Discovery of Sequence-Selective Peptide Binding by Synthetic Receptors Using Encoded Combinatorial Libraries

Vancomycin mimicry: towards new supramolecular antibiotics

Vancomycin is the best-known of the glycopeptide group antibiotics (GPAs), a family of agents which operate by binding the C-terminal deptide D-Ala-D-Ala. This anionic epitope is an interesting target because it plays a central role in bacterial cell wall synthesis, and is not readily modified by evolution. Accordingly, vancomycin has been in use for >60 years but has only provoked limited resistance. Agents which mimic vancomycin but are easier to synthesise and modify could serve as valuable weapons against pathogenic bacteria, broadening the scope of the GPAs and addressing the resistance that does exist. This article gives an overview of vancomycin's structure and action, surveys past work on vancomycin mimicry, and makes the case for renewed effort in the future.

Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers

It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.

Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages

The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)-mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase-substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling.

Conformational selectivity and high-affinity binding in the complexation of N-phenyl amides in water by a phenyl extended calix[4]pyrrole

We report the synthesis of a tetrapyridinium phenyl extended calix[4]pyrrole receptor that shows high binding affinity and selectivity for the complexation of the cis-conformers of N-phenyl amides in water.

We describe the synthesis of a tetrapyridinium phenyl extended calix[4]pyrrole that is soluble in neutral water solution at mM concentrations. We show that, in pure water, the synthesized calix[4]pyrrole receptor selectively binds the cis-(E) conformers of secondary N-phenyl-amides and tertiary N-methyl-N-phenyl-formamide with binding affinities larger than 10³ M^–1. The conformational selectivity is remarkable owing to the energetic preference of amides to adopt the trans-(Z) conformation in solution. In this respect, we used two binding models for the mathematical analyses of the titration data and calculated apparent and intrinsic binding constants. The combined action of hydrogen bonding and the hydrophobic effect that operates in the binding of the amides in water is responsible for the large affinities displayed by the receptor.

High throughput sequencing of cyclic peptide immobilized on a gel-type single bead

Relatively larger scale peptide libraries immobilized on a gel-type solid support consisting of 24 natural and non-natural amino acids by the "split and combine method" have been constructed to find interacting molecules. The diversity was ca. 200 millions of hexapeptides with cysteinyl residues forming cyclotide. Selected beads after screening can be sequenced by the conventional Edman degradation, although several restrictions and the problems are known. To resolve these, a novel combinatorial method involving partial acid hydrolysis followed by liquid chromatography with on-line mass spectrometric analyses has been established. Problems were uncovered in an early stage of the process. Uncertain assignment caused by byproducts derived from a cystine residue and other materials could be resolved by optimal hydrolysis conditions and derivatization before mass spectrometric analysis. Discrimination between Leu and Ile could be performed using high energy collision induced dissociation in the high resolution MALDI-TOF-MS/MS. The present optimized protocol is useful for discovery of sequences of interacting molecules and a second library construction.

Supramolecular protection from the enzymatic tyrosine phosphorylation in a polypeptide

Two pseudopeptidic cages bind the EYE peptide motif of poly(EY) in buffered water, as shown by NMR and fluorescence spectroscopy. This supramolecular interaction protects the Tyr residues from the enzymatic phosphorylation by PTK.

Stereoselective recognition of the Ac-Glu-Tyr-OH dipeptide by pseudopeptidic cages

Pseudopeptidic molecular cages are appealing receptors since they can display different polar and non-polar interaction sites in a modular framework and a controlled disposition. Inspired by previous host-guest knowledge, two pseudopeptidic molecular cages based on serine and threonine (CySer and CyThr, respectively) were designed and synthesized as hosts for the binding of the four possible stereoisomers of the Ac-Glu-Tyr-OH dipeptide, a target sequence of tyrosine kinases. The careful NMR titration experiments in aqueous acetonitrile allowed the determination of the binding constants and reflected a difference in the stability of the corresponding diastereomeric host-guest complexes. The CySer cage proved to be slightly more efficient than the CyThr counterpart, although both showed similar stereoselectivity trends: LL > DD ≥ LD > DL. This stereoselective binding was retained in the gas phase, as shown by ESI-MS competition experiments using the enantiomer-labelled method (EL), as well as CID experiments. Thus, the MS-determined discriminations follow the same trends observed by NMR, suggesting that the stereoselectivity observed for these systems must be mainly dictated by the polar host-guest interactions. Despite the stereoselective binding of short peptide sequences in competitive media being a challenging issue in supramolecular chemistry, our results demonstrate the power of pseudopeptidic cages in molecular recognition with foreseen implications in chemical biology.

Protein recognition using synthetic small-molecular binders toward optical protein sensing in vitro and in live cells

This review describes the recognition and sensing techniques of proteins and their building blocks by use of small synthetic binders.

Bioinspired chemistry based on minimalistic pseudopeptides

For years researchers have tried to understand the molecular behavior of complex biomolecules through the development of small molecules that can partially mimic their function. Now researchers are implementing the reverse approach: using the structural and mechanistic knowledge obtained from those complex systems to design small molecules with defined properties and for specific applications. One successful strategy for constructing bioinspired, minimalistic molecules is to combine natural building blocks that provide functional elements with abiotic fragments that serve as structural scaffolds. Therefore pseudopeptidic compounds, most of them based on C2 symmetric structures, represent a unique opportunity to explore and evaluate this approach. Some of these molecules are as simple as two amino acids connected by a diamino spacer. The results in this Account show how bioinspired minimalistic pseudopeptides can form ordered structures, participate in the recognition and transcription of information events in molecular devices, and catalyze reactions. This strategy allows researchers to design and prepare a variety of open-chain and macrocyclic compounds leading to systems that can self-aggregate to form hierarchically ordered micro- and nanostructures. In addition, small changes in the molecule or external stimuli can regulate the self-aggregation pattern. In the same way, researchers can also tune the molecular movements of simple pseudopeptides through environmental factors, providing a means to control new molecular devices. In addition, some of the prepared model compounds have shown interesting properties in molecular recognition and even as sensors for several targets of interest. Finally we have observed remarkable catalytic activities from these types of molecules, although those results are still far from the efficiency shown by natural peptides. This family of pseudopeptidic compounds offers the opportunity for the more elaborate design of relatively simple abiotic but bioinspired systems that display specific properties. In addition, the results can provide additional information that will increase the molecular understanding of the basic principles that underlie the extraordinary behavior of natural systems.

A multiple multicomponent approach to chimeric peptide-peptoid podands

The success of multi-armed, peptide-based receptors in supramolecular chemistry traditionally is not only based on the sequence but equally on an appropriate positioning of various peptidic chains to create a multivalent array of binding elements. As a faster, more versatile and alternative access toward (pseudo)peptidic receptors, a new approach based on multiple Ugi four-component reactions (Ugi-4CR) is proposed as a means of simultaneously incorporating several binding and catalytic elements into organizing scaffolds. By employing α-amino acids either as the amino or acid components of the Ugi-4CRs, this multiple multicomponent process allows for the one-pot assembly of podands bearing chimeric peptide-peptoid chains as appended arms. Tripodal, bowl-shaped, and concave polyfunctional skeletons are employed as topologically varied platforms for positioning the multiple peptidic chains formed by Ugi-4CRs. In a similar approach, steroidal building blocks with several axially-oriented isocyano groups are synthesized and utilized to align the chimeric chains with conformational constrains, thus providing an alternative to the classical peptido-steroidal receptors. The branched and hybrid peptide-peptoid appendages allow new possibilities for both rational design and combinatorial production of synthetic receptors. The concept is also expandable to other multicomponent reactions.

Nanomolar binding of peptides containing noncanonical amino acids by a synthetic receptor

This paper describes the molecular recognition of phenylalanine derivatives and their peptides by the synthetic receptor cucurbit[7]uril (Q7). The 4-tert-butyl and 4-aminomethyl derivatives of phenylalanine (tBuPhe and AMPhe) were identified from a screen to have 20-30-fold higher affinity than phenylalanine for Q7. Placement of these residues at the N-terminus of model tripeptides (X-Gly-Gly), resulted in no change in affinity for tBuPhe-Gly-Gly, but a remarkable 500-fold increase in affinity for AMPhe-Gly-Gly, which bound to Q7 with an equilibrium dissociation constant (K(d)) value of 0.95 nM in neutral phosphate buffer. Structure-activity studies revealed that three functional groups work in a positively cooperative manner to achieve this extraordinary stability (1) the N-terminal ammonium group, (2) the side chain ammonium group, and (3) the peptide backbone. Addition of the aminomethyl group to Phe substantially improved the selectivity for peptide versus amino acid and for an N-terminal vs nonterminal position. Importantly, Q7 binds to N-terminal AMPhe several orders of magnitude more tightly than any of the canonical amino acid residues. The high affinity, single-site selectivity, and small modification in this system make it attractive for the development of minimal affinity tags.

Anthracene appended pyridinium amide-urea conjugate in selective fluorometric sensing of L-N-acetylvaline salt

A new anthracene labeled pyridinium amide-urea conjugate 1 has been designed and synthesized. The receptor shows a different fluorometric response with L-N-acetylvaline and L-N-acetylalanine salts in CH₃CN in contrast to the other salts of L-N-acetyl α-amino acids and (S)-α-hydroxy acids studied. Upon complexation of the tetrabutylammonium salt of L-N-acetylvaline, the emission of 1 increases accompanied by the formation of a new band at higher wavelength and this characteristic change distinguishes it from other anionic substrates studied. The binding interaction has been studied by ¹H NMR, fluorescence and UV titration experiments.

Affinity purification of multifunctional polymer nanoparticles

We report that multifunctional polymer nanoparticles approximately the size of a large protein can be "purified", on the basis of peptide affinity just as antibodies, using an affinity chromatography strategy. The selection process takes advantage of the thermoresponsiveness of the nanoparticles allowing "catch and release" of the target peptide by adjusting the temperature. Purified particles show much stronger affinity (K(dapp) ≈ nM) and a narrower affinity distribution than the average of particles before purification (K(dapp) > μM) at room temperature but can release the peptide just by changing the temperature. We anticipate this affinity selection will be general and become an integral step for the preparation of "plastic antibodies" with near-homogeneous and tailored affinity for target biomacromolecules.

Cryptand-like anion receptors

The design of supramolecular hosts for anions began with simple diaza bicycles, named katapinands, and has evolved over the last 40 years to a number of elegantly designed receptors capable of binding many different anions. About the same time the term cryptand appeared in reference to another bicyclic compound that was selective for alkaline-earth ions. Since the first report these simple bicycles, a vast arena of hosts has appeared, including acyclic, monocyclic, and other multicyclic supramolecular receptors. Studies of these systems have revealed considerable information about anion coordination chemistry, including the fact that many of these complexes mimic their transition-metal corollaries in terms of coordination numbers. However, for anions interactions occur via H-bonding most often, rather than the coordinate covalent or dative bonds observed in transition-metal coordination. This critical review examines the design of enclosed, primarily bicyclic cryptands as hosts for anions, with a small scattering of higher polyhedra when deemed appropriate to the discussion. In order to show the development (evolution) of the field, key examples of early work will be noted and compared with more recent developments (136 references).

Structural dynamic of a self-assembling peptide d-EAK16 made of only D-amino acids

We here report systematic study of structural dynamics of a 16-residue self-assembling peptide d-EAK16 made of only D-amino acids. We compare these results with its chiral counterpart L-form, l-EAK16. Circular dichroism was used to follow the structural dynamics under various temperature and pH conditions. At 25 degrees C the d-EAK16 peptide displayed a typical beta-sheet spectrum. Upon increasing the temperature above 70 degrees C, there was a spectrum shift as the 218 nm valley widens toward 210 nm. Above 80 degrees C, the d-EAK16 peptide transformed into a typical alpha-helix CD spectrum without going through a detectable random-coil intermediate. When increasing the temperature from 4 degrees C to 110 degrees C then cooling back from 110 degrees C to 4 degrees C, there was a hysteresis: the secondary structure from beta-sheet to alpha-helix and then from alpha-helix to beta-sheet occurred. d-EAK16 formed an alpha-helical conformation at pH0.76 and pH12 but formed a beta-sheet at neutral pH. The effects of various pH conditions, ionic strength and denaturing agents were also noted. Since D-form peptides are resistant to natural enzyme degradation, such drastic structural changes may be exploited for fabricating molecular sensors to detect minute environmental changes. This provides insight into the behaviors of self-assembling peptides made of D-amino acids and points the way to designing new peptide materials for biomedical engineering and nanobiotechnology.

A general method for designing combinatorial peptide libraries decodable by amino acid analysis

Herein we describe an algorithm for designing combinatorial peptide libraries for split-and-mix synthesis on solid support that are decodable by amino acid analysis (AAA) of the beads. AAA is a standard service analysis available in most biochemical laboratories, and it allows one to control the quality of the peptide on each bead, an important feature that is missing from most library decoding protocols. In the algorithm, each AA is assigned to two variable positions in the sequence grouped in a "unique pair". This arrangement limits sequence design because both the number of unique pairs U (setting the maximum number of variable AA) and the maximum number S of different AA per variable position depend on the peptide length N (U=N(N-1)/2), S=N-1). The method is therefore only suitable for focused libraries. An application example is shown for the selection of peptides with N-terminal proline or hydroxyproline catalyzing an aldol reaction from a combinatorial library of 65536 octapeptides. A simple enumeration program is available to help design combinatorial libraries decodable by amino acid analysis. The method applies to linear and cyclic peptides, can be used for nonnatural building blocks, including beta-amino acids, and should help to explore the vast chemistry of linear and cyclic peptide for catalysis and bioactivity.

Artificial Ditopic Arg-Gly-Asp (RGD) Receptors

Covalent fusion of two artificial recognition motifs for arginine and aspartate resulted in a new class of ditopic RGD receptor molecules, 1-4. The two binding sites for the oppositely charged amino acid residues are linked by either flexible linkers of different length (in 1-3) or a rigid aromatic spacer (in 4). These spacers are shown to be critical for the complexation efficiency of the artificial hosts. If the linkers are too flexible, as in 1-3, an undesired intramolecular self-association occurs within the host and competes with, and thereby weakens, substrate binding. The rigid aromatic linker in 4 prevents any intramolecular self-association and hence efficient RGD binding is observed, even in buffered water (association constant of K(a) approximately 3000 m(-1)). A further increase in hydrophobic contacts, as in host 16, can complement the specific Coulomb attractions, thereby leading to an even more stable complex (Ka=5000 m(-1)). The recognition events have been studied with NMR spectroscopy, UV/Vis spectroscopy, and fluorescence titrations.

Chiral macrocycle-catalyzed highly enantioselective phenylacetylene addition to aliphatic and vinyl aldehydes

The 1,1'-binaphthyl macrocycle (S)-2 is found to be an excellent catalyst for the alkyne addition to aldehydes. In the presence of (S)-2 (20 mol %) and Me2Zn (2 equiv) in THF at room temperature, the addition of phenylacetylene to linear or branched aliphatic aldehydes and vinyl aldehydes gave various propargylic alcohols with 89-96% ee.