An NMR conformational analysis of cyclic bradykinin mimics. Evidence for a beta-turn

A detailed NMR study is carried out in acetonitrile/water solutions on three novel cyclic bradykinin antagonist analogues, BKM-824, BKM-870, and BKM-872, to examine their solution structures, and to correlate the structures with bradykinin antagonist and anti-cancer activities. The solution structures of the cyclic peptides are correlated with the structural data for known linear bradykinin antagonists. The sequences are: BKM-824 c[Ava-Ig1-Ser-DF5F-Oic-Arg] where Ava is 5-aminovaleric acid, Ig1 is alpha-(2-indanyl)glycine, F5F is pentafluorophenylalanine, and Oic is (2S,3aS,7aS)-octahydroindole-2-carboxylic acid; BKM-870; c[DArg-Arg-Add-DF5F-Oic-Arg] where Add is 12-aminododecanoic acid; and BKM-872; c[DArg-Arg-Eac-Ser-DF5F-Oic-Arg] where Eac is 6-aminocaproic acid. BKM-824 was the only peptide within this series that possessed a discernable solution structure. The NMR data indicate the presence of a type I beta-turn between residues F5F4 and Ava1, a C-terminal-like end. Molecular dynamics calculations show that a type I beta-turn from DF5F4 to Ava1 does exist although the turn was somewhat distorted. This result differs from the structures seen in linear bradykinin antagonists, which usually possess a type II'beta-turn at the C-terminal end and the presence of a defined turn is correlated with bradykinin antagonist activity. There is no solution structure for BKM-870 and BKM-872 but a correlation between the primary sequence Arg(terminal)-DArg1-Arg2-long chain aliphatic amino acid and anti-cancer activity is evident.     

Fused bicyclic heteroarylpiperazine-substituted l-prolylthiazolidines as highly potent DPP-4 inhibitors lacking the electrophilic nitrile group

Hypoglycemic agents with a mechanism of depeptidyl peptidase IV (DPP-4) inhibition are suitable for once daily oral dosing. It is difficult to strike a balance between inhibitory activity and duration of action in plasma for inhibitors bearing an electrophilic nitrile group. We explored fused bicyclic heteroarylpiperazine substituted at the γ-position of the proline structure in the investigation of l-prolylthiazolidines lacking the electrophilic nitrile. Among them, 2-trifluoroquinolyl compound 8g is the most potent, long-lasting DPP-4 inhibitor (IC(50)=0.37nmol/L) with high selectivity against other related peptidases. X-ray crystal structure determination of 8g indicates that CH-π interactions generated between the quinolyl ring and the guanidinyl group of Arg358 enhances the DPP-4 inhibitory activity and selectivity.     

Solid phase synthesis of human growth hormone-releasing factor analogs containing a bicyclic beta-turn dipeptide.

Three analogs derived from the N-terminal 29-residue fragment of human growth hormone-releasing factor (hGRF) which contained a bicyclic beta-turn dipeptide (BTD) at 7-8, 8-9, and 9-10 positions were synthesized by solid phase methodology to ascertain if the beta-turns are important for the biological activity of hGRF and also to show the applicability of the BTD unit to solid phase synthesis. All three analogs were obtained in good yield and purity indicating that the BTD unit can be used in the usual condition of solid phase synthesis. The capacity of these analogs to release growth hormone (GH) was tested in an in vitro bioassay using rat anterior pituitary cells. All three BTD-containing analogs showed the same maximal GH secretion with parallel dose-response curves to that of hGRF(1-29)NH2, except their relative potencies were very low.     

A potent peptide affinity reagent for the opiate receptor

The synthesis and characterization of a novel enkephalin analogue, Tyr-D-Ala-Gly-Phe-Leu-chloromethyl ketone, is described. The biological potency of the compound in various assays has been determined to be very high. The compound is an alkylating affinity reagent and irreversibly inactivates a defined population of enkephalin receptors in rat brain membrane preparations, as well as irreversibly inhibiting electrically stimulated contractions in the mouse vas deferens tissue preparation.     

Design of novel bicyclic analogues derived from a potent oxytocin antagonist.

Eleven new analogues were synthesized by modification of the potent oxytocin antagonist (OTA) [(S)Pmp(1), D-Trp(2), Pen(6), Arg(8)]-Oxytocin, or PA (parent antagonist), in which (S)Pmp = beta,beta-(3-thiapentamethylene)-beta-mercapto-propionic acid. By internal acylation of Lys, Orn, L-1,4-diaminobutyric acid (Dab), L-1,3-diaminopropionic acid (Dap) at position 4 with the C-terminal Gly of the peptide tail, we prepared cyclo-(4-9)-[Lys(4), Gly(9)]-PA (pA(2) = 8.77 +/- 0.27), 1, and cyclo-(4-9)-[Orn(4), Gly(9)]-PA (pA(2) = 8.81 +/- 0.25), 3, which are equipotent with PA (pA(2) = 8.68 +/- 0.18) in the rat uterotonic assay and cyclo-(4-9)-[Dab(4), Gly(9)]-PA, 4, cyclo-(4-9)-[Dap(4), Gly(9)]-PA, 5, and cyclo-(4-9)-[Pmp(1), Lys(4), Gly(9)]-PA, 2, which were weaker OTAs. Neither 1 nor 3 had activity as agonists or antagonists in the antidiuretic assay. In the pressor assay, both analogues 1 and 3, with pA(2) = 7.05 +/- 0.10 and pA(2) = 6.77 +/- 0.12, respectively, are somewhat weaker antagonists than PA (pA(2) = 7.47 +/- 0.35) showing significant gain in specificity. The [desamido(9)] PA-ethylenediamine monoamide, 6, and the dimer ([desamido(9)]-PA)(2) ethylenediamine diamide, 7, had lower potency in the uterotonic assay than PA. Additionally, we synthesized cyclo-(1-5)-[(HN)Pmp(1), Asp(5)]-PA, 8, inactive in all tests, which suggests that the intact Asn(5) side chain may be critical in the interaction of the OTAs with the oxytocin (OT) receptor. Similarly, cyclo-(5-9)-[Dap(5), Gly(9)]-PA, 9, had very low uterotonic potency. Two derivatives of PA truncated from the C-terminus were internally cyclized to Lys(4), giving rise to cyclo-(4-8)-desGly-NH(2)(9)[Lys(4), Arg(8)]-PA, 10 (pA(2) = 8.35 +/- 0.20), which maintains the high potency of PA and has no activity in the rat antidiuretic assay, and in the rat pressor assay it is about ten times weaker (pA2 = 6.41 +/- 0.15) than PA (pA2 = 7.47 +/- 0.35), thus showing gains in specificity, and to cyclo-(4-7)-desArg-Gly-(NH)(2)(8-9)[Lys(4), Pro(7))-PA, 11, which has much weaker potency than PA. Synthesis of cyclo-(4-6)-desPro-Arg-Gly-(NH)(2)(7-9)[Lys(4)]-PA failed.     

Influence of N-terminal residue stereochemistry on the prolyl amide geometry and the conformation of 5-tert-butylproline type VI beta-turn mimics.

The effects of N-terminal amino acid stereochemistry on prolyl amide geometry and peptide turn conformation were investigated by coupling both L- and D-amino acids to (2S, 5R)-5-tert-butylproline and L-proline to generate, respectively, N-(acetyl)dipeptide N'-methylamides 1 and 2. Prolyl amide cis- and trans-isomers were, respectively, favored for peptides 1 and 2 as observed by proton NMR spectroscopy in water, DMSO and chloroform. The influence of solvent composition on amide proton chemical shift indicated an intramolecular hydrogen bond between the N'-methylamide proton and the acetamide carbonyl for the major conformer of dipeptides (S)-1, that became less favorable in (R)-1 and 2. The coupling constant (3J(NH,alpha)) values for the cis-isomer of (R)-1 indicated a phi2 dihedral angle value characteristic of a type VIb beta-turn conformation in solution. X-ray crystallographic analysis of N-acetyl-D-leucyl-5-tert-butylproline N'-methylamide (R)-lb showed the prolyl residue in a type VIb beta-turn geometry possessing an amide cis-isomer and psi3-dihedral angle having a value of 157 degrees, which precluded an intramolecular hydrogen bond. Intermolecular hydrogen bonding between the leucyl residues of two turn structures within the unit cell positioned the N-terminal residue in a geometry where their phi2 and psi2 dihedral angle values were not characteristic of an ideal type VIb turn. The circular dichroism spectra of tert-butylprolyl peptides (S)- and (R)-1b were found not to be influenced by changes in solvent composition from water to acetonitrile. The type B spectrum exhibited by (S)-1b has been previously assigned to a type VIa beta-turn conformation [Halab L, Lubell WD. J. Org. Chem. 1999; 64: 3312-3321]. The type C spectrum exhibited by the (R)-lb has previously been associated with type II' beta-turn and alpha-helical conformations in solution and appears now to be also characteristic for a type VIb geometry.     

Membranolytic antifungal activity of arenicin-1 requires the N-terminal tryptophan and the beta-turn arginine

To determine the structural requirements of arenicin-1 in exerting antifungal activity, a truncated peptide with an N-terminal deletion and a peptide with an Ala substitution for an Arg in the beta-turn region were characterised by comparison to arenicin-1. The antifungal activities of the analogues were 25–50% lower than arenicin-1. Trp fluorescence and circular dichroism spectroscopy showed that Trp in the N-terminus contributed to peptide penetration and Arg in the beta-turn to conformational transition. These results suggest that Trp in the N-terminus and Arg in the beta-turn play a pivotal role in the membrane-directed antifungal activity of arenicin-1.     

Immobilized metal affinity chromatography in the presence of arginine

Arginine hydrochloride (ArgHCl) is a versatile solvent additive, as it suppresses protein aggregation. ArgHCl has been used for protein refolding and to solubilize proteins from loose inclusion bodies. Immobilized metal affinity chromatography (IMAC) is one of the most commonly used technologies for purification of recombinant proteins. Here we have evaluated compatibility of ArgHCl with IMAC purification for his-tag proteins. ArgHCl clearly interfered with protein binding to Ni-columns. Nevertheless, such interference was greatly reduced at ArgHCl concentration below 200 mM, demonstrating that IMAC purification can be done even in the presence of ArgHCl.     

Support vector machines for the classification and prediction of beta-turn types.

The support vector machines (SVMs) method is proposed because it can reflect the sequence-coupling effect for a tetrapeptide in not only a beta-turn or non-beta-turn, but also in different types of beta-turn. The results of the model for 6022 tetrapeptides indicate that the rates of self-consistency for beta-turn types I, I', II, II', VI and VIII and non-beta-turns are 99.92%, 96.8%, 98.02%, 97.75%, 100%, 97.19% and 100%, respectively. Using these training data, the rate of correct prediction by the SVMs for a given protein: rubredoxin (54 residues. 51 tetrapeptides) which includes 12 beta-turn type I tetrapeptides, 1 beta-turn type II tetrapeptide and 38 non-beta-turns reached 82.4%. The high quality of prediction of the SVMs implies that the formation of different beta-turn types or non-beta-turns is considerably correlated with the sequence of a tetrapeptide. The SVMs can save CPU time and avoid the overfitting problem compared with the neural network method.     

Self-assembled monolayers of globotriaosylceramide (Gb3) mimics: surface-specific affinity with shiga toxins

Self-assembled monolayers (SAMs) of Gb3 mimics having different lengths of alkyl chains were prepared on gold surfaces, and their interactions with galactose-specific lectin (RCA(120)) and Shiga toxins (Stxs) were investigated by a quartz crystal microbalance (QCM) in aqueous solutions. Their interaction with RCA(120) was enhanced owing to the "cluster effect," regardless of the alkyl chain length of the SAMs. The interaction with Stxs was dependent on the alkyl chain length of Gb3 mimics. Stx-1 and Stx-2 showed a stronger affinity to the Gb3C2 SAM with ethyl disulfide and to the Gb3C10 with decyl disulfide, respectively. Gb3 glycoconjugate polymer with no alkyl spacer inhibited the adsorption of Stx-1 to Gb3C10 SAM but did not inhibit the adsorption of Stx-2 to Gb3C10 SAM. The results suggest that the alkyl chain of the glycolipid takes part in the binding to Stx-2 but not to Stx-1, which is also supported by the computer simulation of Stx-1 with a Gb3 model substance.     

1,3-dithianes with acid functionalities: potent inhibitors and candidate affinity probes for the gaba-gated chloride channel

2 ,5 -1,3-Dithianes of the type (CH₃)C-CH(CH₂S)₂CH-C₆H₄-CC-R (R = CO₂H, CH₂CH₂CO₂H and CH₂CH₂PO₃H₂) are potent blockers of the GABA-gated chloride channel with 50% inhibition at 5–10 nM. Functionalization of the acid moieties provides candidate photoaffinity ligands [R = C(O)CHN₂ and CH₂CH₂C(O)CHN₂], affinity columns, and hapten-protein conjugates for antibody production.     

Sequence replacements in the central beta-turn of plastocyanin.

The role of beta-turns in dictating the structure of a beta-barrel protein is assessed by probing the tolerance of the central beta-turn of poplar plastocyanin to substitution by arbitrary sequences. Native plastocyanin binds copper and is colored bright blue. However, when the wild-type Pro47-Ser48-Gly49-Val50 turn sequence is replaced by arbitrary tetrapeptides, the vast majority (92/98 = 94%) of mutant proteins cannot fold into the native blue structure. Characterization of the colorless mutant proteins demonstrates that the majority of substitutions in this type II beta-turn disrupt the native structure severely. Gross structural changes are indicated by major differences in the CD spectra of the mutants relative to the wild-type protein, and by the much larger apparent size of mutant proteins in gel filtration experiments. These mutant proteins do not bind copper. Furthermore, Cys84 forms a disulfide bond readily in the colorless mutant proteins, indicating that it has moved away from the buried position it occupies in the native copper binding site and has become exposed. These results indicate that the central beta-turn in plastocyanin is not merely a default structure arising in response to the surrounding context; rather, sequence information in this turn plays an active role in dictating the location of a chain reversal in the beta-barrel structure. These findings are discussed in terms of their implications for the folding of natural proteins, as well as the design of de novo proteins.     

Exploration of the DTrp-NMeLys motif in the search for potent somatostatin antagonists

Previous studies from this laboratory demonstrated that N-methylation at Lys(5) residue in somatostatin octapeptide antagonist analogues increased the GH release inhibition potency by as much as 300%. We have now further investigated N-methylation of this Lys(5) residue in conjunction with a number of N- and C-terminal modifications previously found to give highly potent somatostatin receptor antagonists. Synthetic analogues were tested in a functional assay for their ability to inhibit somatostatin-inhibited GH release from rat pituitary cells in culture and to displace 125I-labeled somatostatin from CHO cells transfected with the five known human somatostatin receptors. Several interesting observations resulted from the study. Replacement of liphophilic Nal(8) at the C-terminus with a hydrophilic His(8) resulted in the increased affinity and selectivity for type 2 receptor to give the most potent antagonist analogue yet discovered (K(i), 1.5 nM), although in the rat pituitary cells inhibitory activity on somatostatin inhibited GH release decreased somewhat. A His(3) substitution within the cyclic portion of the analogues retained pituitary cell potency and affinity for type 2 receptor as did substitution with Bip(8) and Fpa(1). Replacement of Cpa(1) with Iph(1) did not effect the affinity for type 2 receptor significantly, but did decrease the effects on rat cell GH release. Iph(3) within-ring substitution increased the selectivity for sst(2) appreciably although the affinity for that receptor was considerably decreased. Substitution of Npa(3) resulted in good selectivity for sst(2) receptor. Replacement of Nal(8) with D-Trp(8) also increased the selectivity for type 2 receptor. Use of a 'bivalent ligand' approach in which two peptides were joined by 4,4'-biphenyldicarbonyl as a spacer destroyed the affinity for all the subtypes, however, the bivalent ligand formed with the Ahp spacer displayed significant affinity and high selectivity for the type 2 receptor.     

Simplification of adenophostin A defines a minimal structure for potent glucopyranoside-based mimics of D-myo-inositol 1,4,5-trisphosphate

The synthesis of 1-O-[(3S,4R)-3-hydroxytetrahydrofuran-4-yl]-alpha-D-glucopyranosid e 3,4,3'-trisphosphate (7), a novel Ca2+ mobilising agonist at the Ins(1,4,5)P3 receptor, designed by excision of two motifs of adenophostin A is reported, defining a potential minimal structure for potent glucopyranoside-based agonists of Ins(1,4,5)P3 receptors.     

Selective CB2 agonists with anti-pruritic activity: Discovery of potent and orally available bicyclic 2-pyridones

The CB2 receptor has emerged as a potential target for the treatment of pruritus as well as pain without CB1-mediated side effects. We previously identified 2-pyridone derivatives 1 and 2 as potent CB2 agonists; however, this series of compounds was found to have unacceptable pharmacokinetic profiles with no significant effect in vivo. To improve these profiles, we performed further structural optimization of 1 and 2, which led to the discovery of bicyclic 2-pyridone 18e with improved CB2 affinity and selectivity over CB1. In a mouse pruritus model, 18e inhibited compound 48/80 induced scratching behavior at a dose of 100 mg/kg. In addition, the docking model of 18e with an active-state CB2 homology model indicated the structural basis of its high affinity and selectivity over CB1.     

Toward the development of potent and selective bisubstrate inhibitors of protein arginine methyltransferases

Prototype inhibitors of protein arginine methyltransferases (PRMTs) have been constructed by attaching guanidine functionality via a variable linker to non-reactive amine analogues of the cellular co-factor (S)-adenosyl methionine (AdoMet). Potent inhibition of PRMT1 (IC₅₀ of ～3–6 μM) combined with weak inhibition of the lysine methyltransferase SET7 (～50% of activity at 100 μM) was observed for two such compounds.