A Biomimetic Approach to Asymmetric Acyl Transfer Catalysis

Kinetic Resolution of β-Branched Aldehydes through Peptide-Catalyzed Conjugate Addition Reactions

The catalytic kinetic resolution of racemic β-branched aldehydes offers a straightforward stereoselective entry to aldehydes and addition products. Yet, control over stereoselectivity is difficult due to the conformational flexibility of β-branched aldehydes. Here, we show that the peptide catalyst H-dPro-αMePro-Glu-NH2 resolves β-branched aldehydes through reaction with nitroolefins and provides γ-nitroaldehydes with three consecutive stereogenic centers in high yields and stereoselectivities. Kinetic, NMR spectroscopic, and computational studies provided insights into the selectivity-determining step and origins of the kinetic resolution.

Scaffold-Oriented Asymmetric Catalysis: Conformational Modulation of Transition State Multivalency during a Catalyst-Controlled Assembly of a Pharmaceutically Relevant Atropisomer

A new class of superbasic, bifunctional peptidyl guanidine catalysts is presented, which enables the organocatalytic, atroposelective synthesis of axially chiral quinazolinediones. Computational modeling unveiled the conformational modulation of the catalyst by a novel phenyl urea N-cap, that preorganizes the structure into the active, folded state. A previously unanticipated noncovalent interaction involving a difluoroacetamide acting as a hybrid mono- or bidentate hydrogen bond donor emerged as a decisive control element inducing atroposelectivity. These discoveries spurred from a scaffold-oriented project inspired from a fascinating investigational BTK inhibitor featuring two stable chiral axes and relies on a mechanistic framework that was foreign to the extant lexicon of asymmetric catalysis.

Formation of extraterrestrial peptides and their derivatives

The formation of protein precursors, due to the condensation of atomic carbon under the low-temperature conditions of the molecular phases of the interstellar medium, opens alternative pathways for the origin of life. We perform peptide synthesis under conditions prevailing in space and provide a comprehensive analytic characterization of its products. The application of 13C allowed us to confirm the suggested pathway of peptide formation that proceeds due to the polymerization of aminoketene molecules that are formed in the C + CO + NH3 reaction. Here, we address the question of how the efficiency of peptide production is modified by the presence of water molecules. We demonstrate that although water slightly reduces the efficiency of polymerization of aminoketene, it does not prevent the formation of peptides.

Quantifying Intermolecular Interactions in Asymmetric Peptide Organocatalysis as a Key toward Understanding Selectivity

The kinetic resolution of trans-cyclohexane-1,2-diol with a lipophilic oligopeptide catalyst shows extraordinary selectivities. To improve our understanding of the factors governing selectivity, we quantified the Gibbs free energies of interactions of the peptide with both enantiomers of trans-cyclohexane-1,2-diol using nuclear magnetic resonance (NMR) spectroscopy. For this, we use advanced methods such as transverse relaxation (R2), diffusion measurements, saturation transfer difference (STD), and chemical shift (δ) analysis of peptide-diol mixtures upon varying their composition (NMR titrations). The methods employed give comparable and consistent results. The molecular recognition by the catalyst is approximately 3 kJ mol-1 in favor of the preferentially acetylated (R,R)-enantiomer in the temperature range studied. Interestingly, the difference of 3 kJ mol-1 is also confirmed by results from reaction monitoring of the acylation step under catalytic conditions, indicating that this finding is true regardless of whether the investigation is performed on the acetylated species or on the free catalyst. To arrive at these conclusions, the self-association of both the catalyst and the substrate in toluene was found to play an important role and thus needs to be taken into account in reaction screening.

Ratcheting synthesis

Synthetic chemistry has traditionally relied on reactions between reactants of high chemical potential and transformations that proceed energetically downhill to either a global or local minimum (thermodynamic or kinetic control). Catalysts can be used to manipulate kinetic control, lowering activation energies to influence reaction outcomes. However, such chemistry is still constrained by the shape of one-dimensional reaction coordinates. Coupling synthesis to an orthogonal energy input can allow ratcheting of chemical reaction outcomes, reminiscent of the ways that molecular machines ratchet random thermal motion to bias conformational dynamics. This fundamentally distinct approach to synthesis allows multi-dimensional potential energy surfaces to be navigated, enabling reaction outcomes that cannot be achieved under conventional kinetic or thermodynamic control. In this Review, we discuss how ratcheted synthesis is ubiquitous throughout biology and consider how chemists might harness ratchet mechanisms to accelerate catalysis, drive chemical reactions uphill and programme complex reaction sequences.

A Combined DFT, Energy Decomposition, and Data Analysis Approach to Investigate the Relationship Between Noncovalent Interactions and Selectivity in a Flexible DABCOnium/Chiral Anion Catalyst System

Developing strategies to study reactivity and selectivity in flexible catalyst systems has become an important topic of research. Herein, we report a combined experimental and computational study aimed at understanding the mechanistic role of an achiral DABCOnium cofactor in a regio- and enantiodivergent bromocyclization reaction. It was found that electron-deficient aryl substituents enable rigidified transition states via an anion-π interaction with the catalyst, which drives the selectivity of the reaction. In contrast, electron-rich aryl groups on the DABCOnium result in significantly more flexible transition states, where interactions between the catalyst and substrate are more important. An analysis of not only the lowest-energy transition state structures but also an ensemble of low-energy transition state conformers via energy decomposition analysis and machine learning was crucial to revealing the dominant noncovalent interactions responsible for observed changes in selectivity in this flexible system.

Detection and Verification of a Key Intermediate in an Enantioselective Peptide Catalyzed Acylation Reaction

Until now, the intermediate responsible for the acyl transfer of a highly enantioselective tetrapeptide organocatalyst for the kinetic resolution of trans-cycloalkane-1,2-diols has never been directly observed. It was proposed computationally that a π-methylhistidine moiety is acylated as an intermediate step in the catalytic cycle. In this study we set out to investigate whether we can detect and characterize this key intermediate using NMR-spectroscopy and mass spectrometry. Different mass spectrometric experiments using a nano-ElectroSpray Ionization (ESI) source and tandem MS-techniques allowed the identification of tetrapeptide acylium ions using different acylation reagents. The complexes of trans-cyclohexane-1,2-diols with the tetrapeptide were also detected. Additionally, we were able to detect acylated tetrapeptides in solution using NMR-spectroscopy and monitor the acetylation reaction of a trans-cyclohexane-1,2-diol. These findings are important steps towards the understanding of this highly enantioselective organocatalyst.

Controlling the Site Selectivity in Acylations of Amphiphilic Diols: Directing the Reaction toward the Apolar Domain in a Model Diol and the Midecamycin A1 Macrolide Antibiotic

Seeking to improve the site selectivity of acylation of amphiphilic diols, which is induced by imidazole-based nucleophilic catalysts and directs the reaction toward apolar sites, as we recently reported, we examined a new improved catalytic design and an alteration of the acylating agent. The new catalysts performed slightly better selectivity-wise in the model reaction, compared to the previous set, but notably could be prepared in a much more synthetically economic way. The change of the acylating agent from anhydride to acyl chloride, particularly in combination with the new catalysts, accelerated the reaction and increased the selectivity in favor of the apolar site. The new selectivity-inducing techniques were applied to midecamycin, a natural amphiphilic antibiotic possessing a secondary alcohol moiety in each of its two domains, polar as well as apolar. In the case of the anhydride, a basic dimethylamino group, decorating this substrate, overrides the catalyst’s selectivity preference and forces selective acylation of the alcohol in the polar domain with a more than 91:1 ratio of the monoacylated products. To counteract the internal base influence, an acid additive was used or the acylating agent was changed to acyl chloride. The latter adjustment leads, in combination with our best catalyst, to the reversal of the ratio between the products to 1:11.

Isolating Conformers to Assess Dynamics of Peptidic Catalysts Using Computationally Designed Macrocyclic Peptides

Studying the relationship between catalyst conformational dynamics and selectivity in an asymmetric reaction is a challenge. In this study, cyclic peptides were computationally designed to stabilize different ground state conformations of a highly effective, flexible tetrapeptide catalyst for the atroposelective bromination of N-aryl quinazolinones. Through a combination of computational and experimental techniques, we have determined that dynamic movement of the lead catalyst plays a crucial role in achieving high enantioselectivity in the reaction of study. This approach may also serve as a valuable method for investigating the mechanism of other peptide-catalyzed transformations.

Asymmetric Catalysis Mediated by Synthetic Peptides, Version 2.0: Expansion of Scope and Mechanisms

Low molecular weight synthetic peptides have been demonstrated to be effective catalysts for an increasingly wide array of asymmetric transformations. In many cases, these peptide-based catalysts have enabled novel multifunctional substrate activation modes and unprecedented selectivity manifolds. These features, along with their ease of preparation, modular and tunable structures, and often biomimetic attributes make peptides well-suited as chiral catalysts and of broad interest. Many examples of peptide-catalyzed asymmetric reactions have appeared in the literature since the last survey of this broad field in Chemical Reviews (Chem. Rev. 2007, 107, 5759-5812). The overarching goal of this new Review is to provide a comprehensive account of the numerous advances in the field. As a corollary to this goal, we survey the many different types of catalytic reactions, ranging from acylation to C-C bond formation, in which peptides have been successfully employed. In so doing, we devote significant discussion to the structural and mechanistic aspects of these reactions that are perhaps specific to peptide-based catalysts and their interactions with substrates and/or reagents.

N-Primary-amine tetrapeptide-catalyzed highly asymmetric Michael addition of aliphatic aldehydes to maleimides

The highly asymmetric Michael addition reaction between maleimides and aliphatic aldehydes catalyzed by low-loading β-turn tetrapeptides with excellent yields and enantioselectivities at room temperature was reported. α-Branched and α-unbranched aldehydes both are suitable nucleophiles. N-Aryl, alkyl and hydrogen maleimides all are well tolerated and led to high yields and enantioselectivities. The transformation can be enlarged to the gram scale without decrease in the yield and enantioselectivity. Furthermore, the succinimides were converted into γ-lactams and γ-lactones, showing good practicality of this work. Some reaction intermediates in the proposed reaction mechanism can be captured with the HR-MS method.

Base- and Catalyst-Induced Orthogonal Site Selectivities in Acylation of Amphiphilic Diols

Seeking to selectively functionalize natural and synthetic amphiphiles, we explored acylation of model amphiphilic diols. The use of a nucleophilic catalyst enabled a remarkable shift of the site selectivity from the polar site, preferred in background noncatalyzed or base-promoted reactions, to the apolar site. This tendency was significantly enhanced for organocatalysts comprising an imidazole active site surrounded by long/branched tails. An explanation of these orthogonal modes of selectivity is supported by competitive experiments with monoalcohol substrates.

Catalytic Sulfamoylation of Alcohols with Activated Aryl Sulfamates

We report a new catalytic method for alcohol sulfamoylation that deploys electron-deficient aryl sulfamates as activated group transfer reagents. The reaction utilizes the simple organic base N-methylimidazole, proceeds under mild conditions, and provides intrinsic selectivity for 1° over 2° alcohols (up to >40:1 for certain nucleosides). The requisite aryl sulfamate donors are stable crystalline solids that can be readily prepared on a large scale. Mechanistic considerations support the intermediacy of HNSO₂ "aza-sulfene" in the transfer reaction.

Rational Design of an Organocatalyst for Peptide Bond Formation

Amide bonds are ubiquitous in peptides, proteins, pharmaceuticals, and polymers. The formation of amide bonds is a straightforward process: amide bonds can be synthesized with relative ease because of the availability of efficient coupling agents. However, there is a substantive need for methods that do not require excess reagents. A catalyst that condenses amino acids could have an important impact by reducing the significant waste generated during peptide synthesis. We describe the rational design of a biomimetic catalyst that can efficiently couple amino acids featuring standard protecting groups. The catalyst design combines lessons learned from enzymes, peptide biosynthesis, and organocatalysts. Under optimized conditions, 5 mol % catalyst efficiently couples Fmoc amino acids without notable racemization. Importantly, we demonstrate that the catalyst is functional for the synthesis of oligopeptides on solid phase. This result is significant because it illustrates the potential of the catalyst to function on a substrate with a multitude of amide bonds, which may be expected to inhibit a hydrogen-bonding catalyst.

Asymmetric Formal Synthesis of (+)-Catharanthine via Desymmetrization of Isoquinuclidine

Although (+)-catharanthine is an attractive alkaloid for both clinical research and organic synthetic chemistry, only a limited number of approaches for its catalytic asymmetric synthesis exist. Herein, we describe a novel strategy for synthesizing a chiral intermediate of (+)-catharanthine via phosphoric acid-catalyzed asymmetric desymmetrization of a meso-isoquinuclidine possessing a 1,3-diol unit that was synthesized by a formal amide insertion reaction.

Structure and Reactivity of Highly Twisted N-Acylimidazoles

A modular and efficient synthesis of highly twisted N-acylimidazoles is reported. These twist amides were characterized via X-ray crystallography, NMR spectroscopy, IR spectroscopy, and DFT calculations. Modification of the substituent proximal to the amide revealed a maximum torsional angle of 88.6° in the solid state, which may be the most twisted amide reported for a nonbicyclic system to date. Reactivity and stability studies indicate that these twisted N-acylimidazoles may be valuable, namely as acyl transfer reagents.

Outer-Sphere Control for Divergent Multicatalysis with Common Catalytic Moieties

We herein report two examples of one-pot, simultaneous reactions, mediated by multiple, orthogonal catalysts with the same catalytic motif. First, BINOL-derived chiral phosphoric acids (CPA) and phosphothreonine (pThr)-embedded peptides were found to be matched for two different steps in double reductions of bisquinolines. Next, two π-methylhistidine (Pmh)-containing peptides catalyzed enantio- and chemoselective acylations and phosphorylations of multiple substrates in one pot. The selectivity exhibited by common reactive moieties is adjusted solely by the appended chiral scaffold through outer-sphere interactions.

Computational insight into the mechanism and origins of high selectivities in the acylation of polyamines with 5-benzoyl-5-phenyl-1,5-dihydro-4H-pyrazol-4-one

Amide bonds have gained much attention from numerous scientists and acyl transfer is a good way to form amide bonds. The acylation mechanism of polyamines and their high selectivity in dichloromethane were investigated by the use of the density functional theory (DFT), M06-2X/6-311+G (d, p)//M06-2X/6-31G (d, p) method combined with the solvation SMD model. The calculated results suggest that the reaction process involved two steps: an acylation step and a proton-transfer step, with the former being the rate-limiting step. Meanwhile, with the substituent group effects of amines and 5-acyl-5-phenyl-1,5-dihydro-4H-pyrazol-4-one (BCPP) on the acylation step, different substituent groups of amines have little influence on the kinetic properties of the acylation step, and the para-substituent groups of the phenyl group in BCPP lead to a linear relationship according to the electronegativity of the substituents. Furthermore, regarding the rate-selectivity of amines, the rate-selectivity of primary amines is higher than that of secondary amines, and polyamines very easily take part in acylation owing to the intramolecular hydrogen bond interaction. Moreover, it is harder for the amine group which has an α-position substituent group in polyamines to take part in an acylation reaction compared to the one without an α-position substituent group. The site-selectivity of the acylation process in polyamines is determined by steric hindrance. What's more, the auxiliary analysis of the distortion/interaction analysis and the frontier molecular orbital (FMO) analysis is used to investigate the origins of the rate- and site-selectivities.

Molecular Dynamics Simulations of a Conformationally Mobile Peptide-Based Catalyst for Atroposelective Bromination

It is widely accepted that structural rigidity is required to achieve high levels of asymmetric induction in catalytic, enantioselective reactions. This fundamental design principle often does not apply to highly selective catalytic peptides that often exhibit conformational heterogeneity. As a result, these complex systems are particularly challenging to study both experimentally and computationally. Herein, we utilize molecular dynamics simulations to investigate the role of conformational mobility on the reactivity and selectivity exhibited by a catalytic, β-turn-biased peptide in an atroposelective bromination reaction. By means of cluster analysis, multiple distinct conformers of the peptide and a catalyst-substrate complex were identified in the simulations, all of which were corroborated by experimental NMR measurements. The simulations also revealed that a shift in the conformational equilibrium of the peptidic catalyst occurs upon addition of substrate, and the degree of change varies among different substrates. On the basis of these data, we propose a correlation between the composition of the peptide conformational ensemble and its catalytic properties. Moreover, these findings highlight the importance of conformational dynamics in catalytic, asymmetric reactions mediated by oligopeptides, unveiled through high-level, state-of-the-art computational modeling.

Catalytic enantioselective acyl transfer: the case for 4-PPY with a C-3 carboxamide peptide auxiliary based on synthesis and modelling studies

A series of 4-pyrrolidinopyridine (4-PPY) C-3 carboxamides containing peptide-based side chains have been synthesised and evaluated in the kinetic resolution of a small library of chiral benzylic secondary alcohols. A key design element was the incorporation of a tryptophan residue in the peptide side chain for promoting π-stacking between peptide side chain and the pyridinium ring of the N-acyl intermediate, in which modelling was used as a structure-based guiding tool. Together, a catalyst containing a LeuTrp-N-Boc side chain (catalyst 8) was identified that achieved s-values up to and in slight excess of 10. A transition-state model based on the modelling is proposed to explain the origin of enantioselectivity. This study establishes the usefulness of modelling as a structure-based guiding tool for enantioselectivity optimization as well as the potential for developing scalable peptide-based DMAP-type catalysts for large-scale resolution work.

Applications of Nonenzymatic Catalysts to the Alteration of Natural Products

The application of small molecules as catalysts for the diversification of natural product scaffolds is reviewed. Specifically, principles that relate to the selectivity challenges intrinsic to complex molecular scaffolds are summarized. The synthesis of analogues of natural products by this approach is then described as a quintessential "late-stage functionalization" exercise wherein natural products serve as the lead scaffolds. Given the historical application of enzymatic catalysts to the site-selective alteration of complex molecules, the focus of this Review is on the recent studies of nonenzymatic catalysts. Reactions involving hydroxyl group derivatization with a variety of electrophilic reagents are discussed. C-H bond functionalizations that lead to oxidations, aminations, and halogenations are also presented. Several examples of site-selective olefin functionalizations and C-C bond formations are also included. Numerous classes of natural products have been subjected to these studies of site-selective alteration including polyketides, glycopeptides, terpenoids, macrolides, alkaloids, carbohydrates, and others. What emerges is a platform for chemical remodeling of naturally occurring scaffolds that targets virtually all known chemical functionalities and microenvironments. However, challenges for the design of very broad classes of catalysts, with even broader selectivity demands (e.g., stereoselectivity, functional group selectivity, and site-selectivity) persist. Yet, a significant spectrum of powerful, catalytic alterations of complex natural products now exists such that expansion of scope seems inevitable. Several instances of biological activity assays of remodeled natural product derivatives are also presented. These reports may foreshadow further interdisciplinary impacts for catalytic remodeling of natural products, including contributions to SAR development, mode of action studies, and eventually medicinal chemistry.

Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences

X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H-1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions.

Structural studies of β-turn-containing peptide catalysts for atroposelective quinazolinone bromination

We describe herein a crystallographic and NMR study of the secondary structural attributes of a β-turn-containing tetra-peptide, Boc-Dmaa-D-Pro-Acpc-Leu-NMe2, which was recently reported as a highly effective catalyst in the atroposelective bromination of 3-arylquinazolin-4(3H)-ones. Inquiries pertaining to the functional consequences of residue substitutions led to the discovery of a more selective catalyst, Boc-Dmaa-D-Pro-Acpc-Leu-OMe, the structure of which was also explored. This new lead catalyst was found to exhibit a type I'β-turn secondary structure both in the solid state and in solution, a structure that was shown to be an accessible conformation of the previously reported catalyst, as well.

Cross-strand histidine-aromatic interactions enhance acyl-transfer rates in beta-hairpin peptide catalysts

A reactive tagging methodology was used to select the species most reactive to an acylation reagent from a solid phase library of beta hairpin peptides. Hits bearing an electron-rich aromatic residue across strand from a reactive histidine were found to competitively become N-acylated. In addition to displaying rapid N-acylation rates the hit peptide was additionally deacylated in the presence of a nucleophile, thus closing a putative catalytic cycle. Variants of the hit peptide were studied to elucidate both the magnitude (up to 18,000-fold over background, kcat/kuncat = 94,000,000, or 45-fold over Boc-histidine methyl ester) and mechanism of acyl transfer catalysis. A combination of CH-π, cation-π and HisH(+)-O interactions in the cationic imidazole transition state is implicated in the rate acceleration, in addition to the fidelity of the beta hairpin fold. Moreover, NMR structural data on key intermediates or models thereof suggest that a key feature of this catalyst is the ability to access several different stabilizing conformations along the catalysis reaction coordinate.

Synthetic turn mimetics and hairpin nucleators: Quo Vadimus?

Structural mimicry of peptides has witnessed perceptible progress in the last three decades. Reverse turn and β-hairpin units are the smallest secondary structural motifs that are some of the most scrutinized functional cores of peptides and proteins. The practice of mimicking, without altering the function of the bioactive core, ranges from conformational locking of the basic skeleton to total replacement of structural architecture using synthetic analogues. Development of heterogeneous backbones--using unnatural residues in place of natural ones--has broadened further opportunities for efficient structural rigidification. This feature article endeavours to trail the path of progress achieved hitherto and envisage the possibilities that lie ahead in the development of synthetic turn mimetics and hairpin nucleators.

En route to multicatalysis: kinetic resolution of trans-cycloalkane-1,2-diols via oxidative esterification

We demonstrate the application of a multicatalyst to the oxidation of a broad variety of aldehydes and subsequent enantioselective esterification of the incipient acids with (±)-trans-cycloalkane-1,2-diols.

Asymmetric catalysis at a distance: catalytic, site-selective phosphorylation of teicoplanin

We report three distinct, peptide-based catalysts that enable site-selective phosphorylation of three distinct hydroxyl groups within the complex glycopeptide antibiotic teicoplanin A2-2. Two of the catalysts are based on a design that capitalizes on a catalyst-substrate interaction that mimics the biological mechanism of action for teicoplanin. These catalysts are based on a DXaa-DXaa peptide motif that is known to target the teicoplanin structure in a specific manner. The third was identified through evaluation of a set of catalysts that had been developed for historically distinct projects. Each catalyst contains additional functionality designed to dispose a catalytic moiety (a nucleophilic alkylimidazole) at a different region of the glycopeptide structure. A combination of mass spectrometry and 2D-NMR spectroscopy allowed structural assignment of the distinct phosphorylated teicoplanin derivatives. Mechanistic studies are also reported that support the hypotheses that led to the discovery of the catalysts. In this manner, small molecule catalysts have been achieved that allow rational, catalytic control over reactions at sites that are separated by 11.6, 16.5, and nearly 17.7 Å, based on the X-ray crystal structure of teicoplanin A2-2. Finally, we report the biological activity of the new phosphorylated teicoplanin analogs and compare the results to the natural product itself.