Solid-Phase Total Synthesis of Yaku'amide B Enabled by Traceless Staudinger Ligation

What is the future of click chemistry in drug discovery and development?

INTRODUCTION

The concept of click chemistry was introduced in 2001 as an effective, efficient, and sustainable approach to making functional groups harnessing the thermodynamic properties of a set of known chemical reactions that are based on nature. Some of the most common examples include reactions that produce 1,2,3-triazoles, which have been used with great success in drug discovery and development, and in chemical biology. The reactions unite two molecules quickly and irreversibly, and the reactions can be performed inside living cells, without harming the cell.

AREAS COVERED

The main focus of this perspective is the future of click chemistry in drug discovery and development, exemplified by novel click chemistry approaches and other aspects of the drug development enterprise, like SPAAC and analogous techniques, PROTACs, as well as diversity-oriented click chemistry.

EXPERT OPINION

Drug discovery and development has benefited enormously from the amazing advances that have been made in the field of click chemistry since 2001. The methods most likely to have the most future applications include metal-catalyzed azide-alkyne cycloadditions giving 1,2,3-triazoles, SPAAC for medical diagnostics and vaccine development, other congeners, Sulfur-Fluoride Exchange (SuFEx) and Diversity-Oriented Clicking (DOC), a concept with diverse molecular methodology with the potential for obtaining extensive molecular diversity.

A Brief Guide to Preparing a Peptide-Drug Conjugate

Peptide-drug conjugates (PDCs) have recently emerged as interesting hybrid constructs not only for targeted therapy, but also for the early diagnosis of different pathologies. In most cases, the crucial step in the PDC synthesis is the final conjugation step, where a specific drug is bound to a particular peptide-/peptidomimetic-targeting unit. Thus, this concept paper aims to give a short guide to determining the finest conjugation reaction, by considering in particular the reaction conditions, the stability of the linker and the major pros and cons of each reaction. Based on the recent PDCs reported in literature, the most common and efficient conjugation methods will be systematically presented and compared, generating a short guide to consult while planning the synthesis of a novel peptide-drug conjugate.

Synthesis and Studies of Bulky Cycloalkyl α,β-Dehydroamino Acids that Enhance Proteolytic Stability

Three new bulky cycloalkyl α,β-dehydroamino acids (ΔAAs) have been designed and synthesized. Each residue enhances the rigidity of model peptides and their stability to proteolysis, with larger ring sizes exhibiting greater effects. Peptides containing bulky cycloalkyl ΔAAs are inert to conjugate addition by a nucleophilic thiol. The results suggest that these residues will be effective tools for improving the proteolytic stability of bioactive peptides.

[Total Synthesis and Functional Analysis of Complex Peptidic Natural Products and Their Artificial Analogues]

This review focuses on a new solid-phase synthetic strategy for an anticancer natural product yaku'amide B (1) and its target identification and structure-function relationship study using synthetic analogues and probes. To realize the Fmoc-based solid-phase synthesis of 1, we developed new synthetic methods for enamide formation. Namely, modified traceless Staudinger ligation using alkenyl azides and newly designed phosphinophenol esters enabled stereoselective construction of the (E)- and (Z)-ΔIle moieties. Furthermore, resin-cleavage and C-terminus modification were simultaneously achieved with an ester-amide exchange reaction using C-terminal amine and AlMe₃, which successfully afforded 1 via a full solid-phase route. The developed strategy was applied to the construction of seven E/Z isomers of 1. In the target identification of 1, fluorescent imaging study and affinity pull-down assay using the synthetic probes revealed that 1 exerts potent cytostatic activity by binding to subunits α and β of mitochondrial F_oF₁-ATP synthase. On the basis of the mode of action of 1, we conducted biological evaluation of the seven E/Z-isomers of 1. Assessment of growth inhibition activity and the effect on F_oF₁-ATP synthase indicates that the E/Z-stereochemistry of the three ΔIle residues controls the magnitude of biological functions of 1.

Synthesis and evaluation of potent yaku'amide A analogs

Two full-length analogs of the anticancer peptide yaku'amide A (1a) and four partial structures have been synthesized. These analogs were identified by computational studies in which the three E- and Z-ΔIle residues of the natural product were replaced by the more accessible dehydroamino acids ΔVal and ΔEnv. Of the eight possible analogs, modeling showed that the targeted structures 2a and 2b most closely resembled the three-dimensional structure of 1a. Synthesis of 2a and 2b followed a convergent route that was streamlined by the absence of ΔIle in the targets. Screening of the compounds against various cancer cell lines revealed that 2a and 2b mimic the potent anticancer activity of 1a, thereby validating the computational studies.

Simplified full-length analogs of yaku'amide A were designed with the aid of computations and then synthesized. The analog that was predicted to most closely resemble the structure of the natural product mimicked its anticancer activity.

Generation and Biological Evaluation of Degraded Derivatives of the Three E/Z-Isomers of Yaku'amide B

Potently cytostatic yaku'amide B (1) is a highly unsaturated linear tridecapeptide. During our synthetic studies of the E/Z-isomers of the α,β-dehydroisoleucines of 1, an unexpected retro-aldol reaction proceeded to transform E/Z-isomers 2, 3, and 4 into 2a, 3a, and 4a/4b, respectively. Compounds 2a, 3a, and 4a have a glycine at residue-1 instead of β-hydroxyisoleucine, and the β-hydroxyvaline at residue-8 in 4a is further replaced by glycine in 4b. Evaluation of the growth inhibition activities against MCF-7 cells revealed that 4b was approximately 10-fold weaker than the equipotent 2-4 and 2a-4a, demonstrating the biological importance of a bulky side chain at residue-8.

Bioorthogonal Reactions of Triarylphosphines and Related Analogues

Bioorthogonal phosphines were introduced in the context of the Staudinger ligation over 20 years ago. Since that time, phosphine probes have been used in myriad applications to tag azide-functionalized biomolecules. The Staudinger ligation also paved the way for the development of other phosphorus-based chemistries, many of which are widely employed in biological experiments. Several reviews have highlighted early achievements in the design and application of bioorthogonal phosphines. This review summarizes more recent advances in the field. We discuss innovations in classic Staudinger-like transformations that have enabled new biological pursuits. We also highlight relative newcomers to the bioorthogonal stage, including the cyclopropenone-phosphine ligation and the phospha-Michael reaction. The review concludes with chemoselective reactions involving phosphite and phosphonite ligations. For each transformation, we describe the overall mechanism and scope. We also showcase efforts to fine-tune the reagents for specific functions. We further describe recent applications of the chemistries in biological settings. Collectively, these examples underscore the versatility and breadth of bioorthogonal phosphine reagents.

Dehydropeptide Supramolecular Hydrogels and Nanostructures as Potential Peptidomimetic Biomedical Materials

Supramolecular peptide hydrogels are gaining increased attention, owing to their potential in a variety of biomedical applications. Their physical properties are similar to those of the extracellular matrix (ECM), which is key to their applications in the cell culture of specialized cells, tissue engineering, skin regeneration, and wound healing. The structure of these hydrogels usually consists of a di- or tripeptide capped on the N-terminus with a hydrophobic aromatic group, such as Fmoc or naphthalene. Although these peptide conjugates can offer advantages over other types of gelators such as cross-linked polymers, they usually possess the limitation of being particularly sensitive to proteolysis by endogenous proteases. One of the strategies reported that can overcome this barrier is to use a peptidomimetic strategy, in which natural amino acids are switched for non-proteinogenic analogues, such as D-amino acids, β-amino acids, or dehydroamino acids. Such peptides usually possess much greater resistance to enzymatic hydrolysis. Peptides containing dehydroamino acids, i.e., dehydropeptides, are particularly interesting, as the presence of the double bond also introduces a conformational restraint to the peptide backbone, resulting in (often predictable) changes to the secondary structure of the peptide. This review focuses on peptide hydrogels and related nanostructures, where α,β-didehydro-α-amino acids have been successfully incorporated into the structure of peptide hydrogelators, and the resulting properties are discussed in terms of their potential biomedical applications. Where appropriate, their properties are compared with those of the corresponding peptide hydrogelator composed of canonical amino acids. In a wider context, we consider the presence of dehydroamino acids in natural compounds and medicinally important compounds as well as their limitations, and we consider some of the synthetic strategies for obtaining dehydropeptides. Finally, we consider the future direction for this research area.

Convergent Total Synthesis of Yaku'amide A

Total synthesis of the anticancer peptide natural product yaku'amide A is reported. Its β-tert-hydroxy amino acids were prepared by regioselective aminohydroxylation involving a chiral mesyloxycarbamate reagent. Stereospecific construction of the E- and Z-ΔIle residues was accomplished through a one-pot reaction featuring anti dehydration, azide reduction, and O→N acyl transfer. Alkene isomerization was negligible during this process. These methods enabled a highly convergent and efficient synthetic route to the natural product.

Sustainable Triazine-Based Dehydro-Condensation Agents for Amide Synthesis

Conventional methods employed today for the synthesis of amides often lack of economic and environmental sustainability. Triazine-derived quaternary ammonium salts, e.g., 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM(Cl)), emerged as promising dehydro-condensation agents for amide synthesis, although suffering of limited stability and high costs. In the present work, a simple protocol for the synthesis of amides mediated by 2-chloro-4,6-dimethoxy-1,3,5-triazine (CDMT) and a tert-amine has been described and data are compared to DMTMM(Cl) and other CDMT-derived quaternary ammonium salts (DMT-Ams(X), X: Cl- or ClO4-). Different tert-amines (Ams) were tested for the synthesis of various DMT-Ams(Cl), but only DMTMM(Cl) could be isolated and employed for dehydro-condensation reactions, while all CDMT/tert-amine systems tested were efficient as dehydro-condensation agents. Interestingly, in best reaction conditions, CDMT and 1,4-dimethylpiperazine gave N-phenethyl benzamide in 93% yield in 15 min, with up to half the amount of tert-amine consumption. The efficiency of CDMT/tert-amine was further compared to more stable triazine quaternary ammonium salts having a perchlorate counter anion (DMT-Ams(ClO4)). Overall CDMT/tert-amine systems appear to be a viable and more economical alternative to most dehydro-condensation agents employed today.

Taming the reactivity of alkyl azides by intramolecular hydrogen bonding: site-selective conjugation of unhindered diazides

The intramolecular hydrogen bonding in the α-azido secondary acetamides (α-AzSAs) enabled site-selective integration onto the diazide modular hubs even without steric hindrance.

Synthesis of Azido Acids and Their Application in the Preparation of Complex Peptides

Azido acids are important synthons for the synthesis of complex peptides. As a protecting group, the azide moiety is atom-efficient, easy to install and can be reduced in the presence of many other protecting groups, making it ideal for the synthesis of branched and/or cyclic peptides. α-Azido acids are less bulky than urethane-protected counterparts and react more effectively in coupling reactions of difficult-to-form peptide and ester bonds. Azido acids can also be used to form azoles on complex intermediates. This review covers the synthesis of azido acids and their application to the total synthesis of complex peptide natural products.

1 Introduction

2 Synthesis of α-Azido Acids

2.1 From α-Amino Acids or Esters

2.2 Via α-Substitution

2.3 Via Electrophilic Azidation

2.4 Via Condensation of N-2-Azidoacetyl-4-Phenylthiazolidin- 2-Thi one Enolates with Aldehydes and Acetals

2.5 Synthesis of α,β-Unsaturated α-Azido Acids and Esters

3 Synthesis of β-Azido Acids

3.1 Preparation of Azidoalanine and 3-Azido-2-aminobutanoic Acids

3.2 General Approaches to Preparing β-Azido Acids Other Than Azi doalanine­ and AABA

4 Azido Acids in Total Synthesis

4.1 α-Azido Acids

4.2 β-Azido Acids and Azido Acids Containing an Azide on the Side Chain

5 Conclusions

Proapoptotic Peptide Brush Polymer Nanoparticles via Photoinitiated Polymerization-Induced Self-Assembly

Herein, we report the photoinitiated polymerization-induced self-assembly (photo-PISA) of spherical micelles consisting of proapoptotic peptide-polymer amphiphiles. The one-pot synthetic approach yielded micellar nanoparticles at high concentrations and at scale (150 mg mL-1 ) with tunable peptide loadings up to 48 wt. %. The size of the micellar nanoparticles was tuned by varying the lengths of hydrophobic and hydrophilic building blocks. Critically, the peptide-functionalized nanoparticles imbued the proapoptotic "KLA" peptides (amino acid sequence: KLAKLAKKLAKLAK) with two key properties otherwise not inherent to the sequence: 1) proteolytic resistance compared to the oligopeptide alone; 2) significantly enhanced cell uptake by multivalent display of KLA peptide brushes. The result was demonstrated improved apoptosis efficiency in HeLa cells. These results highlight the potential of photo-PISA in the large-scale synthesis of functional, proteolytically resistant peptide-polymer conjugates for intracellular delivery.

Highly Sensitive Labeling Reagents for Scarce Natural Products

Scarce natural products that possess unique biological activities have been ideal drug leads for decades. However, their identification and structural determinations are problematic owing to sample amount limitation. Inspired by an extremely rare natural product yaku'amide B (10), highly sensitive labeling reagents that would be powerful tools for scarce natural product chemistry were designed and synthesized in this study. By fusion with the key structural motif for the structural revision of 10, the detection sensitivities of amino acid labeling reagents were drastically enhanced in LC-MS analysis. These advanced labeling reagents enabled the detection of infinitesimal amounts of amino acids and peptide hydrolysates. This sensitivity-enhancement design concept was also applicable to reagents for labeling saccharides and reactivity-guided isolation of electrophilic natural products. Details of these reagents, including their practical preparations and extended applications, are also provided.