Discovery and molecular basis of subtype-selective cyclophilin inhibitors.

Although cyclophilins are attractive targets for probing biology and therapeutic intervention, no subtype-selective cyclophilin inhibitors have been described. We discovered novel cyclophilin inhibitors from the in vitro selection of a DNA-templated library of 256,000 drug-like macrocycles for cyclophilin D (CypD) affinity. Iterated macrocycle engineering guided by ten X-ray co-crystal structures yielded potent and selective inhibitors (half maximal inhibitory concentration (IC50) = 10 nM) that bind the active site of CypD and also make novel interactions with non-conserved residues in the S2 pocket, an adjacent exo-site. The resulting macrocycles inhibit CypD activity with 21- to >10,000-fold selectivity over other cyclophilins and inhibit mitochondrial permeability transition pore opening in isolated mitochondria. We further exploited S2 pocket interactions to develop the first cyclophilin E (CypE)-selective inhibitor, which forms a reversible covalent bond with a CypE S2 pocket lysine, and exhibits 30- to >4,000-fold selectivity over other cyclophilins. These findings reveal a strategy to generate isoform-selective small-molecule cyclophilin modulators, advancing their suitability as targets for biological investigation and therapeutic development.

Multimodal small-molecule screening for human prion protein binders.

Prion disease is a rapidly progressive neurodegenerative disorder caused by misfolding and aggregation of the prion protein (PrP), and there are currently no therapeutic options. PrP ligands could theoretically antagonize prion formation by protecting the native protein from misfolding or by targeting it for degradation, but no validated small-molecule binders have been discovered to date. We deployed a variety of screening methods in an effort to discover binders of PrP, including 19F-observed and saturation transfer difference (STD) NMR spectroscopy, differential scanning fluorimetry (DSF), DNA-encoded library selection, and in silico screening. A single benzimidazole compound was confirmed in concentration-response, but affinity was very weak (Kd > 1 mm), and it could not be advanced further. The exceptionally low hit rate observed here suggests that PrP is a difficult target for small-molecule binders. Whereas orthogonal binder discovery methods could yield high-affinity compounds, non-small-molecule modalities may offer independent paths forward against prion disease.

Author Correction: Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Reductive Amination in the Synthesis of Pharmaceuticals.

Reductive amination plays a paramount role in pharmaceutical and medicinal chemistry owing to its synthetic merits and the ubiquitous presence of amines among biologically active compounds. It is one of the key approaches to C-N bond construction due to its operational easiness and a wide toolbox of protocols. Recent studies show that at least a quarter of C-N bond-forming reactions in the pharmaceutical industry are performed via reductive amination. This Review concisely compiles information on 71 medical substances that are synthesized by reductive amination. Compounds are grouped according to the principle of action, which includes drugs affecting the central nervous system, drugs affecting the cardiovascular system, anticancer drugs, antibiotics, antiviral and antifungal medicines, drugs affecting the urinary system, drugs affecting the respiratory system, antidiabetic medications, drugs affecting the gastrointestinal tract, and drugs regulating metabolic processes. A general synthetic scheme is provided for each compound, and the description is focused on reductive amination steps. The green chemistry metric of reaction mass efficiency was calculated for all reactions.

Atom- and Step-Economical Ruthenium-Catalyzed Synthesis of Esters from Aldehydes or Ketones and Carboxylic Acids.

We developed a ruthenium-catalyzed reductive ester synthesis from aldehydes or ketones and carboxylic acids using carbon monoxide as a deoxygenative agent. Multiple factors influencing the outcome of the reaction were investigated. Best results were obtained for commercially available and inexpensive benzene ruthenium chloride; as low as 0.5 mol % of the catalyst is sufficient for efficient reaction. Competitive studies demonstrated that the presence of even 1000 equiv of alcohol in the reaction mixture does not lead to the corresponding ester, which clearly indicates that the process is not a simple reductive esterification but a novel type of Ru-catalyzed redox process.

Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules.

DNA-encoded libraries have emerged as a widely used resource for the discovery of bioactive small molecules, and offer substantial advantages compared with conventional small-molecule libraries. Here, we have developed and streamlined multiple fundamental aspects of DNA-encoded and DNA-templated library synthesis methodology, including computational identification and experimental validation of a 20 × 20 × 20 × 80 set of orthogonal codons, chemical and computational tools for enhancing the structural diversity and drug-likeness of library members, a highly efficient polymerase-mediated template library assembly strategy, and library isolation and purification methods. We have integrated these improved methods to produce a second-generation DNA-templated library of 256,000 small-molecule macrocycles with improved drug-like physical properties. In vitro selection of this library for insulin-degrading enzyme affinity resulted in novel insulin-degrading enzyme inhibitors, including one of unusual potency and novel macrocycle stereochemistry (IC50 = 40 nM). Collectively, these developments enable DNA-templated small-molecule libraries to serve as more powerful, accessible, streamlined and cost-effective tools for bioactive small-molecule discovery.

Hydrogen-free reductive amination using iron pentacarbonyl as a reducing agent.

We developed solvent-free reductive amination without an external hydrogen source using iron pentacarbonyl as a reducing agent. Neither a catalyst nor any other additives were employed. Various types of substrates are suitable for the reaction, including those with low reactivity, e.g. benzophenone. Among others, the protocol tolerates bromo-, cyano-, benzyloxy-, pyrimidyl and styryl moieties.

Dichotomy of Atom-Economical Hydrogen-Free Reductive Amidation vs Exhaustive Reductive Amination.

Rh-catalyzed one-step reductive amidation of aldehydes has been developed. The protocol does not require an external hydrogen source and employs carbon monoxide as a deoxygenative agent. The direction of the reaction can be altered simply by changing the solvent: reaction in THF leads to amides, whereas methanol favors formation of tertiary amines.

Reductive amination catalyzed by iridium complexes using carbon monoxide as a reducing agent.

Development of novel, sustainable catalytic methodologies to provide access to amines represents a goal of fundamental importance. Herein we describe a systematic study for the construction of a variety of amines catalyzed by a well-defined homogeneous iridium complex using carbon monoxide as a reducing agent. The methodology was shown to be compatible with functional groups prone to reduction by hydrogen or complex hydrides.

Dichotomy of Reductive Addition of Amines to Cyclopropyl Ketones vs Pyrrolidine Synthesis.

An interesting catalytic dichotomy was discovered: switching between simple ligand-free catalysts leads to fundamentally different outcomes of reductive reaction between amines and α-carbonylcyclopropanes. Whereas a rhodium catalyst leads to the traditional reductive amination product, ruthenium catalysis enables a novel reaction of pyrrolidine synthesis via ring expansion. The protocols do not require an external hydrogen source and employ carbon monoxide as a deoxygenative agent. The developed methodologies are perfectly compatible with a number of synthetically important functionalities such as ester, carboxyl, bromo, and Cbz moieties.

The synthesis of sterically hindered amines by a direct reductive amination of ketones.

An atom-economical methodology for the synthesis of sterically hindered tertiary amines was developed, which is based on complementary Rh- and Ru-catalyzed direct reductive amination of ketones with primary and secondary amines using carbon monoxide as a deoxygenating agent.

Ruthenium-catalyzed reductive amination without an external hydrogen source.

A ruthenium-catalyzed reductive amination without an external hydrogen source has been developed using carbon monoxide as the reductant and ruthenium(III) chloride (0.008-2 mol %) as the catalyst. The method was applied to the synthesis of antianxiety agent ladasten.

Atom- and step-economical preparation of reduced Knoevenagel adducts using CO as a deoxygenative agent.

A highly efficient one-step Rh-catalyzed preparation of reduced Knoevenagel adducts of various aldehydes and ketones with active methylene compounds has been developed. The protocol does not require an external hydrogen source and employs carbon monoxide as a deoxygenative agent. The use of malonic acid or cyanoacetamide enabled efficient formal deoxygenative addition of methyl acetate or acetonitrile to aldehydes. The developed methodology was applied to the synthesis of the precursors of biomedically important compounds.

Formation of five- and seven-membered rings enabled by the triisopropylsilyl auxiliary group.

A highly convenient synthetic pathway to 2-indanones from aldehydes was established. The introduction of a triisopropylsilyl group greatly facilitated Meinwald rearrangement of the intermediate epoxides and alleviated the necessity of polysubstitution for the clean formation of indenes and cyclopentadienes via cyclodehydration of allylic alcohols; unprecedented freedom with respect to the product structure was thus achieved. The developed methodology could also be applicable to the formation of seven-membered rings leading to dibenzo[7]annulenes and dibenzosuberones.

Enantioselective alkynylation of aldehydes with 1-haloalkynes catalyzed by tethered bis(8-quinolinato) chromium complex.

The first example of Cr-catalyzed asymmetric alkynylation of aldehydes with 1-iodo- and 1-bromoalkynes was developed. The use of tethered bis(8-quinolinato) chromium catalyst (3 mol %) allowed preparation of enantioenriched propargyl alcohols with good yields and enantioselectivities up to 92% ee. 1-Bromoalkynes can be activated by the introduction of a cobalt porphine co-catalyst, which enables shorter reaction times without any loss of enantiocontrol.

Mechanism-guided development of VO(salen)X complexes as catalysts for the asymmetric synthesis of cyanohydrin trimethylsilyl ethers.

Catalyze this! Detailed study of the mechanism of asymmetric cyanohydrin synthesis catalyzed by VO(salen)X complexes (see figure) led to the development of VO(salen)NCS, as the most active vanadium-based catalyst yet developed for this reaction.The mechanism by which oxovanadium(V)(salen) complexes(1) VO(salen)X catalyze the asymmetric addition of trimethylsilyl cyanide to benzaldehyde has been studied. The reaction kinetics indicated that the structure of the counterion (X) had a significant influence on the rate, but not on the enantioselectivity of the reaction. The less coordinating the counterion, the lower the catalytic activity; a trend that was confirmed by a Hammett analysis. Variable temperature kinetics allowed the enthalpies and entropies of activation to be determined for some catalysts, and showed that, for others, the overall reaction order changes from second order to zero order as the temperature is reduced. The order with respect to the catalyst was determined for nine of the VO(salen)X complexes and showed that the less active catalysts were active predominantly as mononuclear species whilst the more active catalysts were active predominantly as dinuclear species. Mass spectrometry confirmed the formation of dinuclear species in situ from all of the VO(salen)X complexes and indicated that the dinuclear complexes contained one vanadium(V) and one vanadium(IV) ion. The latter conclusion was supported by cyclic voltammetry of the complexes, by fluorescence measurements and by the fact that catalyst deactivation occurs when reactions are carried out under an inert atmosphere. Based on this evidence, it has been deduced that the catalysis involves two catalytic cycles: one for catalysis by mononuclear VO(salen)X species and the other for catalysis by dinuclear species. The catalytic cycle involving dinuclear species involves activation of both the cyanide and aldehyde, whereas the catalytic cycle involving mononuclear species activates only the aldehyde, thus explaining the higher catalytic activity observed for catalysts which are predominantly active as dinuclear complexes. Based on these mechanistic results, two new VO(salen)X complexes (X=F and NCS) were predicted to form highly active catalysts for asymmetric cyanohydrin synthesis. VO(salen)NCS was indeed found to be the most active catalyst of this type and catalyzed the asymmetric addition of trimethylsilyl cyanide to thirteen aldehydes. In each case, high yields and enantioselectivities were obtained after a reaction time of two hours at room temperature using just 0.1 mol % of the catalyst.

In an attempt to provide a user's guide to the galaxy of benzylidene, alkoxybenzylidene, and indenylidene ruthenium olefin metathesis catalysts.

The data reported in this paper demonstrate that great care must be taken when choosing an appropriate catalyst for a given metathesis reaction. First-generation catalysts were found to be useful in the metathesis of sterically unhindered substrates. Second-generation catalysts (under optimised conditions) showed good to excellent activities toward sterically hindered and electron-withdrawing group (EWG)-substituted alkenes that do not react using the first-generation complexes. A strong temperature effect was noted on all of the reactions tested. Interestingly, attempts to force a reaction by increasing the catalyst loading were much less effective. Therefore, when possible, it is suggested that metathesis transformations should be carried out with a second-generation catalyst at 70 degrees C in toluene. However, different second-generation catalysts proved to be optimal for different applications and no single catalyst outperformed all others in all cases. Nevertheless, some empirical rules can be deduced from the model experiments, providing preliminary hints for the selection of the optimal catalysts.

VO(salen)(X) catalysed asymmetric cyanohydrin synthesis: an unexpected influence of the nature of anion X on the catalytic activity.

The nature of the anionic ligand X (X = EtOSO3, BF4, Cl, Br, OSO2CF3, F or CN) in vanadium(V)salen complexes [V+ O(salen) X-] was found to have a significant influence on the catalytic activity of the complexes, but not on their enantioselectivities; with the complexes in which X = Cl or F being most active and the complex with X = OSO2CF3 being totally inactive.