The Role of Attractive Non-Covalent Interactions in Peptide Macrocyclization.

The efficiency of macrocyclization reactions relies on the appropriate conformational preorganization of a linear precursor, ensuring that reactive ends are in spatial proximity prior to ring closure. Traditional peptide cyclization approaches that reduce the extent of terminal ion pairing often disfavor cyclization-conducive conformations and can lead to undesired cyclodimerization or oligomerization side reactions, particularly when they are performed without high dilution. To address this challenge, synthetic strategies that leverage attractive noncovalent interactions, such as zwitterionic attraction between chain termini during macrocyclization, offer a potential solution by reducing the entropic penalty associated with linear peptides adopting precyclization conformations. In this study, we investigate the role of (N-isocyanoimino)triphenylphosphorane (Pinc) in facilitating the cyclization of linear peptides into conformationally rigid macrocycles. The observed moderate diastereoselectivity is consistent with the preferential Si-facial addition of Pinc, where the isocyanide adds to the E-iminium ion on the same face as the l-proline amide group. The resulting peptide chain reveals that the activated phosphonium ylide of Pinc brings the reactive ends close together, promoting cyclization by enclosing the carboxylate within the interior of the pentapeptide and preventing the formation of byproducts. For shorter peptides with modified peptide backbones, the cyclization mechanism and outcome are redirected, as nucleophilic motifs such as thiazole and imidazole can covalently trap nitrilium intermediates. The isolation of the intermediate in the unproductive macrocyclization pathway, along with nuclear magnetic resonance and density functional theory studies, provides insights into heterocycle-dependent selectivity. The Pinc-driven macrocyclization process has generated diverse collections of cyclic molecules, and our models offer a comprehensive understanding of observed trends, facilitating the development of other heterocycle-forming macrocyclization reactions.

A Boron Scan of Ethyl Acetoacetate Leads to Versatile Building Blocks.

Discovered in the 19th century, ethyl acetoacetate has been central to the development of organic chemistry, including its pedagogy and applications. In this study, we present borylated derivatives of this venerable molecule. A boron handle has been installed at either α ${{\rm \alpha }}$ - or ß ${\beta }$ -position of acetoacetate by homologation of acyl-MIDA (N-methyliminodiacetic acid) boronates with diazoacetates. Either alkyl or boryl groups were found to migrate with regiochemistry being a function of the steric bulk of the diazo species. Boryl ß ${{\rm \beta }}$ -ketoesters can be further modified into borylated pyrazolones and oximes, thereby expanding the synthetic toolkit and offering opportunities for additional modifications.

Synthesis and Application of Constrained Amidoboronic Acids Using Amphoteric Boron-Containing Building Blocks.

Amidoboronic acid-containing peptidomimetics are an important class of scaffolds in chemistry and drug discovery. Despite increasing interest in boron-based enzyme inhibitors, constrained amidoboronic acids have received little attention due to the limited options available for their synthesis. We describe a new methodology to prepare both α- and ß-amidoboronic acids that impose restrictions on backbone angles. Lewis acid-promoted Boyer-Schmidt-Aube lactam ring expansions using an azidoalkylboronate enabled generation of constrained α-amidoboronic acid derivatives, whereas assembly of the homologous ß-amidoboronic acids was achieved through a novel boronic acid-mediated lactamization process stemming from an α-boryl aldehyde. The results of quantum chemical calculations suggest carboxylate-boron coordination to be rate-limiting for small ring sizes, whereas the tetrahedral intermediate formation is rate limiting in the case of larger rings. As part of this study, an application of ß-amidoboronic acid derivatives as novel VIM-2 metallo-ß-lactamase inhibitors has been demonstrated.

Conformational Control of Macrocycles by Remote Structural Modification.

The conformational analysis of macrocycles is a complex and challenging problem. There are many factors that contribute to this complexity. These include a large number of degrees of freedom, transannular interactions such as hydrogen bonds and hydrophobic interactions, and a range of steric interactions, along with ring strain effects. To a greater extent than within acyclic molecules, these interactions within macrocycles are coupled such that changing one dihedral angle can significantly affect other dihedral angles, further complicating the situation. However, this coupling of bond rotations and transannular interactions enables the transmission of three-dimensional information from one side of a macrocycle to the other. Making relatively small structural modifications to a macrocycle can result in local conformational changes that propagate along the ring to affect distal structural features. The factors that control how such changes can propagate are poorly understood, and it is difficult to predict which modifications will result in significant conformational reorganizations of remote regions of a macrocycle. This review discusses examples where small structural modifications to macrocyclic scaffolds change the conformational preferences of structurally remote regions of the ring. We will highlight evidence provided for conformational changes triggered by remote substituents and explanations of how these changes might occur in an effort to further understand the factors that control such phenomena.

Synthesis of Fluorinated Aminoalkylboronic Acids from Amphoteric α-Boryl Aldehydes.

Our ongoing search for underdeveloped functional group combinations has brought to light α-fluorinated aminoalkylboronic acids, a new class of molecules featuring the B-CF linkage. These compounds can now be generated from secondary amines and α-boryl aldehydes through electrophilic fluorination of boryl enamines or enamides. Fluorinated ß-aminoalkylboronic acids show no signs of degradation under ambient conditions. We present evidence for the involvement of chair-like motifs, favored over the acyclic forms by up to 1.7±0.1 kcal mol-1 in water and held together by an amine-boronate hydrogen bond. Fluorinated ß-aminoalkylboronic acids are stable over a wide pH range and are characterized by a pKa of 3.4, which is the lowest of any alkylboronic acid.

Identification and characterization of the first fragment hits for SETDB1 Tudor domain.

SET domain bifurcated protein 1 (SETDB1) is a human histone-lysine methyltransferase which is amplified in human cancers and was shown to be crucial in the growth of non-small and small cell lung carcinoma. In addition to its catalytic domain, SETDB1 harbors a unique tandem tudor domain which recognizes histone sequences containing both methylated and acetylated lysines, and likely contributes to its localization on chromatin. Using X-ray crystallography and NMR spectroscopy fragment screening approaches, we have identified the first small molecule fragment hits that bind to histone peptide binding groove of the Tandem Tudor Domain (TTD) of SETDB1. Herein, we describe the binding modes of these fragments and analogues and the biophysical characterization of key compounds. These confirmed small molecule fragments will inform the development of potent antagonists of SETDB1 interaction with histones.

Carboxyboronate: A Versatile C1 Building Block.

The synthesis and applications of carboxy-MIDA-boronate, a novel C1 building block, are described. This molecule is accessible via a ruthenium tetraoxide-mediated cleavage of commercially available ethynyl-MIDA-boronate. In the course of this study, carboxy-MIDA-boronate was found to possess ambident reactivity towards nucleophiles. Carboxylic acid derivatization produces a broad range of previously unknown carbamoyl-, oxycarbo- and thiocarboboronates. Carboxy-MIDA-boronate and its derivatives undergo condensations to access borylated heterocycles with boron at positions that are difficult to access using alternate methods. The resulting heterocycles participate in the Suzuki-Miyaura cross-coupling reaction, enabling entry into diverse bis(heteroaryl) motifs. The carbon monoxide-releasing capacity of carboxy-MIDA-boronate was also examined and applied in palladium-catalyzed carbonylation.

Synthesis of Aminoboronic Acid Derivatives from Amines and Amphoteric Boryl Carbonyl Compounds.

Herein, we demonstrate the use of α-boryl aldehydes and acyl boronates in the synthesis of aminoboronic acid derivatives. This work highlights the untapped potential of boron-substituted iminium ions and offers insights into the behavior of N-methyliminodiacetyl (MIDA) boronates during condensation and tautomerization processes. The preparative value of this contribution lies in the demonstration that various amines, including linear and cyclic peptides, can be readily conjugated with boron-containing fragments. A mild deprotection of amino MIDA-boronates enables access to α- and ß-aminoboronic acids in high chemical yields. This simple process should be applicable to the synthesis of a wide range of bioactive molecules as well as precursors for cross-coupling reactions.

Navigating complex peptide structures using macrocycle conformational maps.

Identification of turn motifs that are stabilized by intramolecular hydrogen bonds can be useful in describing the conformation of peptide systems. However, this approach is somewhat insufficient for cyclic peptides because peptide regions that are not positioned within a hydrogen bond can be left with no description. Furthermore, non-regular secondary structures and other rarely-observed conformations can be left without detailed evaluation. Herein, we describe "higher-order" ϕ/ψ plots termed macrocycle conformational maps (MCMs) as a tool for evaluating and comparing the conformations of a series of structurally related macrocyclic peptides.

Illuminating the dark conformational space of macrocycles using dominant rotors.

Three-dimensional conformation is the primary determinant of molecular properties. The thermal energy available at room temperature typically equilibrates the accessible conformational states. Here, we introduce a method for isolating unique and previously understudied conformations of macrocycles. The observation of unusual conformations of 16- to 22-membered rings has been made possible by controlling their interconversion using dominant rotors, which represent tunable atropisomeric constituents with relatively high rotational barriers. Density functional theory and in situ NMR measurements suggest that dominant rotor candidates for the amino-acid-based structures considered here should possess a rotational energy barrier of at least 25 kcal mol-1. Notable differences in the geometries of the macrocycle conformations were identified by NMR spectroscopy and X-ray crystallography. There is evidence that amino acid residues can be forced into rare turn motifs not observed in the corresponding linear counterparts and homodetic rings. These findings should unlock new avenues for studying the conformation-activity relationships of bioactive molecules.

Conformationally stable peptide macrocycles assembled using the Petasis borono-Mannich reaction.

Macrocyclization of linear peptide precursors using the Petasis borono-Mannich reaction affords a diverse range of macrocycles with an endocyclic amine. Analysis of the corresponding macrocyclic structures underscores that the hydrogen bond between an endocyclic amine and the adjacent amide NH is a powerful control element for conformationally homogenous peptide macrocycles.

De Novo Design of Boron-Based Peptidomimetics as Potent Inhibitors of Human ClpP in the Presence of Human ClpX.

Boronic acids have attracted the attention of synthetic and medicinal chemists due to boron's ability to modulate enzyme function. Recently, we demonstrated that boron-containing amphoteric building blocks facilitate the discovery of bioactive aminoboronic acids. Herein, we have augmented this capability with a de novo library design and a virtual screening platform modified for covalent ligands. This technique has allowed us to rapidly design and identify a series of α-aminoboronic acids as the first inhibitors of human ClpXP, which is responsible for the degradation of misfolded proteins.

Author Correction: Amine hemilability enables boron to mechanistically resemble either hydride or proton.

During the revision of this Article prior to publication, a computational study was reported (Vallejos, M. M. & Pellegrinet, S. C. Theoretical study of the BF3-promoted rearrangement of oxiranyl N-methyliminodiacetic acid boronates. J. Org. Chem. 82, 5917-5925; 2017) that evaluates the nucleophilic boryl transfer mechanism predicted in this Article; this reference has now been added as number 19, and the subsequent references renumbered.

Amine hemilability enables boron to mechanistically resemble either hydride or proton.

Tetracoordinate MIDA (N-methyliminodiacetic acid) boronates have found broad utility in chemical synthesis. Here, we describe mechanistic insights into the migratory aptitude of the MIDA boryl group in boron transfer processes, and show that the hemilability of the nitrogen atom on the MIDA ligand enables boron to mechanistically resemble either a hydride or a proton. The first case involves a 1,2-boryl shift, in which boron migrates as a nucleophile in its tetracoordinate form. The second case involves a neighbouring atom-promoted 1,4-boryl shift, in which boron migrates as an electrophile in its pseudo-tricoordinate form. Density functional theory studies and in situ NMR measurements all suggest that MIDA can act as a dynamic switch. These findings encouraged the development of novel migration processes involving boron that exploit the chameleonic behaviour of boron by acting as both a nucleophile and an electrophile, including the first report of a compound with a boronate functionality bound to carbon in the carboxylic acid oxidation state.

The versatility of boron in biological target engagement.

Boron-containing molecules have been extensively used for the purposes of chemical sensing, biological probe development and drug discovery. Due to boron's empty p orbital, it can coordinate to heteroatoms such as oxygen and nitrogen. This reversible covalent mode of interaction has led to the use of boron as bait for nucleophilic residues in disease-associated proteins, culminating in the approval of new therapeutics that work by covalent mechanisms. Our analysis of a wide range of covalent inhibitors with electrophilic groups suggests that boron is a unique electrophile in its chameleonic ability to engage protein targets. Here we review boron's interactions with a range of protein side-chain residues and reveal that boron's properties are nuanced and arise from its uncommon coordination preferences. These mechanistic and structural insights should serve as a guide for the development of selective boron-based bioactive molecules.

Reversible covalent interactions of ß-aminoboronic acids with carbohydrate derivatives.

ß-Aminoalkylboronic acids are capable of binding to carbohydrate derivatives through reversible covalent interactions. An anthracene-bearing ß-aminoboronic acid has been synthesized, enabling determinations of association constants for binding of sugars by fluorescence spectroscopy. The diol-binding properties of ß-aminoboronic acids are also useful in catalysis: one such compound displays remarkably high activity for regioselective O-acylation of a pyranoside derivative.

Borylated oximes: versatile building blocks for organic synthesis.

Herein, we demonstrate the synthesis and functionalization of α-boryl aldoximes from α-boryl aldehydes, with no sign of C-to-N boryl migration. Selective modification of the oxime functionality enables access to a wide range of borylated compounds, such as borylated heterocycles and N-acetoxyamides. By reducing the α-boryl aldoximes, MIDA deprotection yields the corresponding ß-boryl hydroxylamines. As part of this study, we also demonstrate the utility of the boryl aldoxime motif in peptide conjugation.

Multicomponent mapping of boron chemotypes furnishes selective enzyme inhibitors.

Heteroatom-rich organoboron compounds have attracted attention as modulators of enzyme function. Driven by the unmet need to develop chemoselective access to boron chemotypes, we report herein the synthesis of α- and ß-aminocyano(MIDA)boronates from borylated carbonyl compounds. Activity-based protein profiling of the resulting ß-aminoboronic acids furnishes selective and cell-active inhibitors of the (ox)lipid-metabolizing enzyme α/ß-hydrolase domain 3 (ABHD3). The most potent compound displays nanomolar in vitro and in situ IC50 values and fully inhibits ABHD3 activity in human cells with no detectable cross-reactivity against other serine hydrolases. These findings demonstrate that synthetic methods that enhance the heteroatom diversity of boron-containing molecules within a limited set of scaffolds accelerate the discovery of chemical probes of human enzymes.

Nanomolar-Potency Small Molecule Inhibitor of STAT5 Protein.

We herein report the design and synthesis of the first nanomolar binding inhibitor of STAT5 protein. Lead compound 13a, possessing a phosphotyrosyl-mimicking salicylic acid group, potently and selectively binds to STAT5 over STAT3, inhibits STAT5-SH2 domain complexation events in vitro, silences activated STAT5 in leukemic cells, as well as STAT5's downstream transcriptional targets, including MYC and MCL1, and, as a result, leads to apoptosis. We believe 13a represents a useful probe for interrogating STAT5 function in cells as well as being a potential candidate for advanced preclinical trials.