Side chain interactions in aromatic dipeptides

Old Molecules for New Receptors: Trp(Nps) Dipeptide Derivatives as Vanilloid TRPV1 Channel Blockers

The transient receptor potential vanilloid member 1 (TRPV1), an integrator of multiple pain-producing stimuli, is regarded nowadays as an important biological target for the discovery of novel analgesics. Here, we describe the first experimental evidence for the behavior of an old family of analgesic dipeptides, namely Xaa-Trp(Nps) and Trp(Nps)-Xaa (Xaa=Lys, Arg) derivatives, as potent TRPV1 channel blockers. We also report the synthesis and biological investigation of a series of new conformationally restricted Trp(Nps)-dipeptide derivatives with improved TRPV1/NMDA selectivity. Compound 15 b, which incorporates an N-terminal 2S-azetidine-derived Arg residue, was the most selective compound in this series. Collectively, a new family of TRPV1 channel blockers emerged from our results, although further modifications are required to fine-tune the potency/selectivity/toxicity balance.

Replacement of Phe6, Phe7, and Phe11 of D-Trp8-somatostatin-14 with L-pyrazinylalanine. Predicted and observed effects on binding affinities at hSST2 and hSST4. An unexpected effect of the chirality of Trp8 on NMR spectra in methanol

An alanine scan performed in the 1970s suggested that Phe(6) and Phe(11) are required for the binding of somatostatin (SRIF-14). Molecular modeling studies and replacement of Phe(6) and Phe(11) with a cystine bridge affording ligands with the retention of high biological activity, however, led to the alternate conclusion that Phe(6) and Phe(11) stabilize the bioactive conformation of SRIF-14. Subsequent studies revealed that Phe(11) shields Phe(6) in a "herringbone" arrangement. More recently, a report from this laboratory demonstrated that Spartan 3-21G MO calculations can be invaluable in explaining SARs in medicinal chemistry. For example, the ability of benzene and indole rings to bind the Trp(8) binding pocket for SRIF-14 and the inability of pyrazine to do so was explained through differences in electrostatic potentials. To investigate the role of Phe(6) and Phe(11) more fully, we report here the synthesis of two analogues of D-Trp(8)-SRIF in which Phe(6) and Phe(11) were replaced by the pryazinylalanine congeners, respectively. The NMR spectra in D(2)O and the K(i)s fully support the proposition that Phe(11) stabilizes the bioactive conformation through pi-bonding or aromatic edge-to-face interaction and that pyrazinylalanine(6) can be shielded by Phe(11). The data also show unexpectedly that Phe(6), via the pi-bond, interacts with the receptor, consistent with the original interpretation of the alanine scan. Heretofore it had only been known that Lys(9) interacts with an aspartate anion of the receptor. These conclusions are supported by recent studies of Lewis et al. on the effects on K(i)s of Ala(6)-SRIF-14-amide at the five receptor subtargets. We also found that pyrazinylalanine(7)-D-Trp(8)-SRIF-14 does not bind, suggesting a repulsive interaction with the receptor. Taken together, our results not only validate predictions based on Spartan 3-21G MO analysis but also provide valuable information about the nature of the receptor interaction at the molecular level. Finally, the chirality of Trp(8) was unexpectedly found to have a striking effect on NMR spectra in methanol, especially at lower temperatures.

Entry to New Conformationally Constrained Amino Acids. First Synthesis of 3-Unsubstituted 4-Alkyl-4-carboxy-2-azetidinone Derivatives via an Intramolecular Nα-Cα-Cyclization Strategy

A systematic study on the base-assisted intramolecular alkylation of N-benzyl-N-chloroacetyl amino acid derivatives is described. This study resulted in the first concise and versatile route to the preparation of 3-unsubstituted 4-alkyl-4-carboxy-2-azetidinones, to be included into the scarce family of beta-lactams with quaternary centers at the C(4) position. Particularly noteworthy is that the intramolecular N(alpha)-C(alpha)-cyclization of Phe and Leu derivatives afforded the corresponding beta-lactam derivatives with moderate enantioselectivity (up to 56%). It is suggested that, in these particular cases, the cyclization reaction proceeds by way of planar enolate intermediates, which possess dynamic chirality. The described sequence of reactions, that is compatible with commonly used protecting moieties for the alpha-carboxy group, cannot be applied to dipeptides, since the cyclization to the six-membered 2,5-diketopiperazine ring occurs preferentially.

Design of serine protease inhibitors with conformation restricted by amino acid side-chain-side-chain CH/pie interaction

A novel type of conformationally restricted peptides with the structure of H-D-Xaa-Phe-NH-CH2-C6H5 has been developed as inhibitors of serine proteinase chymotrypsin. The D-Xaa-alkyl and Phe-phenyl groups resulted in a formation of the hydrophobic core due to the side-chain-side-chain CH/pie interaction. Their spatial proximity was evidenced by 400 MHz 1H-nmr measurements, observing large upfield shifts of proton signals of D-Xaa-alkyl and nuclear Over-hauser effect (NOE) enhancements between the D-Xaa-alkyl and Phe-phenyl groups. This conformational restriction brought by CH/pie interaction produced an inhibitory structure, in which the C-terminal amide-benzyl group fits the chymotrypsin S1 site and the hydrophobic core binds to the S2 site. The inhibitory conformation was demonstrated crystallographically for the complex between the dipeptide H-D-Leu-Phe-NH-CH2-C6H4(p-F) and gamma-chymotrypsin. Detailed structure-activity studies have substantiated the structure of dipeptides in the active center of the enzyme.

CH/pi interaction in the conformation of peptides. A database study

A study was carried out, with use of the Cambridge Structural Database, to examine the role of the CH/pi interaction in the conformation of peptides. A number of short intramolecular CH/pi distances have been shown in the crystal structure of peptides bearing at least an aromatic residue in the sequence. The molecular structure in the crystal was inspected individually to know whether the conformation is merely a consequence of the so-called packing forces, or the CH/pi interaction plays a role. It has been demonstrated that the CH/pi interaction constitutes one of the key factors in controlling the conformation of peptides.

Use of papain as a model for the structure-based design of cathepsin K inhibitors: crystal structures of two papain-inhibitor complexes demonstrate binding to S'-subsites

Papain has been used as a surrogate enzyme in a drug design effort to obtain potent and selective inhibitors of cathepsin K, a new member of the papain superfamily of cysteine proteases that is selectively and highly expressed in osteoclasts and is implicated in bone resorption. Here we report the crystal structures of two papain-inhibitor complexes and the rational design of novel cathepsin K inhibitors. Unlike previously known crystal structures of papain-inhibitor complexes, our papain structures show ligand binding extending deep within the S'-subsites. The two inhibitor complexes, carbobenzyloxyleucinyl-leucinyl-leucinal and carbobenzyloxy-L-leucinyl-L-leucinyl methoxymethyl ketone, were refined to 2.2- and 2.5-A resolution with R-factors of 0.190 and 0. 217, respectively. The S'-subsite interactions with the inhibitors are dominated by an aromatic-aromatic stacking and an oxygen-aromatic ring edge interaction. The knowledge of S'-subsite interactions led to a design strategy for an inhibitor spanning both subsites and yielded a novel, symmetric inhibitor selective for cathepsin K. Simultaneous exploitation of both S- and S'-sites provides a general strategy for the design of cysteine protease inhibitors having high specificity to their target enzymes.

Chymotrypsin inhibitory conformation of dipeptides constructed by side chain-side chain hydrophobic interactions

A complete series of configurational isomers (L-L, L-D, D-L and D-D) of a dipeptide Leu-Phe benzyl ester have been synthesized and assayed for chymotrypsin. In the conformational analysis by 400 MHz 1H NMR, the L-D and D-L isomers, but not the L-L and D-D isomers, showed fairly large upfield shifts (0.2-0.4 ppm) of Leu-beta CH2 and gamma CH proton signals, indicating the presence of shielding effects from the benzene ring. In addition to distinct signal splitting of Phe-beta CH2, the NOE enhancement observed between Leu-delta CH3 and Phe-phenyl groups revealed that these groups are in close proximity. These data indicated that L-D and D-L isomers form a hydrophobic core between side chains of adjacent Leu and Phe residues. When the dipeptides were examined for inhibition of chymotrypsin using Ac-Tyr-OEt as a substrate, the L-L isomer showed no inhibition, itself becoming a substrate. However, the other three isomers inhibited chymotrypsin in a competitive manner, and the D-L isomer was strongest with Ki of 2.2 x 10(-5) M. It was found that the D-L isomer was only slowly hydrolysed but the L(or D)-D isomer was not. H-D-Phe-L-Leu-OBzl with the inverse sequence of H-D-Leu-L-Phe-OBzl inhibited chymotrypsin more strongly (Ki = 6.3 x 10(-6) M).(ABSTRACT TRUNCATED AT 250 WORDS)

Conformational analysis of mu-selective [D-Ala2,MePhe4]enkephalins

The conformational space of the potent mu-selective opioids [D-Ala2,MePhe4,Gly-ol5]enkephalin (DAGO) and [D-Ala2,MePhe4,Met(O)-ol5]enkephalin (FK 33-824) has been analyzed by 1H-NMR spectroscopy and theoretical calculations involving systematic conformational searching and energy minimizations. A cis-trans equilibrium of the Gly3-MePhe4 amide bond is induced by the N-methyl group, and the more energetically favoured trans isomer is proposed as the biologically relevant form. A compact interaction between the side chains of Tyr1 and D-Ala2 was demonstrated by NOE and ROE effects in both peptides in D2O and DMSO-d6, further supported by shielding of the D-Ala2 methyl protons in both solvents. Analysis of coupling constants, NOE and ROE data indicated significant restriction of the conformational freedom of the MePhe4 side-chain for both peptides in the two solvents. The NMR results and theoretical calculations point towards folded low energy conformations characterized by a beta II-type turn around Gly3-MePhe4. For the trans isomer, a Tyr1-MePhe4 phenyl ring separation between 8.5 and 12.5 A was accompanied by proximity between the D-Ala2 side chain and the C-terminal in low energy conformations. The results are in good agreement with available data on related active enkephalins. The conformational effects induced by simultaneous incorporation of D-Ala2 and MePhe4 in enkephalins is discussed in the light of the enhanced mu-opioid receptor selectivity and activity of these peptides.

Solid phase synthesis of a fully active analogue of cholecystokinin using the acid-stable Boc-Phe (p-CH2) SO3H as a substitute for Boc-Tyr(SO3H) in CCK8

Substitution of the -OSO3H group in the sulfated-tyrosine by the non-hydrolyzable-CH2SO3H group was the first described modification of the sulfate ester that does not affect CCK8 activity. In addition to its capacity to mimic the sulfated tyrosine residue, the amino acid Phe(p-CH2SO3Na) was shown to be stable in acidic media, including HF containing mixtures. The synthesis of Boc-Phe(p-CH2SO3Na)-OH in racemic and resolved forms and its introduction into the sequence of CCK8 by solid phase using standard Boc/benzyl synthesis conditions and BOP as coupling reagent is now reported. The two CCK8 analogues containing the L- or the D-Phe(p-CH2SO3Na) residue, obtained in satisfactory yields, were separated by HPLC and the stereochemistry of Phe(p-CH2SO3Na) residue in each peptide was established by NMR spectroscopy and confirmed by a separate solid phase synthesis in which the pure L isomer was used. Both CCK8 analogues displayed high affinities for peripheral and central receptors (KI approximately 1 nM) and proved to be full agonists in the stimulation of pancreatic amylase secretion. The "stabilized-CCK8 peptide", easily prepared by solid phase, could replace the native peptide in biochemical and pharmacological studies. Moreover the modified amino acid Phe (p-CH2SO3Na) could also be used in solid phase synthesis to prepare a wide variety of CCK analogues and more generally, peptides analogues containing the acid-labile O-sulfated tyrosine.

Synthesis and biological activity of linear and cyclic enkephalins modified at the Gly3-Phe4 amide bond

As part of our continuing effort to define structure-activity relationships for enkephalin and design enzymatically resistant analogs, we report the synthesis and biological activities of linear and cyclic enkephalin analogs modified at the Gly3-Phe4 amide bond. The partial retro-inverso enkephalin analog Tyr-D-Ala-gGly-(R,S)-mPhe-Leu-NH2 and its cyclic counterpart, Tyr-cyclo[D-A2 bu-gGly-(R,S)-mPhe-Leu-], were synthesized as diastereomeric mixtures using solution methodology. The racemic benzylmalonate allowed the linear analog to be synthesized by fragment coupling at the reversed bond. Cyclization of the second analog was carried out at high concentration, eliminating formation of polymer by the use of an insoluble base. All gem-diaminoalkyl residues were prepared by conversion of peptidyl amides with benzene iodonium bis(trifluoroacetate). Diastereomers of both compounds were separable by reverse phase HPLC but those of the linear compound racemized rapidly under conditions of testing and were therefore tested together. All analogs tested had activities ranging from 6 to 14% of the activity of Leu enkephalin, indicating that the Gly3-Phe4 amide bond is important, though not crucial, for receptor binding.

Solution conformation of virginiamycin S. II. The conformation of allohydroxy- and deoxyvirginiamycin S

The experimental results of 1H- and 13C-NMR studies of allohydroxy-, and of deoxyvirginiamycin S strongly confirm the conformation that was proposed earlier for the parent virginiamycin S (Anteunis, Callens and Tavernier (1975) Eur. J. Biochem. 58, 259--268). The changing nature of dipole-induced dipole interaction is responsible for the specific gradually increasing libration of the N-MePhe side chain along the series virginiamycin S, allohydroxy-, deoxyvirginiamycin S. Previous methods for the estimation of rotameric populations around the alpha, beta bonds are critically evaluated and compared to the present results obtained from interpretation of geminal 2J (beta) coupling constants.

H and 13C nuclear magnetic resonance spectra of some peptides with fibrinogen-like reactivity

The 1H and 13C spectra of four peptides, L-Phe-Val-Arg-pNA, D-Phe-Val-Arg-pNA, L-Phe-Pip-Arg-pNA and D-Phe-Pip-Arg-pNA (pNA = p-nitroaniline, Pip = pipecolic acid residue), have been examined, and deductions made about their conformation in solution. The D-Phe peptides, which are cleaved especially rapidly by thrombin in water, have structures (in deuterated DMSO) in which the aromatic ring of the D-Phe residue is folded back over the Val or Pip residue. This arrangement is not found in the L-Phe peptides. It is proposed that this feature (in which Phe could be situated near Val and near the Arg-Gly bond of the A alpha chain in the three-dimensional structure of fibrinogen) may be especially advantageous for binding to the enzyme.

Solution conformation of virginiamycins (staphylomycins)

The 1H (at 300 MHz) and 13C nuclear magnetic resonance spectra of virginiamycins S and S4 and vernamycin Balpha have been unravelled and analyzed. Together with model building and theoretical considerations, this allows the detailed description of their solution conformations. The depside bond can rotate and gives to the backbone some conformational mobility. The orientation of the depsicarbonyl bond depends on the surrounding. Apparent discrepancies between the different methods that are applicable for the disclosure of the nature of peptide H-bonding, have found a rational explanation.