Linkers, acid-labile

For these reasons, an alternative route and more acid labile linkers compared to p-carboxy trityl linker 24a initially used were sought, to avoid high concentrations of TFA for the final cleavage. The synthesis of the alkoxysubstitued linkers 24b (Meisenbach and Voelter 1997) and 24c, which can be synthesised directly on the solid support in five steps, offer the possibility of linkers with tailor-made stability. 

The successful assembly of organic compounds on a solid support represents only part of the challenge in SPOS. After completion of synthetic sequence, the compounds must be cleaved from linkers attached to polymer by a chemical or photochemical reaction, for example, treatment of a polymer-bound compound with acids, bases, nucleophiles, redox reagents, and even photons. Acid-labile linker and amine-cleavable Marshall linker are two major classes of hnkers used in combinatorial synthesis. 

Many acid-labile linkers are used to assemble combinatorial libraries. Compounds are cleaved in the final step by TFA/DCM solution with various concentrations for a certain period of time. Mild cleavage conditions may lead to incomplete cleavage of the desired compound from a solid support. On the other hand harsh conditions may cause compound degradation and side reactions. Harsh conditions will also cause the partial breakdown of resin and the leaching of unidentified impurities into the final products. Harsh cleavage conditions demand the stabihty of all compounds under such conditions. This may limit the scope of combinatorial synthesis... 

For resin-bound carbamates (18-21), indole linker was the most acid-labile linker for this class of compounds. Rink linker ranked second. Resin (20) was cleaved with 0.5% TFA in 20 min. Resin (21) was cleaved with 1% TFA in 2 min. Resins (18) and (19) required higher concentration of TFA. Resin (18) was cleaved with 1% TFA in 5 h. Alternatively, resin (19) was cleaved with 1% TFA in 12 h and with 5% TFA in only 16 min (not shown). 

For resin-bound ureas (22-25), Indole and Rink linkers, generally ranked 1 and 2 in cleavage kinetics, were still the most acid-labile linker for this class of compounds. Resins (24) and (25) were cleaved with 0.5% TFA in 2 and 23 min, respectively. Resins (22) and (23) were cleaved with 1% TFA in more than 10 h. The order of cleavage rates is similar to carbamate compounds. 

The Marshall Unker [23] has been widely used to synthesize compounds that can be cleaved by primary and secondary amines to afford the corresponding amides. Marshall linker was used in the synthesis of three or more diversity-site hbraries because it allowed the addition of one more diversity element at the cleavage step. While the original reported linker [23] involved the oxidation of the Unker before cleavage, the efficient release of the resin-bound compounds using nucleophiles from the unoxidized linker has been reported [16, 24]. Similarly to the acid-labile linkers, the kinetics of the cleavage reaction and time required for this reaction directly affect the synthesis efficiency, purity and yield of the final products. A cleavage study was carried out on seven resin-bound thiophenol esters (34—40) on Marshall Unker with 3 amines (41-43) (Scheme 12.11 and Tab. 12.4). 

Chemical ligation methods for peptide synthesis using thioester chemistry in solution have been previously documented (see Vol. E 22a, Section 4.1.5). Generalized procedures for solid-phase ligation have been developed that simplify the overall procedure. One method uses a safety-catch acid labile linker at the C-terminus and was used for the synthesis of a 71-amino acid chemokine, vMIP I (Section 5.3.2.1). Another procedure uses a selectively cleavable glycolate ester linkage (Section 5.3.2.2). 

Two approaches for solid-phase chemical ligation have been described. Canne et al. have developed an elegant system that utilizes an oxime forming ligation to attach the first peptide to the resin, a selectively cleavable ester link to remove the peptide from the resin as a C-terminal carboxylic acid, and the Acm group to protect the N-terminal cysteine residue)311 A complementary approach has been developed by Brik et al. that utilizes native chemical ligation to attach the first peptide to the solid support, a safety-catch acid labile linker to remove the final polypeptide from the support as a C-terminal amide and either Acm or Msc group for N-terminal cysteine protection)32 ... 

Using the Safety-Catch Acid Labile Linker... 

Figure 3.1. Acidolysis of a typical, acid-labile linker.

Acid-labile linkers are the oldest and still the most commonly used linkers for carboxylic acids. Most are based on the acidolysis of benzylic C-O bonds. Benzyl esters cleavable under acidic conditions were the first type of linker to be investigated in detail. The reason for this was probably the initial choice of polystyrene as an insoluble support for solid-phase synthesis [13]. Polystyrene-derived benzyl esters were initially prepared by the treatment of partially chloromethylated polystyrene with salts of carboxylic acids (Figure 3.3). 

The trialkoxy benzhydrol linker, developed by Rink in 1987 [46] ( Rink acid resin , Figure 3.4) is a further acid-labile linker for carboxylic acids. Esters of this linker can, like trityl esters, be cleaved with acids as weak as acetic acid or HOBt [47], and care must be taken to avoid loss of the product during synthetic operations. 

Resin-bound (4-acyloxy-2-buten-l-yl)silanes, which can be prepared from resin-bound allylsilanes and allyl esters by cross-metathesis, react with dilute TFA to yield free carboxylic acids (Figure 3.7 [75]). However, the scope of this strategy remains to be explored. Similarly, esters of polystyrene-bound (2-hydroxyethyl)silanes readily undergo acidolysis and have been used as acid-labile linkers (Figure 3.7 [76]). 

Figure 3.7. (4-Acyloxy-2-buten-l-yl)silanes and 2-acyloxyethylsilanes as acid-labile linkers for carboxylic acids.

Primary and secondary aliphatic amines can be linked to polymeric supports by acid-labile linkers or by linkers sensitive to nucleophiles. Linkers cleavable by light or by transition metal catalysis have also been described. The main types of linker for amines are sketched in Figure 3.24. 

Benzhydrylamines are better suited than benzylamines as acid-labile linkers for amines. The MBHA linker ( methylbenzhydrylamine ), which is usually used to prepare peptide amides (see Section 3.3), can also be used as a linker for amines (Entry 1, Table 3.21). Hydrogen fluoride is, however, required as the cleavage reagent. Easier to cleave are alkoxy-substituted benzhydrylamines (Entries 2-5, Table 3.21), which can be prepared from the corresponding benzhydryl chlorides [263] or by reductive alkylation [410] or solvolysis [411] of the Rink amide linker. In the case of benzhydrylamines linked to polystyrene as benzyl ethers, treatment with TFA can lead to the release of the linker into solution (acidolysis of the benzylic C-O bond, see Figure 3.18). 

Methoxyphenyl ethers can be cleaved by mild oxidants (Entry 10, Table 7.8). Because many acid-labile linkers are also readily oxidized, care must be taken when applying this deprotection strategy. Benzyl ethers have been removed from Tentagel-or PEGA-bound carbohydrates by catalytic hydrogenation using palladium nanoparticles [112],... 

Because no treatment with acid is required during peptide assembly, peptide synthesis with Fmoc amino acids can be conducted on acid-sensitive supports (e.g. Tenta-gel) and with acid-labile linkers. Wang resin is suitable for most purposes, but other supports, such as Sasrin or 2-chlorotrityl resin, can also be used. CPG, macroporous... 

Kaval, N., Van der Eycken, J., Caroen, J.,Dehaen, W.,Strohmeier, G.A., Kappe, C.O. and Van der Eycken, E., An exploratory study on microwave-assisted solid-phase diels-alder reactions of2(lH)-pyrazinones the elaboration of a new tailor-made acid-labile linker, /. Comb. Chem., 2003, 5, 560-568. 

Benzodiazepines were the first class of heterocyclic compounds to be synthesized on the SynPhase surface. In 1994, Ellman and co-workers24 reported a 192 member library of structurally diverse 1,4-benzodiazepines. These compounds were prepared on Mimotopes pins that were grafted with polyacrylic acid, the surface originally used for antibody epitope elucidation.10 Ellman and co-workers25 subsequently synthesized a 1680-member 1,4-benzodiazepine library on SynPhase Crowns that were grafted with a methacrylic acid/dimethylacrylamide copolymer, one of the first SynPhase surfaces designed for solid-phase synthesis. The synthesis was performed on a preformed linker-template system in order to avoid low aminobenzophenone incorporation in this case the HMP acid-labile linker... 

Bradley described the first solid-phase synthesis of PAMAM dendrimers in 1997 [220]. To this end, phthaloyl-protected norspermidine was coupled to aminomethyl functionalised polystyrene-polyethylene-glycol resin ((PS-PEG)-NH2) through an acid-labile linker (see Fig. 23). PAMAM dendrons were assembled by treating deprotected scaffold-bound resin 24 first with an excess of methyl acrylate... 

In order to investigate dendrimers of a different nature [230], Bradley described the synthesis and transfection efficiency of polyamidourea dendrimers synthesised from isocyanate-containing AB3 monomers [231-234]. The use of this kind of tris-branched building block was addressed to enhance dendrimer synthesis by replacement of the 1,4-addition step typical of PAMAM synthesis and to a rapid increase in terminal functionality. The dendritic structures were synthesised using a divergent, microwave-assisted, solid-phase approach with the dendrimers assembled on polystyrene resin via an acid labile linker (see Fig. 26). In particular, a G3.0 polyamidourea bis-dendron with the peripheral amino groups conjugated to L-lysine residues demonstrated remarkable transfection abilities [234],... 

The linker moves the point of substrate attachment away from the surface of the bead. This has the effect of reducing steric hindrance, thereby making reaction easier. The choice of linker will depend on the nature of the reactions used in the proposed synthetic pathway (Figure 6.5). For example, an acid labile linker, such as HMP (hydroxymethylphenoxy resin), would not be suitable if the reaction pathway contained reactions that were conducted under strongly acidic conditions. Consideration must also be given to the ease of detaching the product from the linker at the end of the synthesis. The method employed must not damage the required product but must also lend itself to automation. 

The use of the Fmoc-protected 4-nitrophenyl carbamate building blocks and resins with acid-labile linkers allows synthesis of the final products with C-terminal carboxylic acid or amide groups (Fig. 6). Unfortunately, Fmoc solid-phase synthesis of oligourea peptidomimetics with C-terminal carboxylic acid also leads to formation of corresponding hydantoin byproducts (53-56) (Fig. 7). In this case hydantoin formation arises as a result of an acid-catalyzed intramolecular cyclizafion reaction. It has been reported that the ratio of desired oligourea pepfidomimetic acid product and hydantoin byproduct is approximately 2 1 (53). However, these two compounds are in principle separable by preparative HPLC. 

The selected example by Maclean et al. [40] reported a 240-member encoded pyrrolidine library, whose synthetic scheme is reported in Figure 9.12. Coupling of the resin bound acid labile linker FIMPB (4-hydroxymethyl-3-methoxyphenoxybutyric acid) with the first monomer set (four Fmoc amino acids, A) was followed by its coding (tags Ti-T3), and by coding of the second monomer set B (tags T4-T6) then the second monomer set (four aldehydes, B) was added and the reactive imines were immediately reacted with the third... 

This is the most widely used class of SP linkers. Historically, the SPS of peptides (see Section 2.1) was developed using building blocks protected with acid-labile groups, thus allowing a convenient simultaneous cleavage and deprotection in the final step of the synthesis. Four commercially available acid-labile linkers are depicted in Fig. 1.7 in resin- and compound-bound forms. The preferred cleavage conditions for each linker are also provided. 

Seven noncommercial acid-labile linkers have been reported recently in the literature and are shown in Figs. 1.8. (1.7-1.10) and 1.9 (1.11-1.13). The THP (tetrahy-dropyran) linker 1.7 (63), which is easily grafted onto Merrifield resin, has been used to support primary alcohols, secondary alcohols, hydroxylamines, and carboxylic acids. It is stable to strong nucleophiles and basic conditions and can be cleaved by... 

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