Synthesis of C-2 Arylated Tryptophan Amino Acids and Related Compounds through Palladium-Catalyzed C–H Activation

Fluorescent coumarin-alkynes for labeling of amino acids and peptides via manganese(I)-catalyzed C-H alkenylation

The late-stage fluorescent labeling of structurally complex peptides bears immense potential for molecular imaging. Herein, we report on a manganese(I)-catalyzed peptide C-H alkenylation under exceedingly mild conditions with natural fluorophores as coumarin- and chromone-derivatives. The robustness and efficiency of the manganese(I) catalysis regime was reflected by a broad functional group tolerance and low catalyst loading in a resource- and atom-economical fashion.

Pd-Catalyzed Picolinamide-Directed Late-Stage Chalcogenation of Tryptophan-Containing Peptides

This report describes the Pd-catalyzed late-stage chalcogenation of tryptophan-containing peptides with disulfides/diselenides in moderate to good yields. It comprises broad substrate scope, functional group diversity, late-stage modification of drug molecules, and various valuable synthetic transformations, including room temperature easy removal of the picolinamide auxiliary, which could be applicable to tune the structure and function of peptides.

C-2 Thiophenyl Tryptophan Trimers Inhibit Cellular Entry of SARS-CoV-2 through Interaction with the Viral Spike (S) Protein

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, by infecting cells via the interaction of its spike protein (S) with the primary cell receptor angiotensin-converting enzyme (ACE2). To search for inhibitors of this key step in viral infection, we screened an in-house library of multivalent tryptophan derivatives. Using VSV-S pseudoparticles, we identified compound 2 as a potent entry inhibitor lacking cellular toxicity. Chemical optimization of 2 rendered compounds 63 and 65, which also potently inhibited genuine SARS-CoV-2 cell entry. Thermofluor and microscale thermophoresis studies revealed their binding to S and to its isolated receptor binding domain (RBD), interfering with the interaction with ACE2. High-resolution cryoelectron microscopy structure of S, free or bound to 2, shed light on cell entry inhibition mechanisms by these compounds. Overall, this work identifies and characterizes a new class of SARS-CoV-2 entry inhibitors with clear potential for preventing and/or fighting COVID-19.

Site-Selective Modification of Peptides via Late-Stage Pd-Catalyzed Tandem Reaction of Phenylalanine with Benzoquinone

An efficient and straightforward approach for site-selective functionalization of phenylalanine and phenylalanine-containing peptide via a Pd-catalyzed tandem reaction has been developed. The robust method underwent dual C-H activation, including C-C coupling with benzoquinone and intramolecular C-N cyclization, providing a feasible and rapid synthetic route to incorporate 4-benzoquinone-indoline fragments into peptides.

Microwave-accelerated cross-dehydrogenative-coupling (CDC) of N-(quinolin-8-yl)amides with acetone/acetonitrile under metal-free conditions

A highly selective remote C(sp³)-H acetonation of N-(quinolin-8-yl)amide scaffolds at the C5-position under microwave irradiation has been developed. In the absence of a transition-metal-catalyst, benzoyl peroxide (BPO)-promoted cross-dehydrogenation coupling (CDC) of N-(quinolin-8-yl)amides with acetone/acetonitrile occurred smoothly to generate the corresponding 5-acetonated/acetonitriled N-(quinolin-8-yl)amides in good yields. The transformation is operationally simple, rapid, easily scaled-up to the gram scale, and shows a broad substrate scope.

Late-stage peptide labeling with near-infrared fluorogenic nitrobenzodiazoles by manganese-catalyzed C-H activation

Late-stage diversification of structurally complex amino acids and peptides provides tremendous potential for drug discovery and molecular imaging. Specifically, labeling peptides with fluorescent tags is one of the most important methods for visualizing their mode of operation. Despite major recent advances in the field, direct molecular peptide labeling by C-H activation is largely limited to dyes with relatively short emission wavelengths, leading to high background signals and poor signal-to-noise ratios. In sharp contrast, here we report on the fluorescent labeling of peptides catalyzed by non-toxic manganese(i) via C(sp²)-H alkenylation in chemo- and site-selective manners, providing modular access to novel near-infrared (NIR) nitrobenzodiazole-based peptide fluorogenic probes.

Late-stage C-H Functionalization of Tryptophan-Containing Peptides with Thianthrenium Salts: Conjugation and Ligation

Bioorthogonal late-stage diversification of structurally complex peptides bears enormous potential for drug discovery and molecular imaging, among other applications. Herein, we report on a palladium-catalyzed C-H arylation of tryptophan-containing peptides with readily accessible and modular arylthianthrenium salts. Under exceedingly mild reaction conditions, the late-stage diversification of structurally complex peptides was accomplished. The tunability and ease of preparation of arylthianthrenium salts allowed the expedient stitching of tryptophan-containing peptides with drug, natural product, and peptidic scaffolds by forging sterically congested biaryl linkages. The robustness of the palladium catalysis regime was reflected by the full tolerance of a plethora of sensitive and coordinating functional groups. Hence, our manifold enabled efficient access to highly decorated, labelled, conjugated, and ligated linear and cyclic peptides.

Insertion of an Amphipathic Linker in a Tetrapodal Tryptophan Derivative Leads to a Novel and Highly Potent Entry Inhibitor of Enterovirus A71 Clinical Isolates

AL-471, the leading exponent of a class of potent HIV and enterovirus A71 (EV-A71) entry inhibitors discovered in our research group, contains four l-tryptophan (Trp) units bearing an aromatic isophthalic acid directly attached to the C2 position of each indole ring. Starting from AL-471, we (i) replaced l-Trp with d-Trp, (ii) inserted a flexible linker between C2 and the isophthalic acid, and (iii) substituted a nonaromatic carboxylic acid for the terminal isophthalic acid. Truncated analogues lacking the Trp motif were also synthesized. Our findings indicate that the antiviral activity seems to be largely independent of the stereochemistry (l- or d-) of the Trp fragment and also that both the Trp unit and the distal isophthalic moiety are essential for antiviral activity. The most potent derivative, 23 (AL-534), with the C2 shortest alkyl urea linkage (three methylenes), showed subnanomolar potency against different EV-71 clinical isolates. This finding was only observed before with the early dendrimer prototype AL-385 (12 l-Trp units) but remained unprecedented for the reduced-size prototype AL-471. Molecular modeling showed the feasibility of high-affinity binding of the novel l-Trp-decorated branches of 23 (AL-534) to an alternative site on the VP1 protein that harbors significant sequence variation among EV-71 strains.

Temperature-induced formation of Pd nanoparticles in heterogeneous nanobiohybrids: application in C-H activation catalysis

The effect of the temperature in the synthesis of Pd nanoparticles in the metal-enzyme biohybrids is evaluated. The effect on the formation, size, and morphology of nanoparticles was evaluated using C. antarctica B lipase as the protein scaffold. XRD analyses confirmed the formation of crystalline Pd(0) as the metal species in all cases. TEM analyses revealed spherical crystalline nanoparticles with average diameter size from 2 nm at 4 °C synthesis to 10 nm obtained at 50 °C synthesis. The thermal phenomenon was also critical in the final hybrid formation using more complex enzymes, where the relation of the protein structure and temperature and the influence of the latter has been demonstrated to be critical in the reducing efficiency of the enzyme in the final Pd nanoparticle formation, in the metal species, or even in the final size of the nanoparticles. Different Pd biohybrids were evaluated as catalysts in the C-H activation of protected l-tryptophan under mild conditions. Pd@CALB4 showed the best results, with >99% conversion for C-2 arylation in methanol at room temperature with a TOF value of 64 min^-1, being 2 or 4 times higher than that of the other synthesized hybrids. This catalyst showed a very high stability and recyclability, maintaining >95% activity after three cycles of use.

Synthesis of Indoles via Domino Reactions of 2-Methoxytoluene and Nitriles

2-Arylindoles are privileged structures widely present in biologically active molecules. New sustainable synthetic routes toward their synthesis are, therefore, in high demand. Herein, a mixed base-promoted benzylic C-H deprotonation of commercially available ortho-anisoles, addition of the resulting anion to benzonitriles, and S_NAr to displace the methoxy group provide indoles. A diverse array of 2-arylindoles is prepared with good yields (>30 examples, yields up to 99%) without added transition metal catalysts.

Pd-Catalyzed Cross-Couplings: On the Importance of the Catalyst Quantity Descriptors, mol % and ppm

This Review examines parts per million (ppm) palladium concentrations in catalytic cross-coupling reactions and their relationship with mole percentage (mol %). Most studies in catalytic cross-coupling chemistry have historically focused on the concentration ratio between (pre)catalyst and the limiting reagent (substrate), expressed as mol %. Several recent papers have outlined the use of “ppm level” palladium as an alternative means of describing catalytic cross-coupling reaction systems. This led us to delve deeper into the literature to assess whether “ppm level” palladium is a practically useful descriptor of catalyst quantities in palladium-catalyzed cross-coupling reactions. Indeed, we conjectured that many reactions could, unknowingly, have employed low “ppm levels” of palladium (pre)catalyst, and generally, what would the spread of ppm palladium look like across a selection of studies reported across the vast array of the cross-coupling chemistry literature. In a few selected examples, we have examined other metal catalyst systems for comparison with palladium.

Amine-Directed Palladium-Catalyzed C-H Halogenation of Phenylalanine Derivatives

An efficient primary-amine-directed, palladium-catalyzed C-H halogenation (X=I, Br, Cl) of phenylalanine derivatives is reported on a range of quaternary amino acid (AA) derivatives thanks to suitable conditions employing trifluoroacetic acid as additive. The extension of this original native functionality-directed ortho-selective halogenation was even demonstrated with the more challenging native phenylalanine as tertiary AA.

Palladium-Catalyzed Direct C2-Biarylation of Indoles

Biaryl and indole units are important structural motifs in several bioactive molecules and functional materials. We have accomplished straightforward access to C2-biarylated indole derivatives through palladium-catalyzed C-H activation strategy with a broad range of substrate scope in yields of 24 to 92%. Besides, the UV/visible absorption and fluorescence properties of the ensuing products were explored. The calculated higher dihedral angle and rotational barrier values for the selected C2-biarylated indoles show that these compounds may display atropisomerism at room temperature.

Direct C4-Acetoxylation of Tryptophan and Tryptophan-Containing Peptides via Palladium(II)-Catalyzed C-H Activation

An efficient regioselective palladium(II)-catalyzed C(sp2)-H 4-acetoxylation of tryptophan and tryptophan-containing peptides is described. This transformation achieves the direct construction of C-O bonds at the tryptophan C4-position and features good functional group tolerance. The 4-hydroxyl compound was obtained by removing acetyl after C4-acetoxylation of tryptophan derivatives and tryptophan-containing dipeptides. This method provides a novel strategy for the synthesis of 4-substituted tryptophan derivatives and modification of tryptophan-containing peptides.

Late-stage stitching enabled by manganese-catalyzed C─H activation: Peptide ligation and access to cyclopeptides

Bioorthogonal late-stage diversification of structurally complex peptides bears enormous potential for drug discovery and molecular imaging. Despite major accomplishments, these strategies heavily rely on noble-metal catalysis. Herein, we report on a manganese(I)-catalyzed peptide C─H hydroarylation that enabled the stitching of peptidic and sugar fragments, under exceedingly mild and racemization-free conditions. This convergent approach represents an atom-economical alternative to traditional iterative peptide synthesis. The robustness of the manganese(I) catalysis regime is reflected by the full tolerance of a plethora of sensitive functional groups. Our strategy enabled an expedient access to challenging cyclic peptides by a modular late-stage macrocyclization of structurally complex peptides.

nSite-Selective, Chemical Modification of Protein at Aromatic Side Chain and Their Emergent Applications

Site-selective chemical modification of protein side chain has probed enormous opportunities in the fundamental understanding of cellular biology and therapeutic applications. Primarily, in the field of biopharmaceutical where formulation of bioconjugates is found to be potential medicine than an individual constituent. In this regard, Lysine and Cysteine are the most widely used endogenous amino acid for these purposes. Recently, the aromatic side chain residues (Trp, Tyr, and His) that are low abundant in protein have gained more attention in therapeutic applications due to their advantages of chemical reactivity and specificity. This review discusses the site-selective bioconjugation methods for aromatic side chains (Trp, Tyr and His) and highlights the developed strategies in the last three years, along with their applications. Also, the review highlights the prevalent methods published earlier. We have examined that metal-catalyzed and photocatalytic reactions are gaining more attention for bioconjugation, though their practical operation is under development. The review has been summarized with the future perspective of protein and peptide conjugations contemplating therapeutic applications and challenges.

Transition metal-catalyzed C–H functionalizations of indoles

This review summarises a wide range of transformations on the indole skeleton, including arylation, alkenylation, alkynylation, acylation, nitration, borylation, and amidation, using transition-metal catalyzed C–H functionalization as the key step.

Late-Stage Diversification of Tryptophan-Derived Biomolecules

Pd-mediated reactions have emerged as a powerful tool for the site-selective and bioorthogonal late-stage diversification of amino acids, peptides and related compounds. Indole moieties of tryptophan derivatives are susceptible to C2 H-activation, whereas halogenated aromatic amino acids such as halophenylalanines or halotryptophans provide a broad spectrum of different functionalisations. The compatibility of transition-metal-catalysed cross-couplings with functional groups in peptides, other biologically active compounds and even proteins has been demonstrated. This Review primarily compiles the application of different cross-coupling reactions to modify halotryptophans, halotryptophan containing peptides or halogenated, biologically active compounds derived from tryptophan. Modern approaches use regio- and stereoselective biocatalytic strategies to generate halotryptophans and derivatives on a preparative scale. The combination of bio- and chemocatalysis in cascade reactions is given by the biocompatibility and bioorthogonality of Pd-mediated reactions.

Late-stage C(sp2)-H and C(sp3)-H glycosylation of C-aryl/alkyl glycopeptides: mechanistic insights and fluorescence labeling

C(sp³)–H and C(sp²)–H glycosylations of structurally complex amino acids and peptides were accomplished through the assistance of triazole peptide-isosteres. The palladium-catalyzed peptide–saccharide conjugation provided modular access to structurally complex C-alkyl glycoamino acids, glycopeptides and C-aryl glycosides, while enabling the assembly of fluorescent-labeled glycoamino acids. The C–H activation approach represents an expedient and efficient strategy for peptide late-stage diversification in a programmable as well as chemo-, regio-, and diastereo-selective fashion.

C–H glycosylations of complex amino acids and peptides were accomplished through the assistance of triazole peptide-isosteres. The palladium-catalyzed glycosylation provided access to complex C-glycosides and fluorescent-labeled glycoamino acids.

Asymmetric N-aminoalkylation of 3-substituted indoles by N-protected N,O-acetals: an access to chiral propargyl aminals

A direct enantioselective N1 aminoalkylation of 3-substituted indoles is efficiently catalyzed by a phosphoric acid catalyst under mild conditions, which could be applied to the modification of tryptophan containing oligopeptides.

Scaffold Simplification Strategy Leads to a Novel Generation of Dual Human Immunodeficiency Virus and Enterovirus-A71 Entry Inhibitors

Currently, there are only three FDA-approved drugs that inhibit human immunodeficiency virus (HIV) entry-fusion into host cells. The situation is even worse for enterovirus EV71 infection for which no antiviral therapies are available. We describe here the discovery of potent entry dual inhibitors of HIV and EV71. These compounds contain in their structure three or four tryptophan (Trp) residues linked to a central scaffold. Critical for anti-HIV/EV71 activity is the presence of extra phenyl rings, bearing one or two carboxylates, at the C2 position of the indole ring of each Trp residue. The most potent derivatives, 22 and 30, inhibit early steps of the replicative cycles of HIV-1 and EV-A71 by interacting with their respective viral surfaces (glycoprotein gp120 of HIV and the fivefold axis of the EV-A71 capsid). The high potency, low toxicity, facile chemical synthesis, and great opportunities for chemical optimization make them useful prototypes for future medicinal chemistry studies.

Fluorogenic Trp(redBODIPY) cyclopeptide targeting keratin 1 for imaging of aggressive carcinomas

Keratin 1 (KRT1) is overexpressed in squamous carcinomas and associated with aggressive pathologies in breast cancer. Herein we report the design and preparation of the first Trp-based red fluorogenic amino acid, which is synthetically accessible in a few steps and displays excellent photophysical properties, and its application in a minimally-disruptive labelling strategy to prepare a new fluorogenic cyclopeptide for imaging of KRT1+ cells in whole intact tumour tissues.

Construction of Spirocyclic Tetrahydro-β-carbolines via Cross-Annulation of Phenols with Tryptamines in Water

Phenols are readily available by degradation of lignin resource. Palladium-catalyzed conversion of phenols to tetrahydro-β-carboline skeletons bearing a spirocycle at the C-1 position in water is reported. Various substituted phenols are successfully cross-annulated with different tryptamines via sequential C(Ar)-O bond cleavage of phenols, C-H bond activation of tryptamines, and C-N/C-C bond formations. This method provides a new protocol of converting lignin phenols into high-value-added compounds, such as natural product Komavine.

Approaches to Obtaining Fluorinated α-Amino Acids

Fluorine does not belong to the pool of chemical elements that nature uses to build organic matter. However, chemists have exploited the unique properties of fluorine and produced countless fluoro-organic compounds without which our everyday lives would be unimaginable. The incorporation of fluorine into amino acids established a completely new class of amino acids and their properties, and those of the biopolymers constructed from them are extremely interesting. Increasing interest in this class of amino acids caused the demand for robust and stereoselective synthetic protocols that enable straightforward access to these building blocks. Herein, we present a comprehensive account of the literature in this field going back to 1995. We place special emphasis on a particular fluorination strategy. The four main sections describe fluorinated versions of alkyl, cyclic, aromatic amino acids, and also nickel-complexes to access them. We progress by one carbon unit increments. Special cases of amino acids for which there is no natural counterpart are described at the end of each section. Synthetic access to each of the amino acids is summarized in form of a table at the end of this article with the aim to make the information easily accessible to the reader.

Late-Stage Diversification through Manganese-Catalyzed C-H Activation: Access to Acyclic, Hybrid, and Stapled Peptides

Bioorthogonal C-H allylation with ample scope was accomplished through a versatile manganese(I)-catalyzed C-H activation for the late-stage diversification of structurally complex peptides. The unique robustness of the manganese(I) catalysis manifold was reflected by full tolerance of sensitive functional groups, such as iodides, esters, amides, and OH-free hydroxy groups, thereby setting the stage for the racemization-free synthesis of C-H fused peptide hybrids featuring steroids, drug molecules, natural products, nucleobases, and saccharides.

Site-selective modification of tryptophan and protein tryptophan residues through PdNP bionanohybrid-catalysed C–H activation in aqueous media

PdNP bionanohybrid catalyzed selective C–H bond arylation of tryptophan residues in proteins in aqueous media at room temperature.

Homogeneous Catalysis: A Powerful Technology for the Modification of Important Biomolecules

Homogeneous catalysis plays an important and ubiquitous role in the synthesis of simple and complex molecules, including drug compounds, natural products, and agrochemicals. In recent years, the wide-reaching importance of homogeneous catalysis has made it an indispensable tool for the modification of biomolecules, such as carbohydrates (sugars), amino acids, peptides, nucleosides, nucleotides, and steroids. Such a synthetic strategy offers several advantages, which have led to the development of new molecules of biological relevance at a rapid rate relative to the number of available synthetic methods. Given the powerful nature of homogeneous catalysis in effecting these synthetic transformations, this Focus Review has been compiled to highlight these important developments.

Additive-Free Pd-Catalysed C-2 Arylation of Tryptophan Derivatives with Diaryliodonium Salts

An efficient, mild and Pd-catalysed C-2 arylation of Fmoc-L-tryptophan with diaryliodonium salts has been developed, giving easy access to C-2 arylated tryptophan derivatives. This protocol tolerates a variety of functional groups and proceeds smoothly in high yields without any additives. In addition, the chemoseletive C–H arylation with unsymmetrical salts is described.

Internal Peptide Late-Stage Diversification: Peptide-Isosteric Triazoles for Primary and Secondary C(sp3 )-H Activation

Secondary C(sp³ )-H arylations were accomplished by palladium catalysis with triazoles as peptide bond isosteres. The unique power of this approach is highlighted by the possibility of achieving secondary C(sp³ )-H functionalizations on terminal peptides as well as the unprecedented positional-selective C(sp³ )-H functionalization of internal peptide positions, setting the stage for modular peptide late-stage diversification.

The α-tertiary amine motif drives remarkable selectivity for Pd-catalyzed carbonylation of β-methylene C-H bonds

The selective C-H carbonylation of methylene bonds in the presence of traditionally more reactive methyl C-H and C(sp2)-H bonds in α-tertiary amines is reported. The exceptional selectivity is driven by the bulky α-tertiary amine motif, which we hypothesise orientates the activating C-H bond proximal to Pd in order to avoid an unfavourable steric clash with a second α-tertiary amine on the Pd centre, promoting preferential cyclopalladation at the methylene position. The reaction tolerates a range of structurally interesting and synthetically versatile functional groups, delivering the corresponding β-lactam products in good to excellent yields.