Monitoring the Progress and the Yield of Solid-Phase Organic Reactions Directly on Resin Supports

Computer vision as a new paradigm for monitoring of solution and solid phase peptide synthesis

We report a strategy for the camera-enabled non-contact colourimetric reaction monitoring and optimisation of amide bond formation, mediated by coupling reagents. For amide bond formation in solution phase, investigation of reactions mediated by HATU, PyAOP, and DIC/Oxyma evidenced correlations between colour parameters extracted from video data and conversion to amide product measured by off-line HPLC analysis of concentration. These correlations, supported by mutual information analysis, were further investigated using video recordings of solid phase peptide synthesis (SPPS), co-analysed by off-line HPLC to track remaining unreacted substrate in solution. An optimisation method of coupling time in SPPS was derived from ΔE (a measurement of colour contrast), giving comparable isolated peptide yield and purity at 65-95% reduced overall reaction time. The same colour data enabled data-rich monitoring of reaction rate attenuation, consisted with computationally-derived measures of amino acid steric bulk. These findings provide a foundation for exploring the use of camera technology and computer vision towards automated and online mechanistic profiling of SPPS.

In-situ X-ray diffraction snapshotting: determination of the kinetics of a photodimerization within a single crystal

In a single-crystal-to-single-crystal (SCSC) transformation, a preformed three-dimensional coordination polymer,[Ni₃(oba)₂(bpe)₂(SO₄)(H₂O)₄]·H₂O (H₂oba = 4,4′-oxydibenzoic acid; bpe = (E)-1,2-di(pyridin-4-yl)ethane) (1), was shown to undergo a [2+2] cycloaddition reaction upon exposure to UV irradiation. The kinetics of this reaction were followed by taking “snapshots” of the solid state transformation using in situ single crystal X-ray crystallography; a first order process was indicated. The reaction rate was influenced by many factors such as the separation of the sample from the UV light source, the heat produced by the UV irradiation, the light flux of the UV lamp used, the size of the single-crystal and the powder samples. The investigation of the kinetics was complemented by ¹H NMR studies. The results clearly demonstrate that in situ single-crystal X-ray diffraction is able to provide useful insights into the gradual formation of the photoproducts and the reaction processes. The work also offers a clear indication that it is possible to use the technique to study the kinetics of other photocycloaddition reactions and SCSC processes in general.

Synthesis and application of monodisperse oligo(oxyethylene)-grafted polystyrene resins for solid-phase organic synthesis

In a preliminary investigation by our group, we found that poly(styrene-oxyethylene) graft copolymers (PS-PEG), for example, TentaGel resins, are advantageous for gel-phase (13)C NMR spectroscopy. Because of the solution-like environment provided by the PS-PEG resins, good spectral quality of the attached moiety can be achieved, which is useful for nondestructive on-resin analysis. The general drawbacks of such resins are low loading capacities and the intense signal in the spectra resulting from the PEG linker (>50 units). Here, we describe the characterization of solvent-dependent swelling and reaction kinetics on a new type of resin for solid-phase organic synthesis (SPOS) that allows an accurate monitoring by gel-phase NMR without the above disadvantages. A series of polystyrene-oligo(oxyethylene) graft copolymers containing monodisperse PEG units (n = 2-12) was synthesized. A strong correlation between the linker (PEG) length and the line widths in the (13)C gel-phase spectra was observed, with a grafted PEG chain of 8 units giving similar results in terms of reactivity and gel-phase NMR monitoring to TentaGel resin. Multistep on-resin reaction sequences were performed to prove the applicability of the resins in solid-phase organic synthesis.

Synthesis and structural characterization of sialic acid-glutamic acid hybrid foldamers as conformational surrogates of alpha-2,8-linked polysialic acid

Surface expression of alpha-(2,8)-linked polymers of sialic acid in adult tissues has been correlated with metastasis of several human cancers. One approach to chemotherapeutic intervention against the spread of these cancers involves the development of immunogenic molecules that elicit an antibody response against alpha-(2,8)-linked polysialic acids. Naturally occurring polysialic acids are not viable candidates because they are present during embryonic development and are recognized as self by the immune system. These natural polymers also have poor pharmacokinetic properties because they are readily degraded by neuraminidase enzymes. We have been interested in developing structural surrogates of polysialic acids in an effort to overcome these limitations. Reported herein are microwave-assisted solid-phase peptide syntheses and structural characterization studies of a series of alpha/delta hybrid peptides derived from Fmoc-Neu2en and Fmoc-Glu(OtBu)-OH. Conformational experiments including circular dichroism, NH/ND exchange, and ROESY in aqueous solution were performed to study the secondary structures of these hybrid foldamers. ROESY data were analyzed with the assistance of XPLOR-NIH that was modified to include parameter and topology files to accommodate unnatural amino acids and the delta amide linkages. The results indicate that stable secondary structure is dependent upon both the amino acid sequence and the configuration of Glu. The most stable foldamer was composed of a total of 6 residues beginning with L-Glu at the carboxy terminus and alternating Neu2en and L-Glu residues. In water, this foldamer adopts a right-handed helical conformation with 3.7 residues per turn, 7.4 A pitch, 5.8 A diameter, and a length of 18.5 A, which is stabilized by both classical C=O...H-N backbone interactions and by pyranose ring O and L-Glu HN H-bonding. These structural features orient the L-Glu carboxylates along the helical backbone with a periodicity that matches the carboxylate positions along the reported G2(+) left-handed helix of alpha-(2,8)-polysialic acid. However, the charge density of the foldamer is one-half that of the natural polymer. These findings provide a fundamental understanding of the factors that influence stable secondary structure in hybrid Neu2en/Glu systems, and the tools we have developed establish a viable platform for the rational design of alpha-(2,8)-polysialic acid surrogates.

Kinetics of resin-supported Mitsunobu esterification and etherification reactions

Solid-phase Mitsunobu reaction is very useful in organic and parallel synthesis. In this work, we optimize the solid-phase Mitsunobu esterification and etherification reactions and investigated their kinetics by single-bead FTIR microspectroscopy method. Thirteen solid-phase Mitsunobu esterification reactions proceeded at rates between 2.5 x 10(-3) and 19 x 10(-3) s(-1), while five etherification reactions at generally slower rates between 3.3 x 10(-3) and 8.9 x 10(-3) s(-1). We discovered that reaction rates, as in solution phase Mitsunobu reactions, linearly correlated to pK(a) values of acids and phenols used in the reaction. By studying side reactions and intermediates, we found that the solid-phase reaction mechanism also bears remarkable similarities to that of solution phase Mitsunobu reaction.

Studies towards the synthesis of methionine aminopeptidase inhibitors: diversification utilizing a ROMP-derived coupling reagent

Efforts to synthesize potential methionine aminopeptidase inhibitors is described. Preliminary SAR and docking studies served as a guide to design the compound libraries. "Chromatography-free" synthesis of various heterocyclic amides was realized by using a high-load, soluble coupling reagent derived via ring-opening metathesis polymerization (ROMP). Subsequent microwave-assisted Suzuki reactions with ortho-substituted arylboronic acids, followed by chromatographic purification afforded a 55-member library in high yields and purities. While the biological testing was not satisfactory, concurrent X-ray crystallography studies revealed key structural features essential for inhibition of methionine aminopeptidase, which directed fruitful results reported in the accompanying manuscript. In addition, in silico Lipinksi profiles and ADME properties of the library are also reported.

Comparative investigation of the cleavage step in the synthesis of model peptide resins: implications for Nalpha-9-fluorenylmethyloxycarbonyl-solid phase peptide synthesis

Based on our studies of the stability of model peptide-resin linkage in acid media, we previously proposed a rule for resin selection and a final cleavage protocol applicable to the Nalpha-tert-butyloxycarbonyl (Boc)-peptide synthesis strategy. We found that incorrect choices resulted in decreases in the final synthesis yield, which is highly dependent on the peptide sequence, of as high as 30%. The present paper continues along this line of research but examines the Nalpha-9-fluorenylmethyloxycarbonyl (Fmoc)-synthesis strategy. The vasoactive peptide angiotensin II (AII, DRVYIHPF) and its [Gly8]-AII analogue were selected as model peptide resins. Variations in parameters such as the type of spacer group (linker) between the peptide backbone and the resin, as well as in the final acid cleavage protocol, were evaluated. The same methodology employed for the Boc strategy was used in order to establish rules for selection of the most appropriate linker-resin conjugate or of the peptide cleavage method, depending on the sequence to be assembled. The results obtained after treatment with four cleavage solutions and with four types of linker groups indicate that, irrespective of the circumstance, it is not possible to achieve complete removal of the peptide chains from the resin. Moreover, the Phe-attaching peptide at the C-terminal yielded far less cleavage (50-60%) than that observed with the Gly-bearing sequences at the same position (70-90%). Lastly, the fastest cleavage occurred with reagent K acid treatment and when the peptide was attached to the Wang resin.

Application of gel-phase19F NMR spectroscopy for optimization of solid-phase synthesis of a hydrophobic peptide from the signal sequence of the mucin MUC1

This paper describes the manual Fmoc/t-Bu solid-phase synthesis of a difficult nine-residue hydrophobic peptide LLLLTVLTV from one of the signal sequences that flank the tandem repeat of the mucin MUC1. Gel-phase 19F NMR spectroscopy was used as a straightforward method for optimization of the solid-phase synthesis. Different approaches were applied for comparative studies. The strategy based on modified solid-phase conditions using DIC/HOAt for coupling, DBU for Fmoc deprotection, and the incorporation of the pseudo proline dipeptide Fmoc-Leu-Thr(psiMe, Me pro)-OH as a backbone-protecting group was found to be superior according to gel-phase 19F NMR spectroscopy. Implementation of the optimized Fmoc protocol enabled an effective synthesis of signal peptide LLLLTVLTV.

Interpretation of the dissolution of insoluble peptide sequences based on the acid-base properties of the solvent

The dissolution process of model insoluble peptide sequences was investigated in view of the electron acceptor (AN) and electron donor (DN) solvent properties. The Alzheimer's disease-inducing (1-42) Abeta-amyloid peptide and its (1-21) fragment, the (66-97) transmembrane bradykinin B2 receptor sequence, and the strongly aggregated VVLGAAIV were selected as models of insoluble peptides. Solvents presenting similar AN and DN values failed, despite their polarities, to dissociate peptide chains (free in solution or bound to a polymer). The maximum solubility of these aggregated sequences was attained in solvents presenting the highest possible (AN-DN) values (in positive or negative mode). The AN-DN values ranged from approximately -20 to +80 and, notably, the lowest dissociation power was ascribed to solvents presenting values of approximately +40. The strong hydrogen bond donor water is located in this region, indicating that, for dissociation of specific insoluble segments, the solvent should appropriately combine its acid/base strength with the potential for van der Waals interactions. We also observed a sequence-dependent pH effect on peptide solubility confirmed through circular dichroism spectroscopy. This approach also revealed a complex but, in many cases, consistent influence of peptide conformation on its solubility degree, even when structure-inducing solvents were added. In conclusion, the random method of selecting solvents to dissolve insoluble and intractable peptide sequences, still in use by some, could be partially supplanted by the strategy described herein, which may be also applicable to other solute dissociation processes.

Heteroleptic Cu(II) Dipyrromethene Complexes Linked via Hydrogen Bonds, Coordinative Bonds, and Covalent Bonds: Probing the Coordination Environment by Electron Paramagnetic Resonance Spectroscopy

meso-Phenyldipyrromethene acetylacetonato copper(II) complexes [Cu(dpm-C6H4R)(acac)] (dpm-C6H4R = phenyl-substituted dipyrromethene, acac = acetylacetonato) with different substituents R at the phenyl moiety were synthesized. These substituents determine the mode of assembly into polymeric chains, namely, via hydrogen bonds, coordinative bonds, or covalent bonds (by immobilization on a polymer). Although the primary coordination sphere around the copper center is essentially identical for all complexes reported in this study (square-planar geometry with N2O2 coordination), subtle differences due to the different microenvironments have been observed in their structures, properties, and reactivity as probed by IR spectroscopy, electron paramagnetic resonance spectroscopy, magnetic measurements, thermal analyses, density functional theory calculations, and reaction with pyridine.

Solid-Phase Synthesis of Photochromic Spiropyrans

[reaction: see text] A convenient solid-phase synthesis of spiropyrans is described. A succinate linker was employed, which allows base-catalyzed cleavage of the desired photochromophore derivatized with a succinimide. Excellent yields and purities were obtained for the compounds that comprise a library of 23 spiropyrans. Opening of the succinimide ring in spiropyran could be realized under mild conditions.

Determination of Site−Site Distance and Site Concentration within Polymer Beads: A Combined Swelling-Electron Paramagnetic Resonance Study

This work proposes a combined swelling-electron paramagnetic resonance (EPR) approach aiming at determining some unusual polymer solvation parameters relevant for chemical processes occurring inside beads. Batches of benzhydrylamine-resin (BHAR), a copolymer of styrene-1% divinylbenzene containing phenylmethylamine groups were, labeled with the paramagnetic amino acid 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amine-4-carboxylic acid (TOAC), and their swelling properties and EPR spectra were examined in DCM and DMF. By taking into account the BHARs labeling degrees, the corresponding swelling values, and some polymer structural characteristics, it was possible to calculate polymer swelling parameters, among them, the volume and the number of sites per bead, site-site distances and site concentration. The latter values ranged from 17 to 170 A and from 0.4 to 550 mM, respectively. EPR spectroscopy was applied to validate the multistep calculation strategy of these swelling parameters. Spin-spin interaction was detected in the labeled resins at site-site distances less than approximately 60 A or probe concentrations higher than approximately 1 x 10(-2) M, in close agreement with the values obtained for the spin probe free in solution. Complementarily, the yield of coupling reactions in different resins indicated that the greater the inter-site distance or the lower the site concentration, the faster the reaction. The results suggested that the model and the experimental measurements developed for the determination of solvation parameters represent a relevant step forward for the deeper understanding and improvement of polymer-related processes.

Colorimetric Tools for Solid-Phase Organic Synthesis

One of the unresolved problems of solid-phase organic synthesis (SPOS) is the availability of general and rapid methods to monitor the transformation of functional groups present in molecules supported on insoluble supports. Color tests, far from providing the ultimate solution, may help in detection (and sometimes in quantification) of different functional groups. In this short review, we have collected most of the methods available and applied in SPOS with an Experimental Section that describes the procedure we have successfully applied to bead analyses in our laboratories.

Gel-phase19F NMR spectral quality for resins commonly used in solid-phase organic synthesis; a study of peptide solid-phase glycosylations

The spectroscopic properties for seven different commercial resins used in solid-phase synthesis were investigated with (19)F NMR spectroscopy. A fluorine-labeled dipeptide was synthesized on each resin, and the resolution of the (19)F resonances in CDCl(3), DMSO-d(6), benzene-d(6) and CD(3)OD were measured with a conventional NMR spectrometer, i.e. without using magic angle spinning. In general, resins containing poly(ethylene glycol) chains (ArgoGel, TentaGel and PEGA) were found to be favorable for the (19)F NMR spectral quality. Three serine containing tri-, penta-, and heptapeptides were then prepared on an ArgoGel resin functionalized with a fluorine-labeled linker. The resin bound peptides were glycosylated utilizing a thiogalactoside glycosyl donor carrying fluorine-labeled protective groups. Monitoring of the glycosylations with gel-phase (19)F NMR spectroscopy allowed each glycopeptide to be formed in similar 80% yield, using a minimal amount of glycosyl donor (3 x 2 equivalents). In addition, it was found that the glycosylation yields were independent of peptide length.

Physicochemical and chromatographic evaluation of benzhydrylamine-resin as an anion exchanger solid support

Benzhydrylamine-resin (BHAR), a copolymer of styrene-divinylbenzene containing phenylmethylamine groups, used as solid support for peptide synthesis, was examined regarding physicochemical and anion exchanger chromatographic properties. The greater the ionic strength of the medium the poorer the solvation of beads. This effect is less pronounced the higher the amino group content of BHAR. The BHAR chromatographic behavior was compared with commercial cationic resins in columns of constant cation binding capacity. Three negatively charged heparan sulfate disaccharides were successfully purified in a 2.4 mmol/g BHAR that showed as good or better anion exchange performance than classical tertiary or quaternary amino group-containing resins. The BHAR chromatographic resin exclusion limit was estimated to be 30 kDa based on purification experiments of heparins of different molecular weight.

Understanding the effects of the polymer support on reaction rates and kinetics: knowledge toward efficient synthetic design

Solid-phase organic synthesis (SPOS) has an ever-expanding role in the field of organic synthesis. Partially out of difficulty, and partially from the rapid speed of progress, few basic studies on the role of the physical structure of the resin have been undertaken, and the dissemination of the existing knowledge has been slow. Major advances have been made in the understanding of the many factors that govern a SPOS reaction's performance as a function of the choice of solid support.

Single-bead analysis in combinatorial chemistry

Notable limitations have previously prevented the wide application of split synthesis. However, recent developments in highly condensed and miniaturized biological screening and single-bead analysis methods have argued for a revival of split combinatorial synthesis. Although there are still many challenges, we are now in a much better position to accomplish high-throughput analysis and screening of one-bead-one-compound libraries.

Solid-phase synthesis of novel isoxazolocyclobutanones and isoxazolinocyclobutenones

[reaction: see text] The preparation of novel isoxazolocyclobutanone and isoxazolinocyclobutenone derivatives via a traceless solid-phase sulfone linker strategy is described. Key steps in the solid-phase protocol reported here include (i) sulfinate right arrow sulfone alkylation, (ii) four-member ring formation by sulfone dianion alkylation, (iii) heterocycle formation by nitrile oxide 1,3-dipolar cycloaddition, and (iv) traceless product release by cyclobutanol right arrow cyclobutanone oxidation with concomitant linker cleavage by sulfinate elimination.

Static secondary ion mass spectrometry to monitor solid-phase peptide synthesis

Insights into the direct monitoring of supported peptide synthesis were realized through the design of time of flight static secondary ion mass spectrometry (TOF-S-SIMS) experiments. The mass spectrometric method was carried out at the resin bead level and was found reproducible (intra- and inter-day assays), sensitive (femtomol level) and non-destructive (only 0.01% of the peptides were destroyed by the primary ion beam bombardment). The nature of the peptide-resin linkage governed the recovery of ions characterizing the whole peptide sequence. A S-SIMS cleavable bond was thus required solely in that position to achieve the release of the growing structures from the insoluble support into the gas phase without any fragmentation. Results are presented with standard solid-phase resins allowing linkage through an amide or an ester bond. The latter was orthogonally broken upon the bombardment and thus constituted a convenient S-SIMS cleavable bond.