Fragment-Based Discovery of a Series of Allosteric-Binding Site Modulators of ß-Glucocerebrosidase.

ß-Glucocerebrosidase (GBA/GCase) mutations leading to misfolded protein cause Gaucher's disease and are a major genetic risk factor for Parkinson's disease and dementia with Lewy bodies. The identification of small molecule pharmacological chaperones that can stabilize the misfolded protein and increase delivery of degradation-prone mutant GCase to the lysosome is a strategy under active investigation. Here, we describe the first use of fragment-based drug discovery (FBDD) to identify pharmacological chaperones of GCase. The fragment hits were identified by using X-ray crystallography and biophysical techniques. This work led to the discovery of a series of compounds that bind GCase with nM potency and positively modulate GCase activity in cells.

Fragment-Based Discovery of Allosteric Inhibitors of SH2 Domain-Containing Protein Tyrosine Phosphatase-2 (SHP2).

The ubiquitously expressed protein tyrosine phosphatase SHP2 is required for signaling downstream of receptor tyrosine kinases (RTKs) and plays a role in regulating many cellular processes. Genetic knockdown and pharmacological inhibition of SHP2 suppresses RAS/MAPK signaling and inhibit the proliferation of RTK-driven cancer cell lines. Here, we describe the first reported fragment-to-lead campaign against SHP2, where X-ray crystallography and biophysical techniques were used to identify fragments binding to multiple sites on SHP2. Structure-guided optimization, including several computational methods, led to the discovery of two structurally distinct series of SHP2 inhibitors binding to the previously reported allosteric tunnel binding site (Tunnel Site). One of these series was advanced to a low-nanomolar lead that inhibited tumor growth when dosed orally to mice bearing HCC827 xenografts. Furthermore, a third series of SHP2 inhibitors was discovered binding to a previously unreported site, lying at the interface of the C-terminal SH2 and catalytic domains.

X-ray Screening of an Electrophilic Fragment Library and Application toward the Development of a Novel ERK 1/2 Covalent Inhibitor.

Fragment-based drug discovery (FBDD) has become an established method for the identification of efficient starting points for drug discovery programs. In recent years, electrophilic fragment screening has garnered increased attention from both academia and industry to identify novel covalent hits for tool compound or drug development against challenging drug targets. Herein, we describe the design and characterization of an acrylamide-focused electrophilic fragment library and screening campaign against extracellular signal-regulated kinase 2 (ERK2) using high-throughput protein crystallography as the primary hit-finding technology. Several fragments were found to have covalently modified the adenosine triphosphate (ATP) binding pocket Cys166 residue. From these hits, 22, a covalent ATP-competitive inhibitor with improved potency (ERK2 IC50 = 7.8 µM), was developed.

Structure-Based Design of Potent and Orally Active Isoindolinone Inhibitors of MDM2-p53 Protein-Protein Interaction.

Inhibition of murine double minute 2 (MDM2)-p53 protein-protein interaction with small molecules has been shown to reactivate p53 and inhibit tumor growth. Here, we describe rational, structure-guided, design of novel isoindolinone-based MDM2 inhibitors. MDM2 X-ray crystallography, quantum mechanics ligand-based design, and metabolite identification all contributed toward the discovery of potent in vitro and in vivo inhibitors of the MDM2-p53 interaction with representative compounds inducing cytostasis in an SJSA-1 osteosarcoma xenograft model following once-daily oral administration.

Fragment-based drug discovery: opportunities for organic synthesis.

This Review describes the increasing demand for organic synthesis to facilitate fragment-based drug discovery (FBDD), focusing on polar, unprotected fragments. In FBDD, X-ray crystal structures are used to design target molecules for synthesis with new groups added onto a fragment via specific growth vectors. This requires challenging synthesis which slows down drug discovery, and some fragments are not progressed into optimisation due to synthetic intractability. We have evaluated the output from Astex's fragment screenings for a number of programs, including urokinase-type plasminogen activator, hematopoietic prostaglandin D2 synthase, and hepatitis C virus NS3 protease-helicase, and identified fragments that were not elaborated due, in part, to a lack of commercially available analogues and/or suitable synthetic methodology. This represents an opportunity for the development of new synthetic research to enable rapid access to novel chemical space and fragment optimisation.

Oxalyl Boronates Enable Modular Synthesis of Bioactive Imidazoles.

Described herein is the preparation of oxalyl boronate building blocks and their application for the construction of heterocycles. The oxalyl unit, readily accessible through commercially available starting materials, enables a modular approach for the synthesis of imidazoles. A variety of aromatic, heteroaromatic, and alkyl carboxaldehydes were condensed with oxalyl boronates to afford substituted boryl imidazoles in a regiocontrolled fashion. Subsequent palladium-catalyzed cross-coupling with haloarenes furnished the desired trisubstituted imidazole scaffolds. To demonstrate the utility of these scaffolds, potent inhibitors of the serine/threonine-protein kinase STK10 were synthesized.

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.

Access to Cyclic Amino Boronates via Rhodium-Catalyzed Functionalization of Alkyl MIDA Boronates.

Herein, we describe the rhodium-catalyzed C-H amination reaction of 1,2-boryl sulfamate esters derived from amphoteric α-boryl aldehydes. Depending on the substitution pattern of the boryl sulfamate ester, a diverse range of five- or six-membered ring heterocycles are accessible using this transformation. The highly chemoselective nature of the C-H functionalization reaction preserves the alkyl boronate functional group, which enables the synthesis of B-C-N and B-C-C-N motifs that are present in a number of hydrolase inhibitors.

Condensation-Driven Assembly of Boron-Containing Bis(Heteroaryl) Motifs Using a Linchpin Approach.

Herein, we describe the bromomethyl acyl boronate linchpin--an enabling reagent for the condensation-driven assembly of novel bis(heteroaryl) motifs. This building block is readily accessible from commercially available starting materials. A variety of 2-amino- and 2-methylpyridines were reacted with MIDA-protected bromomethyl acylboronate to afford 2-boryl imidazo[1,2-a]pyridine and 2-boryl indolizine derivatives, respectively, in excellent yields. Subsequent condensation with hydroxyamidines and hydrazonamides converted the intermediate heterocycles into novel boron-containing bis(heteroaryl) units characterized by high thermal stability.

Facile synthesis of borofragments and their evaluation in activity-based protein profiling.

The discovery of enzyme inhibitors relies on synthetic methods that enable rapid and modular construction of small molecules. Heterocyclic fragments designed to maximize enthalpic interactions with their protein targets represent a particularly desirable class of molecules. Here we describe a reagent that enables straightforward construction of "borofragments", in which a heterocycle is separated from the boron center by two or three rotatable bonds. The stability of these molecules depends on the MIDA group which likely acts as a slow-release element under biological conditions. Borofragments can be used to discover inhibitors of enzymes that use catalytic oxygen nucleophiles. We have employed this method to identify inhibitors of ABHD10 and the predicted carboxypeptidase CPVL. This technique should be applicable to other classes of targets.

Boron-containing enamine and enamide linchpins in the synthesis of nitrogen heterocycles.

The use of α-boryl enamine and enamide linchpins in the synthesis of nitrogen heterocycles has been demonstrated. Boryl enamines provide ready access to the corresponding α-halo aldehydes, which undergo regioselective annulation to form borylated thiazoles. A condensation/amidation sequence converts α-boryl aldehydes into stable α-boryl enamides without concomitant C → N migration. We also show that palladium-catalyzed cyclization of α-boryl enamides leads to synthetically versatile isoindolones. These molecules can be subsequently used to access polycyclic scaffolds.

Stereocontrolled disruption of the Ugi reaction toward the production of chiral piperazinones: substrate scope and process development.

The factors determining diastereoselectivity observed in the multicomponent conversion of amino acids, aziridine aldehyde dimers, and isocyanides into chiral piperazinones have been investigated. Amino acid-dependent selectivity for either trans- or cis-substituted piperazinone products has been achieved. An experimentally determined diastereoselectivity model for the three-component reaction driven by aziridine aldehyde dimers has predictive value for different substrate classes. Moreover, this model is useful in reconciling the previously reported observations in multicomponent reactions between isocyanides, α-amino acids, and monofunctional aldehydes.

Development of the direct Suzuki-Miyaura cross-coupling of primary B-alkyl MIDA-boronates and aryl bromides.

The development of a palladium-catalyzed sp(3)-sp(2) Suzuki-Miyaura cross-coupling of B-alkyl-N-methyliminodiacetyl (B-alkyl MIDA) boronates and (hetero)aryl bromides is reported. This transformation is tolerant of a variety of functional groups (F, NO2, CN, Cl, COCH3, and CHO). B-Alkyl MIDA boronates allow an efficient cross-coupling reaction directed toward the synthesis of unsymmetrical methylene diaryls as well as alkylated arenes in good to excellent yields.

Stereocontrolled synthesis of 1,2- and 1,3-diamine building blocks from aziridine aldehyde dimers.

Vicinal aziridine-containing diamines have been obtained with high syn-stereoselectivity from readily available aziridine aldehyde dimers in the Petasis borono-Mannich reaction. Subsequent solvent- and/or nucleophile-dependent ring-opening of the aziridine ring yields functionalized 1,2- and 1,3-diamines with high regioselectivity. The ring opening is also influenced by the substitution at the C3 position of the aziridine. A mechanistic rationale for the highly syn-selective three-component reaction is proposed.

Evaluation of a chiral cubane-based Schiff base ligand in asymmetric catalysis reactions.

Recently, a novel chiral cubane-based Schiff base ligand was reported to yield modest enantioselectivity in the Henry reaction. To further explore the utility of this ligand in other asymmetric organic transformations, we evaluated its stereoselectivity in cyclopropanation and Michael addition reactions. Although there was no increase in stereocontrol, upon computational evaluation using both M06L and B3LYP calculations, it was revealed that a pseudo six-membered ring exists, through H-bonding of a cubyl hydrogen to the copper core. This decreases the steric bulk above the copper center and limits the asymmetric control with this ligand.

Oxidative geminal functionalization of organoboron compounds.

Excellent tolerance: Stable acylboronates equipped with N-methyliminodiacetyl (MIDA) boryl groups ([B]) were prepared by using a sequence of oxidative manipulations at the boron-bound carbon center (green in scheme). Chemoselective transformations of these acylated organoboron building blocks yielded a range of multifunctionalized boron derivatives and supplied access to valuable borylated heterocycles (see scheme).

Chemoselective palladium-catalyzed α-allylation of α-boryl aldehydes.

Herein we report the development of an α-allylation reaction of α-boryl aldehydes that preserves the carbon-boron bond under Pd(0)/Pd(II) catalysis. A variety of α-boryl aldehydes and allylic alcohols participate in this chemoselective transformation. The α-allylated products were obtained as single regioisomers.

Boroalkyl group migration provides a versatile entry into α-aminoboronic acid derivatives.

A reaction exemplifying migration of boron-substituted carbon is described. We show that α-boroalkyl groups of transient boroalkyl acyl azide intermediates readily migrate from carbon to nitrogen. This process allows access to a new class of stable molecules, α-boryl isocyanates, from α-borylcarboxylic acid precursors. The methodology facilitates synthesis of a wide range of α-aminoboronic acid derivatives, including α,α-disubstituted analogues.