Efficient solid-phase synthesis of peptide-based phosphine ligands: towards combinatorial libraries of selective transition metal catalysts

A new methodology for the solid-phase synthesis of peptide-based phosphine ligands has been developed. Solid supported peptide scaffolds possessing either primary or secondary amines were synthesised using commercially available Fmoc-protected amino acids and readily available Fmoc-protected amino aldehydes for reductive alkylation, in standard solid-phase peptide synthesis (SPPS). Phosphine moieties were introduced by phosphinomethylation of the free amines as the final solid-phase synthetic step, immediately prior to complexation with palladium(II), thus avoiding tedious protection/deprotection of the phosphine moieties during the synthesis of the ligands. The extensive use of commercial building blocks and standard SPPS makes this methodology well suited for the generation of solid-phase combinatorial libraries of novel ligands. Furthermore, it is possible to generate several different phosphine ligand libraries for every peptide scaffold library synthesised, by functionalising the scaffold libraries with different phosphine moieties. The synthesised ligands were characterised on solid support by conventional (31)P NMR spectroscopy and, cleaved from the support, as their phosphine oxides by HPLC, (1)H NMR, (31)P NMR and high resolution ESMS. Palladium(II) allyl complexes were generated from the resin bound ligands and to demonstrate their catalytic properties, palladium catalysed asymmetric allylic substitution reactions were performed. Good yields and moderate enantioselectivity was obtained for the selected combination of catalysts and substrate, but most importantly the concept of this new methodology was proven. Screening of ligand libraries should afford more selective catalysts.     

Differentially-protected steroidal triamines; scaffolds with potential for medicinal, supramolecular, and combinatorial chemistry

Cholic acid 2a has been converted into two new orthogonally-protected triamino scaffolds, 13 and 14. The synthesis proceeds via the bis-Boc-NH-substituted azide 10, for which an improved preparation is described. After removal of the Boc groups, the two axial amines are differentiated through a novel monoprotection employing 1-(2-nitrobenzenesulfonyloxy)-benzotriazole 29. Regioselectivity of > or 50 : 1 is achieved, presumably reflecting an exceptional sensitivity to steric hindrance. Protection of the remaining amino group as Boc or Alloc gives the scaffolds in approximately 40% overall yield from cholic acid. Scaffold 13 has been sequentially deprotected and derivatised with N-carbamoyl amino acids, to give a model for tripodal peptide libraries.     

5,5-Dimethylproline dipeptides: an acid-stable class of pseudoproline

Commercially available Fmoc-protected l-amino acids were employed and coupled to l-allylglycine. Cross metathesis with 2-methyl-2-butene using second generation Grubbs’ catalyst gave l-prenylglycine-containing dipeptides. Treatment with trifluoromethanesulfonic acid resulted in cyclisation and subsequent formation of acid-stable 5,5-dimethyl-l-proline dipeptides for direct insertion into linear peptide sequences.     

Efficient loading of sulfonamide safety-catch linkers by Fmoc amino acid fluorides

[reaction: see text] Fmoc-protected amino acid fluorides were found to be excellent reagents for the acylation of sulfonamide safety-catch linkers (SCL) suitable for the subsequent preparation of peptide C-terminal thioesters. High loadings were obtained on different types of resins with low levels of epimerization.     

Synthesis and Reactivity of 5‐Bromopenta‐2,4‐diynenitrile (BrC5N): an Access to π‐Conjugated Scaffolds

The synthesis of 5‐bromopenta‐2,4‐diynenitrile (BrC₅N) in three steps from commercially available compounds is reported. Reacting 5‐bromopenta‐2,4‐diynenitrile with secondary amines led to the formation of stable butadiynamines or enynenitriles, depending on the nature of the amine reactant. The reaction of 5‐bromopenta‐2,4‐diynenitrile with simple terminal alkynes in the presence of secondary amines, copper, and palladium catalysts, provided a straightforward access to original polyfunctional carbon‐rich scaffolds. In this work, different alkynes and secondary amines were tested, which allowed for the preparation of a family of substituted dienes. Given the high synthetic potential of 5‐bromopenta‐2,4‐diynenitrile, we also prepared iodinated counterparts of this compound, that is, 5‐iodopenta‐2,4‐diynenitrile and its lower homologue 3‐iodopropiolonitrile. The UV‐visible spectrum of some relevant compounds was also recorded.     

Synthesis of novel exocyclic amino nucleosides by parallel solid-phase combinatorial strategy

A versatile parallel solid-phase combinatorial strategy was developed for the synthesis of large nucleoside libraries. Twelve libraries L1-12 of 1152 novel exocyclic triazinylamino nucleosides and one library L13 of 82 new substituted clitocine derivatives were synthesized in high quality as natural product mimic nucleosides on the semi-automated synthesizer. The polystyrene MMT-Cl resin was selected and utilized. The key intermediate resins 5 and 9 loaded with the corresponding scaffolds were prepared and validated with various amines before parallel synthesis. After a variety of amino building blocks were validated, 56 primary amines in 12 groups (building block set A) and 24 secondary amines in 3 groups (building block set B) were selected and utilized to combinatorialize the first and the second reactive sites on scaffold 5 for the synthesis of libraries L1-12. Eighty-two amines (building block set C) were utilized for the synthesis of clitocine library L13. Thirteen libraries of 1234 novel exocyclic amino nucleosides were all analyzed and characterized by high throughput LC-MS. 81.3-100% of the library members in 13 libraries show more than 60% purity, and 65.7-92.7% of the library members in these libraries show 80-100% purity. The strategy can be widely used for the synthesis of other diverse nucleoside libraries.     

Approaches to the solid phase of a cyclotriveratrylene scaffold-based tripodal library as potential artificial receptors

Two versatile tripodal cyclotriveratrylene (CTV)-based scaffolds (7 and 9) have been prepared for the solid phase construction of libraries of tripodal artificial synthetic receptors. A 2197-member library of CTV-based tripodal receptor molecules, 20[1-13,1-13,1-13], was prepared on the solid phase using split-mix synthesis. The CTV-based receptors contain three peptide arms; one of them is attached to the solid phase and is different from the other two identical peptide arms.     

Synthesis and mass spectrometry studies of branched oxime ether libraries. Mapping the substitution motif via linker stability and fragmentation pattern.

The oxime ether chemistry has recently been used as a convenient approach to preparing potentially highly diverse combinatorial libraries. The synthetically easiest way to form the libraries is convergent, i.e., via reaction of a branched scaffold containing two or more aminooxy linker groups, with a variety of carbonyl substituents. We show here that such reactions between aldehydes and ketones of different structure with the scaffolds containing different types of aminooxy groups can lead to the formation of virtually all expected components in the model mixtures 1-3 formed from three scaffolds (7-9) and eight substituents (R(1)-R(8)). One important problem with the branched libraries is that the libraries formed from the more complex scaffolds, such as 11, contain multiple regioisomers. The results of extensive analysis of a variety of library components by mass spectrometry presented here show that the differences in the MS-MS fragmentation energies for different linkers yield regiochemical information essential for identification of individual library components.     

Solid-phase synthesis of a tyrphostin ether library

The solid-phase synthesis of a 4500-member (30 x 15 x 10) tyrphostin library is demonstrated utilizing the Irori-directed sorting system. Fmoc-protected PL-Rink resin was used as the solid support. After Fmoc-deprotection, aryl aldehydes were attached to the resin through reductive amination. Acylation of the resulting secondary amines with cyanoacetic acid was followed by a Knoevenagel condensation with phenolic aldehydes. Mitsunobu coupling of primary alcohols to the resin-bound phenols yielded the final library of compounds 1.     

Efficient synthesis of tertiary amines from secondary amines

Reliable N-alkylations of secondary amines have been developed. By using DIAD and TPP (or PS-TPP) a variety of secondary amines can be converted to the corresponding tertiary amines in good to excellent yields with diverse alkylhalides; no formation of quaternary amine salts are observed. These protocols are amenable to combinatorial chemistry libraries, and are also useful for the syntheses of secondary amines by an acid lysis of the cleavable tertiary amino resins.     

A novel α,α-diaminoacetic acid derivative for the introduction of the α-oxo aldehyde functionality into peptides

A Fmoc-protected α,α^′-diaminoacetic acid derivative acting as a masked glyoxylic acid equivalent was prepared in one step from glyoxylic acid and introduced into peptide chains after solid-phase peptide elongation. Deprotection and cleavage of the peptide from the solid support using trifluoroacetic acid was followed by unmasking of the glyoxylyl group in the presence of a base. This reagent allowed the synthesis of a glyoxylyl peptide using nonoxidizing conditions.     

Dynamic combinatorial libraries of macrocycles derived from phthalic aldehydes and α,ω-diamines

Dynamic combinatorial chemistry methodology was used to obtain eleven new polyazamacrocycles derived from isophthalic and terephthalic aldehyde and α,ω-diamines. Simple templates, such as alkali metal salts, were found to amplify large macrocycles: 45-membered [3+3]hexaazacrown and 60-membered [4+4]octaazacrown. Parent imine libraries were converted into corresponding secondary libraries of amines using a fast reduction protocol. Methyl carbamate protection of amine group allowed convenient isolation of polyazamacrocycles in very good yields.     

Chemical and Ribosomal Synthesis of Topologically Controlled Bicyclic and Tricyclic Peptide Scaffolds Primed by Selenoether Formation

Bicyclic and tricyclic peptides have emerged as promising candidates for the development of protein binders and new therapeutics. However, convenient and efficient strategies that can generate topologically controlled bicyclic and tricyclic peptide scaffolds from fully‐unprotected peptides are still much in demand, particularly for those amenable to the design of biosynthetic libraries. In this work, we report a reliable chemical and ribosomal synthesis of topologically controlled bicyclic and tricyclic peptide scaffolds. Our strategy involves the combination of selenoether cyclization followed by disulfide or thioether cyclization, yielding desirable bicyclic and tricyclic peptides. This work thus lays the foundation for developing peptide libraries with controlled topology of multicyclic scaffolds for in vitro display techniques.     

Dynamic Amino Acid Side-Chains Grafting on Folded Peptide Backbone**

An efficient strategy for the synthesis of large libraries of conformationally defined peptides is reported, using dynamic combinatorial chemistry as a tool to graft amino acid side chains on a well-ordered 3D (3-dimension) peptide backbone. Combining rationally designed scaffolds with combinatorial side chains selection represents an alternative method to access peptide libraries for structures that are not genetically encodable. This method would allow a breakthrough for the discovery of protein mimetic for unconventional targets for which little is known.     

A versatile annulation protocol toward novel constrained phosphinic peptidomimetics

The development of a novel 3-center 2-component annulation reaction between alpha,omega-carbamoylaldehydes and suitably monoalkylated phosphinic acids is reported. Depending on the starting alpha,omega-carbamoylaldehyde, diverse phosphinic scaffolds varying in the size of their rigidity element, the nature and stereochemistry of substituents, and the participation of heteroatoms in the azacyclic ring system can be obtained in one synthetic step and in high yield. In addition, this methodology allows the synthesis of Fmoc-protected constrained aminophosphinic acids that can be easily converted to suitable pseudodipeptide building blocks compatible with the requirements of peptide synthesis on the solid phase. Finally, the careful choice of both substituents and protecting groups can provide functionally diverse, orthogonally protected constrained scaffolds for extended derivatization of the target phosphinic peptidomimetic structures.     

General and Facile Route to Isomerically Pure Tricyclic Peptides Based on Templated Tandem CLIPS/CuAAC Cyclizations

We report a one‐pot ligation/cyclization technology for the rapid and clean conversion of linear peptides into tricyclic peptides that is based on using tetravalent scaffolds containing two benzyl bromide and two alkyne moieties. These react via CLIPS/CuAAC reactions with cysteines and azides in the peptide. Flexibility in the scaffolds is key to the formation of isomerically pure products as the flexible scaffolds T4 ₁ and T4 ₂ mostly promote the formation of single isomeric tricycles while the rigid scaffolds T4 ₃ and T4 ₄ do not yield clean products. There seems to be no limitation to the number and types of amino acids present as 18 canonical amino acids were successfully implemented. We also observed that azides at the peptide termini and cysteine residues in the center gave better results than compounds with the functional groups placed the other way round.     

The use of proteotypic peptide libraries for protein identification

This paper describes an algorithm to apply proteotypic peptide sequence libraries to protein identifications performed using tandem mass spectrometry (MS/MS). Proteotypic peptides are those peptides in a protein sequence that are most likely to be confidently observed by current MS-based proteomics methods. Libraries of proteotypic peptide sequences were compiled from the Global Proteome Machine Database for Homo sapiens and Saccharomyces cerevisiae model species proteomes. These libraries were used to scan through collections of tandem mass spectra to discover which proteins were represented by the data sets, followed by detailed analysis of the spectra with the full protein sequences corresponding to the discovered proteotypic peptides. This algorithm (Proteotypic Peptide Profiling, or P3) resulted in sequence-to-spectrum matches comparable to those obtained by conventional protein identification algorithms using only full protein sequences, with a 20-fold reduction in the time required to perform the identification calculations. The proteotypic peptide libraries, the open source code for the implementation of the search algorithm and a website for using the software have been made freely available. Approximately 4% of the residues in the H. sapiens proteome were required in the proteotypic peptide library to successfully identify proteins.     

Tethered libraries: solid-phase synthesis of substituted urea-linked bicyclic guanidines

The general concept of tethered combinatorial libraries of compounds in which two pharmacophores are found is described. In particular, an improved method for the solid-phase synthesis of bicyclic guanidines from reduced N-acylated dipeptides, and its use in the synthesis of urea-linked bicyclic guanidines, is described. The exhaustive reduction of glutamine-containing resin-bound N-acylated dipeptides, using borane-THF, generated compounds containing three secondary amines and one primary amine. Following selective trityl protection of the primary amine, treatment of the three secondary amines with thiocarbonyldiimidazole (CSIm2) and mercuric acetate (Hg(OAc)2) generated the resin-bound bicyclic guanidines. Following trityl deprotection, an Fmoc-amino acid was coupled. Upon removal of the Fmoc protecting group, the resulting primary amine was treated with hexyl isocyanate to generate the urea-linked bicyclic guanidines. The desired products were cleaved from the resin using hydrogen fluoride. The selection of building blocks and characterization of controls for the synthesis of a combinatorial library is discussed.     

Modular synthesis of amine-functionalized oxazolines

Substituted oxazoline amines have been prepared in high yield from beta-amino alcohols and Fmoc-protected alpha-amino acids using CCl(4), PPh(3), and Hünig's base in a one-pot procedure followed by base-mediated deprotection. [reaction: see text]     

Solid-phase synthesis of hydroxysteroid derivatives using the diethylsilyloxy linker

Four different types of hydroxysteroids (primary alcohol, secondary alcohols, and phenol), bearing either an oxirane or an azide as a precursor of molecular diversity, were linked in good yields to solid support using the butyldiethylsilane polystyrene (PS-DES) resin. These molecules were then used as scaffolds to generate hydroxysteroid derivatives containing two levels of diversity. The proposed libraries were tested by running steroidal alcohols through a model sequence of reactions (solid-phase coupling, aminolysis of oxirane or reduction of azide, amidation, and final cleavage). As a result, two linked secondary alcohols (17beta-hydroxy-spiro-3(R)-oxirane-5alpha-androstane and 3beta-hydroxy-spiro- 17(S)-oxirane-5alpha-androstane) and a primary alcohol (spiro-17(S)-oxirane-3-(hydroxymethyl)-1,3,5(10)-estratriene) afforded good overall yields (>45%) and high HPLC purities (>90%) of hydroxysteroids derivatized as alkylamides without purification. One limitation was noted for the fourth library: the phenolic steroid linked by the diethylsilyloxy linker gave a poor overall yield of 8% of the desired model compound. Finally, the diethylsilyloxy linker was used successfully for a rapid solid-phase synthesis of a model library of twenty C19-steroid derivatives (3beta-amido-3alpha-hydroxy-5alpha-androstane-17-ones), with an average yield of 53% and average HPLC purity of 97% without purification steps.