Diastereoselective synthesis of highly functionalized fluoroalkene dipeptide isosteres and its application to Fmoc-based solid-phase synthesis of a cyclic pentapeptide mimetic

Design, synthesis and evaluation of bioactivity of peptidomimetics based on chloroalkene dipeptide isosteres

Ample biologically active peptides have been found, identified and modified for use in drug discovery to date. However, several factors, such as low metabolic stability due to proteolysis and non-specific interactions with multiple off-target molecules, might limit the therapeutic use of peptides. To enhance the stability and/or bioactivity of peptides, the development of "peptidomimetics," which mimick peptide molecules, is considered to be idealistic. Hence, chloroalkene dipeptide isosteres (CADIs) was designed, and their synthetic methods have been developed by us. Briefly, in a CADI an amide bond in peptides is replaced with a chloroalkene structure. CADIs might be superior mimetics of amide bonds because the Van der Waals radii (VDR) and the electronegativity value of a chlorine atom are close to those of the replaced oxygen atom. By a developed method of the "liner synthesis", N-tert-butylsulfonyl protected CADIs can be synthesized via a key reaction involving diastereoselective allylic alkylation using organocopper reagents. On the other hand, by a developed method of the "convergent synthesis", N-fluorenylmethoxycarbonyl (Fmoc)-protected carboxylic acids can be also constructed based on N- and C-terminal analogues from corresponding amino acid starting materials via an Evans syn aldol reaction and the Ichikawa allylcyanate rearrangement reaction involving a [3.3] sigmatropic rearrangement. Notably, CADIs can also be applied for Fmoc-based solid-phase peptide synthesis and therefore introduced into bioactive peptides including as the Arg-Gly-Asp (RGD) peptide and the amyloid β fragment Lys-Leu-Val-Phe-Phe (KLVFF) peptide, which are correlated with cell attachment and Alzheimer's disease (AD), respectively. These CADI-containing peptidomimetics stabilized the conformation and enhanced the potency of the cyclic RGD peptide and the cyclic KLVFF peptide.

Substitution Effects of Alkene Dipeptide Isosteres on Adjacent Peptide Bond Rotation

Alkene dipeptide isosteres (ADIs) are promising surrogates of peptide bonds that enhance the bioactive peptide resistance to enzymatic hydrolysis in medicinal chemistry. In this study, we investigated the substitution effects of an ADI on the energy barrier of cis-trans isomerization in the acetyl proline methyl ester (Ac-Pro-OMe) model. The (E)-alkene-type proline analog, which favors a cis-amide conformation, exhibits a lower rotational barrier than native Ac-Pro-OMe. A van't Hoff analysis suggests that the energy barrier is primarily reduced by enthalpic repulsion. It was concluded that although carbon-carbon double bonds and pyrrolidine rings individually increase the rigidity of the incorporation site, their combination can provide structural flexibility and disrupt bioactive conformations. This work provides new insights into ADI-based drug design.

Au(I)-Catalyzed Regioselective Hydrofluorination of Propargylamines Using Aqueous HF

Gold-catalyzed regioselective hydrofluorination of alkynes using aqueous HF has been achieved by employing an amide directing group. For both aryl- and alkyl-substituted propargylamines, the fluorination occurred at the site distal to the amino group.

Design and synthesis of efficient fluororethylene-peptidomimetic inhibitors of dipeptidyl peptidase III (DPP3)

Dipeptidyl peptidase III (DPP3) is a ubiquitously expressed zinc-dependent peptide cutting enzyme and selectively hydrolyses amide bonds to cleave N-terminal dipeptide fragments off of physiologically important oligopeptides. DPP3 has been found in a multitude of different types of cells and appears to be involved in various physiological processes (e.g. nociception, blood pressure control, protein turnover). Using the slowly converted peptide substrate tynorphin (VVYPW) as starting point, we have replaced the scissile bond with a fluoroethylene bioisostere to design ground state inhibitors, which led to the so far most effective peptide-based inhibitor of DPP3.

Chloroalkene dipeptide isosteres as peptidomimetics

To date various biologically active peptides have been discovered, characterized and modified for drug discovery. However, the utilization of peptides as therapeutics involves some limitation due to several factors, including low metabolic stability owing to proteolysis and non-specific interactions with multiple off-target molecules. Hence, the development of "peptidomimetics," in which a part or whole of a molecule is modified, is a desirable strategy to enhance the stability or bioactivity of peptide-based drugs. In this situation, we have designed and developed a synthetic method for chloroalkene dipeptide isosteres (CADIs), which involves replacement of an amide bond in peptides with a chloroalkene structure and are classified as peptidomimetics. By a developed synthetic method, an N-tert-butylsulfonyl protected CADI can be obtained utilizing diastereoselective allylic alkylation with organocopper reagents as a key reaction. This CADI can be transformed into an N-fluorenylmethoxycarbonyl protected CADI in short steps. In addition, CADIs are used in Fmoc-based solid-phase peptide synthesis and introduced into a bioactive peptide. Protocols for practical preparation of some CADIs and peptide mimetics containing a CADI are described as detailed recipes.

Intermolecular fluoroamination of allenes towards substituted vinyl fluorides

Allene difunctionalization: Selectfluor mediated intermolecular aminofluorination of allenes with triazole and tetrazole nucleophiles towards vinyl fluorides.

Computational assessment of thioether isosteres

Replacement of the sulfur atom in biologically active diaryl and heteroaryl thioethers (Ar-S-Ar', HAr-S-Ar, and HAr-S-HAr') with any of several one-atom or two-atom linkers can be expected to reduce the susceptibility of the analogue to metabolic oxidation, a well-documented problem for thioethers intended for medicinal chemistry applications. Ab initio calculations indicate how well various proposed thioether isosteric groups, including some new and unusual ones, may perform structurally and electronically in replacing the bridging sulfur atom. Four of these are calculationally evaluated as proposed substructures in Axitinib analogues. The predicted binding behavior of the latter within two different previously crystallographically characterized protein-Axitinib binding sites (VEGFR2 kinase and ABL1 T315I gatekeeper mutant kinase), and an assessment of their suitability and anticipated shortcomings, are presented.

Activation of C–F bonds α to C–C multiple bonds

A closer look is given to the successful approaches to the C(sp³)–F activation of benzylic, allylic, propargylic and allenylic fluorides.

Recent progress in the racemic and enantioselective synthesis of monofluoroalkene-based dipeptide isosteres

Monofluoroalkenes are fluorinated motifs that can be used to replace amide bonds. In order to be incorporated into peptides, it is normally necessary to first synthesize a dipeptide where the amide bond has been replaced with a monofluoroalkene. In that context, this review will present the racemic and enantioselective synthesis of monofluoroalkene-based dipeptide isosteres described since 2007. Some applications of those compounds will also be presented.

Synthesis of Gly-ψ[(Z)CF═CH]-Phe, a Fluoroalkene Dipeptide Isostere, and Its Incorporation into a Leu-enkephalin Peptidomimetic

A new Leu-enkephalin peptidomimetic designed to explore the hydrogen bond acceptor ability of the third peptide bond has been prepared and studied. This new analog is produced by replacing the third amide of Leu-enkephalin with a fluoroalkene. An efficient and innovative synthesis of the corresponding dipeptide surrogate Fmoc-Gly-ψ[(Z)CF═CH]-Phe-OH is described. The key step involves the alkylation of a tin dienolate from the less hindered face of its chiral sulfonamide auxiliary derived from camphor. Once its synthesis was complete, its incorporation into the peptidomimetic sequence was achieved on a solid support with chlorotrityl resin following the Fmoc strategy. The peptidomimetic was characterized using competition binding with [¹²⁵I]-deltorphin I on membrane extracts of HEK293 cells expressing the mouse delta opioid receptor (DOPr) and based on its abilities to inhibit the electrically induced contractions of the mouse vas deferens and to activate the ERK1/2 signaling pathway in DRGF11/DOPr-GFP cells. Together with our previous observations, our findings strongly suggest that the third amide bond of Leu-enkephalin primarily acts as a hydrogen bond acceptor in DOPr. Consequently, this amide bond can be successfully replaced by an ester, a thioamide, or a fluoroalkene without greatly impacting the binding or biological activity of the corresponding analogs. The lipophilicity (LogD_7.4) of the active analog was also measured. It appears that fluoroalkenes are almost as efficient at increasing the lipophilicity as normal alkenes.

Progress toward rationally designed small-molecule peptide and peptidomimetic CXCR4 antagonists

Over the last 5 years, X-ray structures of CXCR4 in complex with three different ligands (the small-molecule antagonist IT1t, the polypeptide antagonist CVX15 and the viral chemokine antagonist vMIP-II) have been released. In addition to the inherent scientific value of these specific X-ray structures, they provide a reliable structural foundation for studies of the molecular interactions between CXCR4 and its key peptide ligands (CXCL12 and HIV-1 gp120), and serve as valuable templates for further development of small-molecule CXCR4 antagonists with therapeutic potential. We here review recent computational studies of the molecular interactions between CXCR4 and its peptide ligands – based on the X-ray structures of CXCR4 – and the current status of small-molecule peptide and peptidomimetic CXCR4 antagonists.

Direct fluorination of styrenes

We have developed a practical method to synthesize fluorostyrene compounds. A mild and regioselective mono-fluorination reaction occurred smoothly for various di- and trisubstituted styrenes in the presence of RuCl3 and N-fluorobenzenesulfonimide (NFSI). A tandem alkyne hydroarylation-olefin fluorination reaction was also developed using an Au catalyst.

Introduction of fluorine and fluorine-containing functional groups

Over the past decade, the most significant, conceptual advances in the field of fluorination were enabled most prominently by organo- and transition-metal catalysis. The most challenging transformation remains the formation of the parent C-F bond, primarily as a consequence of the high hydration energy of fluoride, strong metal-fluorine bonds, and highly polarized bonds to fluorine. Most fluorination reactions still lack generality, predictability, and cost-efficiency. Despite all current limitations, modern fluorination methods have made fluorinated molecules more readily available than ever before and have begun to have an impact on research areas that do not require large amounts of material, such as drug discovery and positron emission tomography. This Review gives a brief summary of conventional fluorination reactions, including those reactions that introduce fluorinated functional groups, and focuses on modern developments in the field.

Stereoselective synthesis of mono-fluoroalkenes

Recent developments in the stereoselective synthesis of fluoroalkenes, which include hydrofluorination of alkyne, fluorination of alkenylmetal, condensation methods, dehydrofluorination of gem-difluoro compounds, and a cross-coupling reaction using fluorohaloalkenes or fluoroalkenylmetal, are described in this chapter.

Practical synthesis of fluorine-containing α- and β-amino acids: recipes from Kiev, Ukraine

Naturally occurring compounds containing a C-F bond are extremely rare; only a handful of fluorine-containing carboxylic acids have been described so far. By contrast, man-made fluorine-containing derivatives of all major classes of biologically important compounds are extremely promising medicinal targets used in the elucidation of biochemical, metabolic transformations and the development of new pharmaceuticals. Among the fluorine-containing derivatives of natural products, fluorinated analogs of amino acids are of particular interest and medicinal potential. This article presents a concise review of various synthetic methods, developed by the Kiev's school of bioorganic chemistry, for the preparation of fluorine-containing analogs of α- and β-amino acids, α-hydroxy acids, amines, as well as their phosphorus and sulfur-derived compounds, in enantiomerically pure form. One of the major methodological goals of the study was practicality, which is understood by us as stereochemical generality, operational convenience and synthetic affordance for each reaction step and isolation of the target products. The synthetic methods developed by our group can be roughly divided in two general categories: fluorine-adaptation of known synthetic approaches and discovery of new reactions. The former approach is most prominently represented by asymmetric homologation of nucleophilic glycine equivalents using fluorinated substrates via alkyl halide alkylations, aldol and Michael addition reactions. A plethora of discovered unexpected reaction outcomes, in particular stereochemical, are emphasized in this review and the particular role of fluorine, in altering the 'normal' reaction result, is explained. The latter direction is notably represented by the novel 1,3-proton shift reaction, a biomimetic reductive amination of fluorinated carbonyl compounds to the corresponding amines and amino acids, as well as the development of α-fluoroalkyl epoxides as true fluorinated synthons for generalized asymmetric synthesis of various biologically relevant compounds. Despite the highly anticipated potential of fluorine-containing amino compounds, their medicinal chemistry still remains underexplored. The major obstacle, in our opinion, is that these selectively fluorinated compounds are generally unavailable to the medicinal chemists for comprehensive, systematic study. We hope this review of synthetic methods will highlight and bring attention to particular types of fluorinated amino acids and related compounds readily available on a laboratory scale using methods developed by our group.

Enantioselective synthesis of α-fluoro-β(3)-amino esters: synthesis of enantiopure, orthogonally protected α-fluoro-β(3)-lysine

The scope of a tandem conjugate addition-fluorination sequence performed on α,β-unsaturated esters using the enantiopure lithium amide derived from (S)-N-benzyl-N-(α-methylbenzyl)amine, and the electrophilic fluorinating agent N-fluorobenzenesulfonimide has been investigated. Using this method, α-fluoro-β(3)-amino esters can be obtained in up to quantitative yield and 80:20 to >99:1 dr. This simple methodology does not rely on the use of α-amino acids from the chiral pool and thus provides the potential for the preparation of enantiopure α-fluoro-β(3)-amino acids with a wide variety of side chains. Its utility was demonstrated through the synthesis of orthogonally protected (2S,3S)-α-fluoro-β(3)-lysine.

A general preparation of (Z)-1-fluorostilbene derivatives for the design of conformationally restricted peptidomimetics

The preparation of (Z)-1-fluoro-2-bromostyrenes provides a general route for the formation of (Z)-1-fluorostilbene derivatives as configurationally stable spacial linkers for the design of conformationally restricted peptidomimetics. Palladium-catalyzed aryl Suzuki and Stille cross-coupling reactions have been surveyed to proceed with complete retention of fluoroalkene geometry, and permit the direct incorporation of a variety of aryl and heteroaromatic substituents.

Synthesis and biological evaluation of selective CXCR4 antagonists containing alkene dipeptide isosteres

A set of cyclic peptide analogues of a selective CXCR4 antagonist FC131 [cyclo(-d-Tyr-Arg-Arg-Nal-Gly-)] were synthesized and bioevaluated. Using (E)-alkene and (Z)-fluoroalkene dipeptide isosteres for Arg-Arg and Arg-Nal substructures, indispensable or the partial contribution of the two peptide bonds to the CXCR4 antagonism and anti-HIV activity was demonstrated. FC131 and the analogues were shown to selectively inhibit SDF-1 binding to CXCR4, whereas no inhibition of binding of SDF-1 to CXCR7 was observed.

Regio- and stereoselective synthesis of fluoroalkenes by directed Au(I) catalysis

Au-catalyzed hydrofluorination reactions of a range of functionalized alkynes are reported. In the presence of an appropriate directing group, localized with particular spacing from the pendant alkyne, regioselective and predictable conversion of the alkyne to the Z-vinyl fluoride may be achieved. In selected cases, yields and selectivities are excellent. Additional experiments with two directing groups installed have established some initial principles with respect to a hierarchy of directing groups and their capacity for influencing hydrofluorination regioselectivity.

Amino acid-based synthesis of trifluoromethylalkene dipeptide isosteres by alcohol-assisted nucleophilic trifluoromethylation and organozinc-copper-mediated S(N)2' alkylation

A novel synthetic approach to Xaa-Yaa-type (Z)-trifluoromethylalkene dipeptide isostere (CF(3)-ADI) has been developed. Starting from readily available l-phenylalanine and l-alanine, several CF(3)-ADIs were obtained through nucleophilic trifluoromethylation of gamma-keto esters and S(N)2' alkylation of trifluoromethylated mesylates. The influence of a trifluoromethyl group on the diastereoselectivity of the S(N)2' reaction is also discussed.

Synthesis of amide-type fluoroalkene dipeptide isosteres by an intramolecular redox reaction

We previously achieved NHC-mediated preparation of ester-type fluoroalkene dipeptide isosteres (ES-FADIs, 4) by an intramolecular redox reaction. In the present study, a cyanide ion-mediated reaction was successfully applied to the conversions of gamma,gamma-difluoro-alpha,beta-enoylsilane 1 or 2 to amide-type fluoroalkene isosteres (AM-FADIs, 5 or 6). The use of catalytic cyanide ion allowed synthesis of chiral auxiliary incorporated FADI 15b which was then subjected to a diastereoselective alpha-alkylation reaction to yield alpha-substituted FADIs 17. Furthermore, the presented amidation protocol was used for straightforward incorporation of FADI into peptidyl resin.

Peptide bond mimicry by (E)-alkene and (Z)-fluoroalkene peptide isosteres: synthesis and bioevaluation of alpha-helical anti-HIV peptide analogues

The alpha-helix structures of the anti-HIV fusion inhibitory peptides are stabilized by the amino acid sequence and by intrachain hydrogen bonds. The study of peptide analogues using (E)-alkene and (Z)-fluoroalkene dipeptide isosteres demonstrated the substantial, yet position-dependent, contribution of hydrogen bonds to the alpha-helix stability and anti-HIV bioactivity.

Palladium-catalyzed substitution of allylic fluorides

As unusual substrates for the Tsuji-Trost allylation reaction, allylic fluorides are responsive to palladium-catalyzed substitution. Their activity towards this reaction fits in the series OCO(2)Me>OBz>>F>>OAc. The classic stereoretention mechanism that involves sequential inversions does not operate in this case. Several distinct cases are considered.