Click chemistry as a macrocyclization tool in the solid-phase synthesis of small cyclic peptides

Despite the vast number of techniques developed for the cyclization of small peptides, cyclization efficiency remains problematic in peptides that lack turn-promoting structures. Here we demonstrate the utility of click chemistry as a macrocyclization tool in the solid-phase synthesis of cyclic tetra-, penta-, hexa-, and heptapeptides. On-resin cyclization is completed at room temperature within 6 h, resulting in predominantly monomer with small amounts of cyclomultimer byproducts.     

A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides

We studied here the binding of the mastoparan X peptide to a zwitterionic lipid bilayer (POPC) and demonstrated that nitrile-derivatized amino acids can be used to determine the hydration state (or change in hydration state) of specific sites of membrane-interactive peptides (upon binding). We have also shown that polarized ATR-FTIR measurements can further be used to uncover information regarding the spatial orientation of individual side chains as well as their conformational preference within the lipid bilayer.     

A new method for the preparation of unprotected peptides on biocompatible resins with application in combinatorial chemistry

[formula: see text] A synthetic strategy for the preparation of side chain free peptides on biocompatible solid supports is described. Final peptide detachment is afforded in mild basic conditions with no presence of scavengers or other additives, thus allowing single peptide-resin beads to be cleaved in mass spectrometry sample plates for direct sequencing using MALDI-TOF post-source decay. This methodology offers clear advantages for the development of one-bead--one-compound combinatorial libraries in addition to parallel and regular synthesis of peptides.     

An improved method for the synthesis of cellulose membrane-bound peptides with free C termini is useful for PDZ domain binding studies

SPOT synthesis permits parallel synthesis and screening of thousands of cellulose membrane-bound peptides to study protein-protein interactions in a proteomic context. Recognition of C-terminal residues is one of the most common binding features of PDZ domains. Unfortunately, most solid support-bound peptide libraries lack a free C terminus due to C-terminal fixation on the solid support. To overcome this restriction, we developed a robust methodology based on our previous strategy for generating peptides with authentic C termini. To validate this improved method, we screened a human peptide library of 6223 C termini with the syntrophin PDZ domain. Furthermore, using the same library, new peptide ligands derived from membrane proteins and receptors were found for the ERBIN PDZ domain. Finally, we identified the protein kinase breakpoint cluster region, which is known as a negative regulator of cell proliferation and oncogenic transformation, as an ERBIN ligand.     

A new general algorithmic method in reaction syntheses using linear algebra

We discuss here a new general linear algebraic method (both model and algorithm) for describing and generating (among others) minimal reactions and also minimal mechanisms in stoichiometry, or dimensionless groups in physics as well. (Further applications in process network syntheses will be discussed in .) With some minor modifications of the input this method can be extended for several related questions: for generating direct and overall reactions, direct (steady state) mechanisms, for finding the possible resulting (overall) reactions among all possible mechanisms, etc.Computational results in section 4 show the speed of our algorithm.We give also mathematical background and results in sections 3, 5 and 6. However, we do not restrict ourselves to mathematics only, we also talk on the language of chemistry, too.The theoretical results in sections 3.2, 3.3, 5 and the computational examples in section 4 are completely new, further theoretical results will appear in and in .     

A new turn structure for the formation of beta-hairpins in peptides

Previous studies by Gellman and co-workers have elegantly shown that mirror-image beta-turns based upon d-Pro-Gly are especially good at stabilizing beta-hairpins and have demonstrated that peptide 1 [Arg-Trp-Gln-Tyr-Val-d-Pro-Gly-Lys-Phe-Thr-Val-Gln-NH2] folds into a well-defined beta-hairpin [Espinosa, J. F.; Gellman, S. H. Angew. Chem., Int. Ed. 2000, 39, 2330-2333]. The present study establishes that the amino acid ornithine (Orn) also forms a turn structure that is excellent at stabilizing beta-hairpins when linked through the delta-amino group and that this turn is comparable to d-Pro-Gly in ability to induce beta-hairpin formation. Thus, 1H NMR chemical shift and NOE studies establish that Orn-containing analogue 2 [Arg-Trp-Gln-Tyr-Val-deltaOrn-Lys-Phe-Thr-Val-Gln-NH2] is comparable in structure to peptide 1. The present study also establishes that the Orn turn is superior to Asn-Gly turns and that replacement of the deltaOrn with epsilonLys or d-deltaOrn generates structures that do not fold significantly.     

A new base-catalyzed cleavage reaction for the preparation of protected peptides

A new base-catalyzed elimination reaction employing the hindered, non-nucleophilic bases tetramethylguanidine or 1,8-diazabicyclo-[5.4.0.]undec-7-ene has been developed for the removal of protected peptides from a 2-[4-(hydroxymethyl)phenyl-acetoxy]propionyl-resin. The proposed reaction mechanism involved cleavage of the ester bond between the peptide and resin via a base-catalyzed elimination. The protected peptide-resin cleavage reaction is mild, rapid and proceeds in good yield with a very simple work- up procedure. Four protected peptide-resins varying in size from seven to sixteen residues were prepared using the 2-[4-(hydroxymethyl)phenyl-acetoxy]- propionyl-resin and then cleaved in the protected form to demonstrate the utility of the new cleavage technique. The protected peptide cleavage products can be used in the preparation of larger peptides by fragment condensation.     

A new iterative linear integral isoconversional method for the determination of the activation energy varying with the conversion degree

The conventional linear integral isoconversional methods may lead to important errors in the determination of the activation energy when the significant variation of the activation energy with the conversion degree occurs. Vyazovkin proposed an advanced nonlinear isoconversional method, which allows the activation energy to be accurately determined [Vyazovkin, J Comput Chem 2001, 22, 178]. However, the use of the Vyazovkin method raises the problem of the time‐consuming minimization without derivatives. A new iterative linear integral isoconversional method for the determination of the activation energy as a function of the conversion degree has been proposed, which is capable of providing valid values of the activation energy even if the latter strongly varies with the conversion degree. Also, the new method leads to the correct values of the activation energy in much less time than the Vyazovkin method. The application of the new method is illustrated by processing of theoretically simulated data of a strongly varying activation energy process. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

A new approach to macrocyclization via alkene formation in catalytic diazo decomposition. Synthesis of patulolides A and B

[reaction: see text] Effective synthetic uses of bisdiazocarbonyl compounds for the selective construction of diverse macrocycles, including the synthesis of patulolides A and B, by catalytic "carbene dimer" formation are reported. Control of stereochemistry and efficient methods for product isomerization or kinetic isomer differentiation have been achieved.     

A new arithmetic for linear free radical copolymerization

As a consequence of their method of production, polymer chains are polydisperse in size, composition and sequence distribution. In this work we present a new method of uniquely identifying these “polymer isomers” termed “Digital Encoding of Polymeric Chains”. The method involves replacing distinguishable features of the chain such as monomer units, branches, etc. with a number. This unique sequence of numbers provides a digital code, which, depending on the base of the arithmetic used (binary, ternary) can be translated into a unique decimal equivalent number. We have applied this technique to the case of binary copolymerization in a CSTR at steady state and show how the sequence spectra of the chain populations are conveniently obtained. Furthermore, the technique shows that rich information about the copolymerization kinetics, reactivity ratios and termination mode can be obtained from analysis of the short chains of the distribution. The implications for this in parameter estimation and controlled polymerization are discussed in this paper.     

A new method for the detection of racemization during peptide synthesis: stereoselective hydrolysis of diastereomeric peptides by leucine aminopeptidase

A suitably protected dipeptide of configuration L -D , e.g. Z-L -Ala-D -Ala is coupled with an all L alanine peptide, e.g. L -Ala-L -Ala-ONb

1 Abbreviations according to the IUPAC-IUB rules, ‘Symbols for Amino-Acid Derivatives and Peptides, Recommendations (1971)’'. see e.g. J. biol. Chemistry 247, 977 (1972). In particular the following abbreviations have been used: Z = benzyloxycarbonyl-, -ONb = p-nitrobenzyloxy-, -ONSu = succinimido-oxy-. Additional abbreviations are LAP = leucine aminopeptidase, DCCI = N,N′-dicyclohexylcarbodiimide, DMF = dimethylformamide.

. The blocking groups are removed and the free peptide hydrolyzed by leucine amino peptidase (E.C. 3.4.1.1). This enzyme shows absolute L -specificity for the penultimate peptide bond from the amino end and therefore cleaves only the all L peptide formed through racemization. The amount of free alanine determined by amino acid analysis gives a multiple of the degree of racemization. The sensitivity of the test allows 0.1% of (L -Ala)₄ to be detected in the synthesis of L -Ala-D -Ala-L -Ala-L Ala. Coupling of Z-L -Ala-D -Ala and Z-L -Ala-D -Phe with di- and trialanine peptides has been studied using DCCI and DCCI + 1-hydroxybenzotriazole as coupling reagents. The degree of racemization was around 80% for the coupling by DCCI in DMF but was reduced to 0.2–0.4% in the presence of 2 equivalents of 1-hydroxybenzotriazole. Coupling using the succinimide esters Z-L -Ala-D -Ala-ONSu and Z-L -Ala-D -Phe-ONSu resulted in 0.8 to 10% racemization, depending on the solvent and base used.     

A new method for the standardisation of hypobromite

Summary The oxidation of ferrocyanide by hypobromite and the optical density of the yellow colour of ferricyanide thus developed has been studied with the aid of a Hilger Spekker Absorptiometer Model H 760. A violet filter having maximum transmission in the range of 420–450 m was used. Series of experiments showed that quantitative oxidation of ferrocyanide occurred in the p_N range 8–8.5 (bicarbonate buffer) and the colorimetric titration may be used for the standardisation of hypobromite. The results compared favourably with those obtained by amperometric titration of hypobromite against sodium arsenite as a primary standard.Sincere thanks of the authors are due to Prof. S. S. Joshi, D. Sc. (London), F. R. I. C. (London), F. N. I., F. A. Sc. for kind interest and facilities for the work.