Conformationally stable and constrained macrocarbocyclic pseudopeptide mimics of beta-hairpin structures

Subjecting a D-Pro-L-Pro template harboring N- and C-terminal omega-alkenyl amino acids to a ring-closure metathesis reaction afforded the corresponding macrocyclic alkenes. A cis-alkene analogue crystallized with one molecule each of water and chloroform, which were retained even after heating at 100 degrees C. By using the reduced macrocyclic product as a template, the metathesis could be repeated twice on newly installed omega-alkenyl amino acids to give three-tiered macrocarbocyclic pseudopeptides as mixtures of conformers. NMR studies revealed the high conformational stability of these motifs.     

Tailored polymer-supported templates in dynamic combinatorial libraries: simultaneous selection, amplification and isolation of synthetic receptors

The thermodynamically controlled synthesis and isolation of macrocyclic receptors from dynamic combinatorial libraries has been achieved in a single step using a polymer-supported template. The templates were cinchona alkaloids which show interesting enantio- and diastereoselective molecular recognition events in libraries based on pseudo-dipeptide building blocks. The synthetic routes used to derivatise the alkaloids and attach them to polymer supports minimised any influence of the tethering linkage on the templating activity. Systematic studies have been carried out to probe how the polymer morphology and the template loading affect the selectivity and isolation yield of the macrocyclic receptors. Molecular recognition between solid-phase bound templates and selected receptors also enabled their affinity-type chromatographic separation.     

Synthesis, spectral studies and antibacterial activity of novel macrocyclic Co(II) compounds

Ten novel macrocyclic Co(II) compounds have been synthesized by treating four N(4) and six N(2)O(2) donor macrocycles with cobalt chloride in methanol. These compounds were characterized by elemental, IR, (1)H, (13)C NMR, mass, electronic spectral analysis, molar conductance and magnetic susceptibility measurements. Thermal behavior of these compounds has been studied by the thermogravimetric analysis. An octahedral geometry has been proposed for all of these complexes. All the macrocycles and macrocyclic Co(II) compounds along with existing antibacterial drugs were screened for antibacterial activity against Gram +ve and Gram -ve bacteria. All these compounds were found to be more active when compared to streptomycin and ampicillin.     

Synthesis of the Phenylpyridal Scaffold as a Helical Peptide Mimetic

Phenylpyridal‐ and phenyldipyridal‐based scaffolds have been designed and synthesized as novel helical peptide mimetics. The synthesis required optimisation and selective alkylation in producing 2,6‐functionalized 3‐hydroxypyridine derivatives for a convergent scheme. The pyridine analogues were coupled by a series of Suzuki/Stille types cross‐coupling reactions. A series of biaryl and ter‐aryl substituted heterocycles were produced. The synthetic approach was concise and high yielding allowing large variability at the wanted side‐chain attachment points. A number of compounds were synthesised to show the versatility of the strategy.     

Structural examination of ring-closing metathesis-derived 15-member macrocycles as Grb2 SH2 domain-binding tetrapeptide mimetics

Ring-closing metathesis (RCM) was employed to join carboxy-terminal alkenyl glycine side chains together with vinyl- and allyl-functionality appended to the beta-methylene of amino-terminal phosphotyrosyl (pTyr) mimetics. This required the synthesis of a variety of new pTyr mimetics, including a novel aza-containing analogue. Many of the resulting 15-member macrocyclic tetrapeptide mimetics exhibited low nanomolar Grb2 SH2 domain-binding affinities in spite of the fact that differing ring junction stereochemistries and geometries of the RCM-derived double bond were employed. The finding that significant latitude exists in the structural requirements for ring closure may facilitate the development of therapeutically relevant macrocyle-based Grb2 SH2 domain-binding antagonists. The synthetic approaches used in this study may also find application to peptide mimetics directed at other biological targets.     

Synthesis and Solution Conformation of β‐Hairpin Mimetics Utilizing a Template Derived from (2S,3R,4R)‐Diaminoproline

A novel template was synthesized for stabilizing β‐hairpin conformations in cyclic peptide mimetics. The template is a diketopiperazine derived formally from L ‐aspartic acid and (2S,3R,4R)‐diaminoproline, the latter being available by an efficient synthetic route from vitamin C. The template was incorporated by solid‐phase peptide synthesis into a cyclic loop mimetic containing the sequence (‐Ala‐Asn‐Pro‐Asn‐Ala‐Ala‐template‐). This mimetic was shown by NMR to adopt a stable β‐hairpin conformation in (D₆)DMSO solution. The template may prove to be generally useful for creating small‐molecule mimetics of hairpin loops on proteins of diverse function.     

Designed peptides with homochiral and heterochiral diproline templates as conformational constraints

Diproline segments have been advanced as templates for nucleation of folded structure in designed peptides. The conformational space available to homochiral and heterochiral diproline segments has been probed by crystallographic and NMR studies on model peptides containing L-Pro-L-Pro and D-Pro-L-Pro units. Four distinct classes of model peptides have been investigated: a) isolated D-Pro-L-Pro segments which form type II' beta-turn; b) D-Pro-L-Pro-L-Xxx sequences which form type II'-I (betaII'-I, consecutive beta-turns) turns; c) D-Pro-L-Pro-D-Xxx sequences; d) L-Pro-L-Pro-L-Xxx sequences. A total of 17 peptide crystal structures containing diproline segments are reported. Peptides of the type Piv-D-Pro-L-Pro-L-Xxx-NHMe are conformationally homogeneous, adopting consecutive beta-turn conformations. Peptides in the series Piv-D-Pro-L-Pro-D-Xxx-NHMe and Piv-L-Pro-L-Pro-L-Xxx-NHMe, display a heterogeneity of structures in crystals. A type VIa beta-turn conformation is characterized in Piv-L-Pro-L-Pro-L-Phe-OMe (18), while an example of a 5-->1 hydrogen bonded alpha-turn is observed in crystals of Piv-D-Pro-L-Pro-D-Ala-NHMe (11). An analysis of pyrrolidine conformations suggests a preferred proline puckering geometry is favored only in the case of heterochiral diproline segments. Solution NMR studies, reveal a strong conformational influence of the C-terminal Xxx residues on the structures of diproline segments. In L-Pro-L-Pro-L-Xxx sequences, the Xxx residues strongly determine the population of Pro-Pro cis conformers, with an overwhelming population of the trans form in L-Xxx=L-Ala (19).     

Cyclodextrin‐Templated Porphyrin Nanorings

α‐ and β‐Cyclodextrins have been used as scaffolds for the synthesis of six‐ and seven‐legged templates by functionalizing every primary CH₂OH with a 4‐pyridyl moiety. Although these templates are flexible, they are very effective for directing the synthesis of macrocyclic porphyrin oligomers consisting of six or seven porphyrin units. The transfer of chirality from the cyclodextrin templates to their nanoring hosts is evident from NMR and circular dichroism spectroscopy. Surprisingly, the mean effective molarity for binding the flexible α‐cyclodextrin‐based template within the six‐porphyrin nanoring (74 M ) is almost as high as for the previously studied rigid hexadentate template (180 M ). The discovery that flexible templates are effective in this system, and the availability of a template with a prime number of binding sites, open up many possibilities for the template‐directed synthesis of larger macrocycles.     

A short route to the macrocyclic core of biaryl ether-based cyclopeptides

A new route based on an intramolecular Horner-Wadsworth-Emmons type olefination of amidophosphonates has been developed for the construction of a 17-membered macrocyclic scaffold related to some biologically important biaryl ether-based cyclic peptides.     

新型大环席夫碱化合物的合成及其抗菌活性研究

利用Ca2＋, Ba2＋离子作为模板离子, 由2,4-二羟基-5-乙酰苯乙酮与烷基二胺[即1,3-丙二胺, 1,4-丁二胺, 1,6-己二胺]反应, 分别合成了系列新型席夫碱大环化合物Ln (n＝3, 4, 6). 对合成得到的新型大环席夫碱化合物采用元素分析, 1H NMR, IR, 紫外-可见光谱和MS等进行组成和结构表征, 体外抗菌活性也被试验.     

A Multicomponent Conjugation Strategy to Unique N‐Steroidal Peptides: First Evidence of the Steroidal Nucleus as a β‐Turn Inducer in Acyclic Peptides

Constraining small peptides into specific secondary structures has been a major challenge in peptide ligand design. So far, the major solution for decreasing the conformational flexibility in small peptides has been cyclization. An alternative is the use of topological templates, which are able to induce and/or stabilize peptide secondary structures by means of covalent attachment to the peptide. Herein a multicomponent strategy and structural analysis of a new type of peptidosteroid architecture having the steroid as N‐substituent of an internal amide bond is reported. The approach comprises the one‐pot conjugation of two peptide chains (or amino acid derivatives) to aminosteroids by means of the Ugi reaction to give a unique family of N‐steroidal peptides. The conjugation efficiency of a variety of peptide sequences and steroidal amines, as well as their consecutive head‐to‐tail cyclization to produce chimeric cyclopeptide–steroid conjugates, that is, macrocyclic lipopeptides, was assessed. Determination of the three‐dimensional structure of an acyclic N‐steroidal peptide in solution proved that the bulky, rigid steroidal template is capable of both increasing significantly the conformational rigidity, even in a peptide sequence as short as five amino acid residues, and inducing a β‐turn secondary structure even in the all‐s‐trans isomer. This report provides the first evidence of the steroid skeleton as β‐turn inducer in linear peptide sequences.     

Synthesis of novel 2,4,6-trisubstituted pyrimidine derivatives and their in vitro antimicrobial activity

A series of novel pyrimidines (6a–6i) has been synthesized from corresponding chalcones and isonicotinimidamide.HCl in the presence of potassium carbonate involving Michael addition followed by cycloaddition. All newly synthesised chalcones and pyrimidines were screened for in vitro antimicrobial activity against various Gram positive, Gram negative bacterial and fungal strains. Most of compounds displayed high antimicrobial activity compared to standard drugs Penicillin, Streptomycin and Ampothericin-B.     

大环Schiff碱希土配合物的合成及表征

大环化合物及其配合物的研究近来十分活跃,模板反应是合成新型大环配合物的主要手段。通常采用主族金属元素及过渡金属元素离子作模板,而用Ln~(3+)作模板则较少见。本文用自制的呋喃二甲醛—2,5为原料,以Ln~(3+)为模板,合成并表征了一系列大环配合物。     

Context-dependence of the contribution of disulfide bonds to beta-hairpin stability

Incorporation of disulfide bonds to stabilize protein and peptide structures is not always a successful strategy. To advance current knowledge on the contribution of disulfide bonds to beta-hairpin stability, a previously reported beta-hairpin-forming peptide was taken as a template to design a series of Cys-containing peptides. The conformational behavior of these peptides in their oxidized, disulfide-cyclized peptides, and reduced, linear peptides, was investigated on the basis of NMR parameters: NOEs, and 1H and 13C chemical shifts. We found that the effect of disulfide bonds on beta-hairpin stability depends on its location within the beta-hairpin structure, being very small or even destabilizing when connecting two hydrogen-bonded facing residues. When the disulfide bond is linking non-hydrogen-bonded facing residues, we estimated that its contribution to the free-energy change of beta-hairpin folding is approximately -1.0 kcal mol(-1). This value is larger than those reported for most beta-hairpin-stabilizing cross-strand side-chain-side-chain interactions, except for some aromatic-aromatic interactions, in particular the Trp-Trp one, and the cation-pi interaction between Trp and the non-natural methylated Arg/Lys. As disulfide bonds are frequently used to stabilize peptide conformations, our conclusions can be useful for peptide, peptidomimetic, and protein design, and may even extend to other chemical cross-links.     

Cyclic peptide helices: a hybrid beta-hairpin/beta-helical supersecondary structure

This communication describes the design and characterization of a new peptide motif that is a hybrid of beta-hairpin and beta-helical structures. This motif was supported by CD and IR spectrocopies in nonpolar organic solvents and was confirmed by NMR spectroscopy and structure calculations using NMR-derived restraints. The beta-hairpin/beta-helical motif represents a potentially attractive new structural template for a variety of possible applications in biomolecular design, such as ligands for macromolecular targets and building blocks for new protein architectures.     

Intermolecular packing and alignment in an ordered beta-hairpin antimicrobial peptide aggregate from 2D solid-state NMR

The aggregation and packing of a membrane-disruptive beta-hairpin antimicrobial peptide, protegrin-1 (PG-1), in the solid state are investigated to understand its oligomerization and hydrogen-bonding propensity. Incubation of PG-1 in phosphate buffer saline produced well-ordered nanometer-scale aggregates, as indicated by 13C and 15N NMR line widths, chemical shifts, and electron microscopy. Two-dimensional 13C and 1H spin diffusion experiments using C-terminus strand and N-terminus strand labeled peptides indicate that the beta-hairpin molecules in these ordered aggregates are oriented parallel to each other with like strands lining the intermolecular interface. In comparison, disordered and lyophilized peptide samples are randomly packed with both parallel and antiparallel alignments. The PG-1 aggregates show significant immobilization of the Phe ring near the beta-turn, further supporting the structural ordering. The intermolecular packing of PG-1 found in the solid state is consistent with its oligomerization in lipid bilayers. This solid-state aggregation approach may be useful for determining the quaternary structure of peptides in general and for gaining insights into the oligomerization of antimicrobial peptides in lipid bilayers in particular.     

Template Syntheses

Although the principle of template synthesis has been known since the sixties, surprising discoveries and new applications in the field of supramolecular chemistry over the last decade have provoked a boom in the subject. The synthesis of supramolecular species has been made much more efficient, or even in some cases possible, by the introduction of template ions or molecules. It is not just metal ions that can act as templates. Neutral molecules, electrostatic interactions, and hydrogen bonds also support the formation of binary and tertiary complexes. Energetically favorable conformations then lead to the formation of a specific desired product in high yield. In addition to the discussion of metal ions and neutral molecules as templates, covalent, positive, and negative templates are differentiated. Kinetic and thermodynamic aspects will also be considered in this review, together with the influence of templates on the phenomenon of self-organization. Further developments and applications include the synthesis of oligonucleotides, peptide blocks capable of forming secondary structure, and template polymers. Template synthesis of defined molecular cavities ultimately leads to “inclusion chemistry on a nanometer scale.”     

Preparation of diazabicyclo[4.3.0]nonene-based peptidomimetics

Several functionalized diazabicyclo[4.3.0]nonenes and other heterocycles have been prepared as potential peptidomimetic scaffolds. A novel and efficient method has been developed for the preparation of N-substituted gamma-lactams 13. Preparation of amidine-containing 1,5-diazabicyclo[4.3.0]nonenes 43 and 44 has been achieved through Hg-mediated cyclization of the precursor N-aminopropyl-gamma-thiolactams and subsequent functional group manipulation. Bicycle 43 represents a novel scaffold for potential peptide turn mimetics, whereas 44 could potentially be employed as an alpha-helix template attached to the C-terminus of peptides. These compounds are novel additions to the current range of small-molecule constrained peptidomimetics.     

新型缺电子联吡啶大环化合物的模板合成

通过富电子对苯二酚醚链衍生物和缺电子联吡啶间的模板效应, 成功地合成了一种新型联吡啶大环化合物, 利用元素分析、核磁共振和质谱等手段对新化合物进行了表征。     

Utilization of 3'-carboxy-containing tyrosine derivatives as a new class of phosphotyrosyl mimetics in the preparation of novel non-phosphorylated cyclic peptide inhibitors of the Grb2-SH2 domain

A new class of phosphotyrosyl (pTyr) mimetics, distinct from the conventional pTyr mimetic design of adding non-hydrolyzable acidic functionalities to the 4'-position of phenylalanine, was created by introducing carboxy-containing groups to the 3'-position of tyrosine. The effect of the chain length of the carboxy substituent was examined. Reported herein is the chiral pool synthesis of the new pTyr mimetics, and their first use in a novel non-phosphorylated Grb2-SH2 domain binding motif with the 5-amino-acid sequence Xx1-Leu-(3'-substituted-Tyr)-Ac6c-Asn. The highest affinity was exhibited by the 3-L-(2-carboxyethyl)tyrosine-containing sulfoxide-cyclized peptide , with an IC50 = 1.1 microM, providing a promising new template for further development of potent Grb2-SH2 domain inhibitors with reduced charge and peptidic nature, but improved selectivity and bioavailability.