Conformational study of Ac-Xaa-Pro-NHMe dipeptides: proline puckering and trans/cis imide bond

The conformational study on 20 Ac-Xaa-Pro-NHMe dipeptides has been carried out using an empirical potential function ECEPP/3 in order to investigate the factors responsible for the preference of proline puckering of the peptides with the trans or cis imide bond preceding the proline. The general conformational preference for down- and up-puckered dipeptides is calculated as trans-down > trans-up > cis-down > cis-up, which is reasonably in accord with that estimated by analyzing X-ray structures of proteins and the result for the single proline residue. The overestimated occurrence of trans-down conformations of proline seems to be caused by excluding long-range interactions that short dipeptides cannot have. The average computed occurrence of dipeptides with cis imide bonds is about 3%, somewhat lower than the value calculated for Ac-Pro-NHMe, which is close to experimental estimates obtained from X-ray structures of proteins. In particular, the interaction of the aromatic side chain of Xaa residue with the proline ring appears not to be strong enough to stabilize the stacked conformations of small dipeptides with cis imide bonds. The propensity to adopt trans or cis imide bond and to form secondary structures of Xaa-Pro sequences is discussed and compared with results obtained from X-ray structures of proteins.     

Nanomolar inhibitors of the peptidyl prolyl cis/trans isomerase Pin1 from combinatorial peptide libraries

The peptidyl prolyl cis/trans isomerase Pin1 has been implicated in the development of cancer, Alzheimer's disease and asthma, but highly specific and potent Pin1 inhibitors remain to be identified. Here, by screening a combinatorial peptide library, we identified a series of nanomolar peptidic inhibitors. Nonproteinogenic amino acids, incorporated into 5-mer to 8-mer oligopeptides containing a d-phosphothreonine as a central template, yielded selective inhibitors that blocked cell cycle progression in HeLa cells in a dose-dependent manner.     

Analogs of oxytocin containing a pseudopeptide Leu-Gly bond of cis and trans configuration*

Analogs of deamino-oxytocin wherein the Leu-Gly peptide bond has been replaced by a tetrazole moiety or by a double bond of trans configuration were synthesized and their biological activities evaluated. Trans double bond was found to be the most appropriate substitution for the amide bond (uterotonic activity 24% of the deamino-oxytocin). In the case of all three analogs low but prolonged galactogogic activity was found and the ratio of uterotonic in vitro and in vivo activity was surprisingly high (ranging from 4.5 to 20).     

Investigation of cis/trans proline isomerism in a multiply occurring peptide fragment from human salivary proline-rich glycoprotein

The solution-state conformations of eight proline-containing peptide fragments found in human salivary proline-rich glycoprotein (PRG) were investigated in 2 × distilled water (treated with metal ion chelating resin) using ¹³C-nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy. The peptide sequences and acronyms were as follows: PRG9-2 = NH₂-G(I)-P(2)-CONH₂, PRG9-3 = NH₂-G(1)-P(2)-P(3)-CONH₂,PRG9-4 = NH₂-G(1)-P(2)-P(3)-P(4)-CONH₂, PRG9-5 = NH₂-G(1)-P(2)-P(3)-P(4)-H(5)-CONH₂,PRG9-6 = NH₂-G(1)-P(2)-P(3)-P(4)-H(5)-P(6)-CONH₂, PRG9-7 = NH₂-G(1)-P(2)-P(3)-P(4)-H(5)-P(6)-G(7)-CONH₂, PRG9-8 = NH₂-G(1)-P(2)-P(3)-P(4)-H(5)-P(6)-G(7)-K(8)-CONH₂ and PRG9-9 = NH₂-G(1)-P(2)-P(3)-P(4)-H(5)-P(6)-G(7)-K(8)-P(9)-CONH₂. Sequence-specific resonance assignments from the ¹³C-NMR spectra indicated that the trans proline isomer dominated the conformations of the peptides. CD results clearly showed the presence of the poly-l -proline II helix as the major conformation in PRG9-3 → PRG9-5, supplemented by β- and/or γ-turns in PRG9-6 → PRG9-9. These data suggest that in “metal free” water, native PRG could contain several small poly-l -proline II helices along with β- and/or γ-turns. Since proline is the major amino acid present in native PRG, these localized conformations may contribute to PRG's global conformation and act as a primary force in determining its biological activities.     

Pharmacological study on Alzheimer's drugs targeting calcium/calmodulin-dependent protein kinase II

In the brain of Alzheimer's disease patients, down-regulation of both cholinergic and glutamatergic systems have been found and is thought to play an important role in impairment of cognition, learning, and memory. Nefiracetam is a pyrrolidine-related nootropic drug exhibiting various pharmacological actions such as a cognitive-enhancing effect. The present study was undertaken to elucidate mechanisms underlying the action of nefiracetam on glutamatergic receptors and intracellular protein kinases. N-Methyl-D-aspartate (NMDA)-evoked currents were recorded from rat cortical neurons in long-term cultured primary neurons using the whole-cell patch-clamp technique. NMDA-evoked currents were greatly and reversibly potentiated by bath application of nefiracetam, resulting in a bell-shaped dose-response curve. The maximum potentiation of 170% relative to the control was produced at 10 nM. Treatment with an inhibitor of the glycine binding site of the NMDA receptor, 7-chlorokynurenic acid, at 1 μM prevented augmentation of NMDA-evoked currents by nefiracetam. In rat hippocampal CA1 slices, field excitatory postsynaptic potentials were recorded by stimulation of Schaffer collateral/commissural pathways. Nefiracetam treatment significantly enhanced long-term potentiation (LTP) with the same bell-shaped dose-response curve. Furthermore, nefiracetam-induced LTP enhancement was closely associated with calcium/calmodulin-dependent protein kinase II (CaMKII) activation with concomitant increase in phosphorylation of AMPA-type glutamate receptor subunit 1 (GluA1) (Ser-831) as a postsynaptic CaMKII substrate. In conclusion, nefiracetam enhances NMDA-receptor function through stimulation of its glycine binding site and nefiracetam-induced CaMKII activation likely contributes to improvement of cognition, learning, and memory.     

Support vector machines for prediction of peptidyl prolyl cis/trans isomerization

Abstract: A new method for peptidyl prolyl cis/trans isomerization prediction based on the theory of support vector machines (SVM) was introduced. The SVM represents a new approach to supervised pattern classification and has been successfully applied to a wide range of pattern recognition problems. In this study, six training datasets consisting of different length local sequence respectively were used. The polynomial kernel functions with different parameter d were chosen. The test for the independent testing dataset and the jackknife test were both carried out. When the local sequence length was 20‐residue and the parameter d = 8, the SVM method archived the best performance with the correct rate for the cis and trans forms reaching 70.4 and 69.7% for the independent testing dataset, 76.7 and 76.6% for the jackknife test, respectively. Matthew's correlation coefficients for the jackknife test could reach about 0.5. The results obtained through this study indicated that the SVM method would become a powerful tool for predicting peptidyl prolyl cis/trans isomerization.     

Carrier-based strategies for targeting protein and peptide drugs to the lungs

With greater interest in delivery of protein and peptide-based drugs to the lungs for topical and systemic activity, a range of new devices and formulations are being investigated. While a great deal of recent research has focused on the development of novel devices, attention must now be paid to the formulation of these macromolecular drugs. The emphasis in this review will be on targeting of protein/peptide drugs by inhalation using carriers and ligands.     

A Nuclear Magnetic Resonance (NMR) Method for the Determination of the cis/trans Isomeric Content of Chlorprothixene

Proton NMR spectroscopy was applied to the assignment of the isomeric identity of commercially available chlorprothixene. Nuclear Overhauser effect studies confirmed that the clinically useful isomer is the cis (Z) configuration. An NMR method for determining the isomeric content of chlorprothixene was developed based on integration of the ratio of areas of signal strength of the cis-N-methyl in comparison to the trans-N-methyl resonances.     

Tuning the DNA conformational perturbations induced by cytotoxic platinum-acridine bisintercalators: effect of metal cis/trans isomerism and DNA threading groups

Four highly charged, water soluble platinum-acridine bisintercalating agents have been synthesized. Depending on the cis/trans isomerism of the metal and the nature of the acridine side chains, bisintercalation induces/stabilizes the classical Watson-Crick B-form or a non-B-form. Circular dichroism spectra and chemical footprinting experiments suggest that 4, the most active derivative in HL-60 cells, produces a structurally severely perturbed DNA with features of a Hoogsteen base-paired biopolymer.     

Cis/trans conformational equilibrium across the N‐methylphenylalanine2‐ N‐methylphenylalanine3 peptide bond of arginine vasopressin analogs

Abstract: Two cyclic analogs of vasopressin, ‐Pro‐Arg‐Gly‐NH₂ ( 1 ) and ‐Pro‐Arg‐Gly‐NH₂ ( 2 ) were synthesized by the solid phase method. Their structure was determined in aqueous solution by two‐dimensional NMR techniques and simulated annealing algorithm from an extended template in X‐PLOR. The total chemical shift correlation spectroscopy and rotating‐frame Overhauser enhancement spectroscopy of the peptides displayed four distinct sets of residual proton resonances. This suggests that both analogs adopt four families of conformations in H₂O/D₂O (9 : 1) (one major and three minor species). In further analysis only signals of major species (M) and of one minor species (m₁) were considered. The major species of both peptides include a trans peptide bond between the first and second residue, and a cis form between the second and third residue. In the minor species, all peptide bonds were found to exist in trans geometry.     

Pharmacological modulation of the natriuretic peptide system

The natriuretic peptide (NP) system is a cardioprotective hormonal system that fails to meet its cardioprotective end point during the development of cardiovascular complications such as hypertension and heart failure. The use of NPs or orally-active drugs that enhance the function of the NP system, are being explored for the treatment of such disorders. Much of the recent research has focused on vasopeptidase inhibitors that can inhibit neutral endopeptidase (NEP) and angiotensin-converting enzyme (ACE) and thereby augment NP signalling while attenuating the renin–angiotensin–aldosterone system. These drugs offer several beneficial effects over conventional ACE inhibitors but the vasoactive peptide bradykinin, which is partly responsible for their beneficial effects, leads to serious side effects such as angioedema. The hope that these compounds will replace conventional drugs is fading away but they might be useful in targeted refractory populations immune to conventional drugs. The trends from the recent published patents suggest that pharmaceutical companies are exploring new strategies that include inhibition of endothelin-converting enzyme along with ACE and/or NEP. This comprehensive review will address the patents as well as basic and clinical pharmacology of leading compounds that exploit various strategies to modulate the NP system. This includes recombinant NPs, NP receptor ligands, vasopeptidase inhibitors and novel molecules that offer new strategic insights into the modulation of the NP system for the treatment of cardiovascular complications.     

Characterization of benzodiazepinooxazoles: crystal and molecular structure of trans and cis isomers of oxazolam.

The stereochemistry of the trans and cis isomers of 2(S)- and 2(R)-oxazolam is described. A total of four molecular structures of the 11b(R) and 11b(S) diastereomers of 2(S)- and 2(R)-oxazolam have been revealed by X-ray diffraction techniques. 2(S)-Oxazolam crystallizes in space group P2(1)/c, with cell dimensions a = 16.180(2) A, b = 8.791(2) A, c = 13.574(2) A, and beta = 102.07(1) degrees. The molecule in an asymmetric unit exhibited disorder at the 2-carbon (C2) atom, and the structures for trans and cis isomers have been resolved crystallographically. 2(S)-Oxazolam forms polymeric chains with intermediation of ethanol through hydrogen bonding. 2(R)-Oxazolam crystallizes in space group P1, with cell dimensions a = 7.754(1) A, b = 8.654(1) A, c = 15.795(2) A, alpha = 104.09(1) degrees, beta = 91.19(1) degrees, and gamma = 114.00(1) degrees. A similar disorder at the C2 position has been elucidated by a mixture of trans- and cis-2(R)-oxazolams. The two 2(R)-oxazolam molecules form a dimer with a hydrogen bond net. The structural details, focusing on the conformation and molecular complex formation of both oxazolams, have been discussed in connection with the oxazolidine ring stability and the crystal polymorph.     

Intramolecular water bridge and a distorted trans peptide bond in the crystal structure of α-L-glutamyl-L-aspartic acid hydrate

The crystal structure of the monohydrated form of α-L-glutamyl-L-aspartic acid, C₁₉H₁₄N₂O₇ · H₂O, has been determined from three-dimensional X-ray diffractometer data. The dipeptide crystallizes in the triclinic space group P1 with one formula unit in a cell of dimensions a = 7.806(3), b = 8.473(5), c = 4.965(2)Å, α = 101.50(3), β = 100.81(3), γ = 104.72(3)°. The structure was solved by direct methods and refined by full-matrix least-squares methods to a final value of the weighted R factor (on F) of 0.047 based on 1647 unique observations with I ≥ 0.01 (I). The dipeptide crystallizes as a zwitterion with the amino terminus protonated and the main chain carboxyl group ionized. The peptide bond conformation is trans, though the ω angle of 161.3° is highly distorted from the ideal 180° value. The adoption of an unusual 13-membered “intramolecularly” hydrogen bonded ring structure with resulting α-turn character is responsible for distortion of the peptide bond. The solid-state conformation of the hydrate thus differs considerably from the previously reported unhydrated pseudopolymorphic structure of α-L-Glu-L-Asp.     

Pharmacological targeting of adipocytes/fat metabolism for treatment of obesity and diabetes

Obesity is now recognized as a rapidly increasing worldwide threat to health, largely as a result of causing diabetes. Thus, considerable efforts are underway in the pharmaceutical industry to find drugs to treat this condition. Target validation in various academic and industrial laboratories has revealed a number of potential molecular targets in fat cells or adipocytes. By definition, obesity is too much fat, and we here review efforts to treat obesity and, by proxy, diabetes by modulating the metabolic state of adipocytes.