Flexible Synthesis and Evaluation of Diverse Anti-Apicomplexa Cyclic Peptides

The Zinc-Binding Group Effect: Lessons from Non-Hydroxamic Acid Vorinostat Analogs

Histone deacetylases (HDACs) are enzymes pursued as drug targets in various cancers and several non-oncological conditions, such as inflammation and neurodegenerative disorders. In the past decade, HDAC inhibitors (HDACi) have emerged as relevant pharmaceuticals, with many efforts devoted to the development of new representatives. However, the growing safety concerns regarding the established hydroxamic acid-based HDAC inhibitors tend to drive current research more toward the design of inhibitors bearing alternative zinc-binding groups (ZBGs). This Perspective presents an overview of all non-hydroxamic acid ZBGs that have been incorporated into the clinically approved prototypical HDACi, suberoylanilide hydroxamic acid (vorinostat). This provides the unique opportunity to compare the inhibition potential and biological effects of different ZBGs in a direct way, as the compounds selected for this Perspective differ only in their ZBG. To that end, different strategies used to select a ZBG, its properties, activity, and liabilities are discussed.

Chemotherapeutics for Toxoplasma gondii: Molecular Biotargets, Binding Modes, and Structure-Activity Relationship Investigations

Toxoplasmosis, an infectious zoonotic disease caused by the apicomplexan parasite Toxoplasma gondii (T. gondii), is a major worldwide health problem. However, there are currently no effective options (chemotherapeutic drugs or prophylactic vaccines) for treating chronic latent toxoplasmosis infection. Accordingly, seeking more effective and safer chemotherapeutics for combating this disease remains a long-term and challenging objective. In this paper, we summarize possible molecular biotargets, with an emphasis on those that are druggable and promising, including, without limitation, calcium-dependent protein kinase 1, bifunctional thymidylate synthase-dihydrofolate reductase, and farnesyl diphosphate synthase. Meanwhile, as important components of medicinal chemistry, the binding modes and structure-activity relationship profiles of the corresponding inhibitors were also illuminated. We anticipate that this information will be helpful for further identification of more effective chemotherapeutic interventions to prevent and treat zoonotic infections caused by T. gondii.

Divergent Access to Histone Deacetylase Inhibitory Cyclopeptides via a Late-Stage Cyclopropane Ring Cleavage Strategy. Short Synthesis of Chlamydocin

A unified step-economical strategy for accessing histone deacetylase inhibitory peptides is proposed, based on the late-stage installation of multiple zinc-binding functionalities via the cleavage of the strained cyclopropane ring in the common pluripotent cyclopropanol precursor. The efficacy of the proposed diversity-oriented approach has been validated by short stereoselective synthesis of natural product chlamydocin, containing a challenging-to-install fragment of (2S,9S)-2-amino-8-oxo-9,10-epoxydecanoic acid (Aoe) and a range of its analogues, derivatives of 2-amino-8-oxodecanoic and 2-aminosuberic acids.

The Xanthate Route to Ketones: When the Radical Is Better than the Enolate

The alkylation of enolates is one of the backbones of ketone chemistry, yet in practice it suffers from numerous limitations due to problems of regiochemistry (including O- versus C-alkylation), multiple alkylations, self-condensation, competing elimination, and incompatibility with many polar groups that have to be protected. Over the years, various solutions have been devised to overcome these difficulties, such as the employment of auxiliary ester or sulfone groups to modify the p K_a of the enolizable hydrogens, the passage by the corresponding hydrazones, the use of transition-metal-catalyzed redox systems to formally alkylate ketones with alcohols, etc. Most of these hurdles disappear upon switching to α-ketonyl radicals. Radicals are tolerant of most polar functions, and radical additions to flat sp² centers are generally easier to accomplish than enolate substitution at tetrahedral sp³ carbons. The main stumbling block, however, has been a lack of generally applicable methods for the generation and intermolecular capture of α-ketonyl radicals. We have found over the past years that the degenerative exchange of xanthates represents in many ways an ideal solution to this problem. It overcomes essentially all of the difficulties faced by other radical processes because of its unique ability to reversibly store reactive radicals in a dormant, nonreactive form. The lifetime of the radicals can therefore be significantly enhanced, even in the concentrated medium needed for bimolecular additions, while at the same time regulating their absolute and relative concentrations. The ability to perform intermolecular additions to highly functionalized alkene partners opens up numerous possibilities for rapid and convergent access to complex structures. Of particular importance is the elaboration of ketones that are prone to self-condensation, such trifluoroacetone, and of base-sensitive ketones, such as chloro- and dichloroacetone, since the products can be used for the synthesis of a myriad fluorinated and heteroaromatic compounds of relevance to medicinal chemistry and agrochemistry. The formal distal dialkylation of ketones, also of utmost synthetic interest, is readily accomplished, allowing convenient access to a wide array of useful ketone building blocks. Cascade processes can be implemented and, in alliance with powerful classical reactions (aldol, alkylative Birch reductions, etc.), furnish a quick route to complex polycyclic scaffolds. Furthermore, the presence of the xanthate group in the adducts can be exploited to obtain a variety of arenes and heteroarenes, such as pyrroles, thiophenes, naphthalenes, and pyridines, as well as enones, dienes, and cyclopropanes. Last but not least, the reagents and most of the starting materials are exceedingly cheap, and the reactions are safe and easy to scale up.

Hydroxyl Ketone-Based Histone Deacetylase Inhibitors To Gain Insight into Class I HDAC Selectivity versus That of HDAC6

Little is known about the biological and structural features that govern the isoform selectivity for class I histone deacetylases (HDACs) over HDAC6. In addition to that for known inhibitors, like benzamides, psammaplin A, and cyclodepsipeptide-derived thiols, selectivity was also observed for naturally occurring cyclopeptide HDAC inhibitors with an aliphatic flexible linker and ketonelike zinc-binding group (ZBG). The present study reports that this isoform selectivity is mainly due to the linker and ZBG, as replacement of the cyclopeptide cap region by a simple aniline retained class I HDAC isoform selectivity toward HDAC6 in enzymatic assays. The best cyclopeptide-free analogues preserved efficacy against Plasmodium falciparum and cancer cell lines. Molecular modeling provided hypotheses to explain this selectivity and suggests different behaviors of the flexible linker on HDAC1 and HDAC6 pockets, which may influence, on the basis of the strength of the ZBG, its coordination with the zinc ion.

Selective synthesis of three product classes from imine and carboxylic acid precursors via direct imine acylation

Three divergent procedures allow the selective generation of δ-lactams, β-lactams and tetrahydropyrimidinones from common imine and carboxylic acid precursors.

Diversity-oriented synthesis of analogues of the novel macrocyclic peptide FR-225497 through late stage functionalization

A concise synthetic approach to a class of biologically interesting cyclic tetrapeptides is reported which involves a late-stage functionalization of a macrocyclic scaffold through cross metathesis in an attempt to create diversity. The utility of this protocol is demonstrated through the preparation of three structural analogues of the important naturally occurring histone deacetylase inhibitor FR-225497.

[Structural diversity oriented synthesis to explore the living world]

Structural diversity oriented synthesis aims to fulfill the unoccupied tridimensional "chemical space" gap left by traditional chemical libraries. Through the development of novel synthetic strategies relying on divergent reactions, chemist is now able to realize in only two or three steps such library that ensures the access of a large number of products having a good quality in term of structural diversity. A few examples are presented to illustrate how this can be done in the context of increasing molecular complexity and diversity devoted to the discovery and optimization of bioactive compounds.

Small head-to-tail macrocyclic α-peptoids

A convenient and efficient methodology for the head-to-tail macrocyclization of small 3-mer, 4-mer, and 5-mer α-peptoid acids (9-, 12-, and 15-atom N-substituted glycine oligomers) is described. The cyclic trimer has a ccc amide sequence in the crystal structure, whereas the tetramer has ctct and the pentamer has ttccc stereochemistry. NMR analysis reveals rigid structures in solution. These synthetic macrocycles may prove useful in medicinal and materials applications.

Linear and cyclic hybrids of alternating thiophene-amino acid units: synthesis and effects of chirality on conformation and molecular packing

The dipeptide isostere 5-aminothiophene carboxylic acid has been combined with L-phenylalanine moieties to provide linear and cyclic hybrid oligopeptides. A suitable protecting group strategy and appropriate coupling methods have been developed to guarantee a high degree of enantiopurity of the resulting amides. Cyclic tetraamides have been efficiently obtained by macrocyclization of the linear derivatives. In the case of racemized cyclization precursors, two diastereomeric macrocycles (S,S/R,R and meso) have been isolated. Their crystal structures show clear effects of the stereogenic centers on the ring conformations and molecular packing.