor was also stable against human plasma proteases. Further inhibitor design revealed that the toxic dansyl group could be replaced by 4-tert-butylbenzenesulfonyl group and 1- or 2-naphthalenesulfonyl group for in vivo studies.(ABSTRACT TRUNCATED AT 250 WORDS)

Does the edge-to-face interaction between aromatic rings occur in cyclolinopeptide A analogues?

We measured 1H-NMR, fluorescence and CD spectra of cyclolinopeptide A (CLA), its tyrosine analogues with each or both phenylalanines substituted by tyrosine (c-[LeuIleIleLeuValProProTyrPhe], c-[LeuIleIleLeuValProProPheTyr] and c-[LeuIleIleLeuValProProTyrTyr]), and their linear counterparts with the starting sequence leu-Ile-Ile-Leu-Val-Pro-Pro-Phe-Phe (LA). It follows from CD spectra that the conformations of all cyclic peptides are similar to that of CLA; the conformations of linear peptides are more diversified, with the conformation of [Tyr9]LA being most similar to CLA. NMR studies suggest that aromatic rings in cyclic peptides are situated perpendicular to each other, manifesting edge-to-face pairing. Accordingly, the residue in position 9 is shielded ('edge'), and a residue in position 8 is the shielding one ('face'). This effect is not present in the case of linear peptides. Fluorescence quantum yields were much lower for cyclic peptides than for linear ones, indicating the interaction of closely located aromatic chromophores. Those quantum yields depend on the relative position of Tyr in the peptide chain. Another factor influenced by the position in the peptide chain is the optical activity of aromatic side chains (optically active in position 8, inactive in position 9). This phenomenon could be explained by the differences in the side-chain conformation of both aromatic residues.

Synthesis and biological studies on analogs of cyclolinopeptide A with a shortened peptide chain.

Continuing our work on the immunosuppressive activity of cyclolinopeptide A (CLA), a cyclic nonapeptide of the sequence: c-(-Leu-Ile-Ile-Leu-Val-Pro-Pro-Phe-Phe), we synthesized a series of 6 linear analogs of CLA, successively shortened at the N-terminus of the peptide chain. Immunosuppressive activity of acetates as well as trifluoroacetates of these peptides was investigated using PFC (humoral immunity) and DTH (cellular immunity) tests. It was found that the immunosuppressive potency of the peptides examined diminishes with shortening of the peptide chain. Octapeptide I with the sequence Ile-Ile-Leu-Val-Pro-Pro-Phe-Phe was found to be the most active of the whole series. The immunosuppressive activity increased again for a tripeptide fragment of CLA of the sequence Pro-Phe-Phe. The immunosuppressive activity of octapeptide probably depends on the suppression of IL-1, IL-6 and TNF production by the cells involved in immune and inflammatory response.

Synthesis and immunosuppressive activity of glycine containing linear analogs of cyclolinopeptide A.

We demonstrated that a linear peptide Gly-Ile-Ile-Leu-Val-Pro-Pro-Phe, the analog of a cyclic nonapeptide c-(Leu-Ile-Ile-Leu-Val-Pro-Pro-Phe-Phe) possesses a distinct immunosuppressive activity. We synthesized a series of eight other analogs of the linear peptide. The series consists of the nonapeptides protected on N- and/or C-terminus by acetyl-, succinyl-, and amido- functions and of Gly-Ile-Ile-Leu-Val-Pro-Pro-Phe-Phe elongated on N- and/or C-terminus by additional glycine residues. It was found that the protection of the terminal functional groups of the peptide slightly increases its immunosuppressor potency. At the same time the elongation of the peptide chain on both termini by additional glycine residues evokes a distinct increase of the immunosuppressive activity.

Immunosuppressive activity of alanine analogs of cyclolinopeptide A.

The immunosuppressive activity of a linear peptide related to cyclolinopeptide A, Leu-Ile-Ile-Leu-Val-Pro-Pro-Phe-Phe, and its nine analogs, where each successive amino acid residue was substituted by alanine, was investigated using the plaque forming cell and delayed type hypersensitivity tests for the humoral and cellular immune response, respectively. The linear peptide was less active than its cyclic counterpart in the humoral, and equally active in the cellular immune response. All alanine analogs showed quite strong immunosuppressive potencies in the humoral immune response tested in vitro. In the in vivo humoral immune response their activities were much less differentiated than it was observed in the in vitro experiments. All alanine analogs retain the immunosuppressive activity in the cellular immune response. However, their activities are practically not differentiated, and it is impossible to decide which amino acid side chains of the parent peptide are the most important for generation of the immunosuppressive effects. CD spectra of alanine analogs show that, in comparison with the parent peptide, conformational equilibria of these peptides are shifted towards unordered conformations. This finding correspond well to the results of the biological tests which show that all alanine analogs are less biologically active than the parent peptide. The results of CD measurements suggest also that interaction of the hydrophobic residues located at the ends of the peptide chain may be of importance for stabilization of the folded structure of the investigated compounds.

Immunosuppressive activity of antamanide and some of its analogues.

In connection with our discovery of a strong immunosuppressive activity of cyclolinopeptide A (CLA), we investigated immunosuppressive properties of antamanide and a number of its analogues, including symmetrical antamanide, and compared them with the activities of cyclosporin A and CLA. The peptides were investigated by using plaque forming cell (PFC), graft-versus-host (GvH), delayed type hypersensitivity (DTH), and autologous rosette formation cell (ARFC) tests. Antamanide and symmetrical antamanide exhibit an immunosuppressive activity lower than CLA. Linear antamanide fragments are also active. At higher concentrations of the latter peptides, toxic effects occur.

Immunosuppressive activity of tyrosine analogues of cyclolinopeptide A.

Immunosuppressive properties of six tyrosine analogues of cyclolinopeptide A were studied and compared with the activity of cyclosporin A. The peptides were investigated using PFC (in vitro) and DTH tests.

Immunoregulatory activity of substance P fragments.

The C-terminal SP7-11 pentapeptide (Phe-Phe-Gly-Leu-Met-NH2) was found to suppress in vitro the immune response in a dose of 1-5 micrograms/ml. It produced also a distinct immunosuppression in vivo, by both per os and intraperitoneal, applications. In contrast, the N-terminal SP1-4 fragment (Arg-Pro-Lys-Pro) suppressed the response at a dose of 0.1 microgram/ml, but stimulated it slightly at higher doses (1-5 micrograms/ml). A structural analog of SP1-4 (Gly-Pro-Arg-Pro tetrapeptide) was found to be a strong immunosuppressor at a dose of 5 micrograms/ml, indicating the importance of N-terminal basic residue for the immunoregulatory activity of intact SP.

Conformational preferences of sequential fragments of the hinge region of human IgA1 immunoglobulin molecule: II.

The mean solution conformation of tetrapeptide fragments of the hinge region of human IgA1 molecule was investigated by CD and 13C-NMR methods. Distinct conformational differences for the partial sequences were found. Tetrapeptides with the Thr-Pro-Ser-Pro sequence were found to show a clear preference for the beta-turn conformation. Conformational equilibria of these peptides are only slightly affected by acetylation or pH changes. In the case of Pro-Thr-Pro-Ser tetrapeptides conformational equilibria are dominated by unordered forms.

Conformational preferences of the sequential fragments of the hinge region of the human IgA1 immunoglobulin molecule.

The mean solution conformation of tetrapeptide fragments spanning the hinge region of human IgA1 was investigated by CD and 13C-NMR methods. Distinct conformational differences for the partial sequences of IgA1 were found. In a series of tetrapeptides having the Thr-Pro-Pro-Thr sequence, the Pro-Pro fragment was ordered to the structure of a type II polyproline helix, but with unordered forms prevailing in the equilibria. In the case of the Pro-Pro-Thr-Pro sequence, a distinct preference for the beta-turn conformation was found. Acetylation of this tetrapeptide shifts the equilibrium towards unordered forms containing some elements of the type II polyproline helix. The peptide Thr-Pro-Ser-Pro exists predominantly in the beta-turn conformation whereas Pro-Ser-Pro-Ser-NH2 has, for the most part an unordered conformation.

Changes of dipole moments in the series of Boc-(ProLeuGly)n-OBzl oligopeptides and their possible explanation. A preliminary survey.

It was found that the dipole moments in the series of Boc-(ProLeuGly)n-OBzl oligopeptides (n = 1-5) measured in dioxane solution demonstrate a distinct concentration dependence beginning from dodecapeptide. This effect may be connected with the appearance of aggregated (triple-helical?) structure in conformation equilibrium. The tendency to minimize the dipole moment of the system may be of some importance in the creation of supercoiled structures of polypeptides.