Acid Building Blocks Research Articles

Synthesis of Non-canonical Tryptophan Variants via Rh-catalyzed C-H Functionalization of Anilines.

Tryptophan and its non-canonical variants play critical roles in pharmaceutical molecules and enzymes. Facile access to this privileged class of amino acids from readily available building blocks remains a long-standing challenge. Here, we report a regioselective synthesis of non-canonical tryptophans bearing C4-C7 substituents via Rh-catalyzed annulation between structurally diverse tert-butyloxycarbonyl (Boc)-protected anilines and alkynyl chlorides readily prepared from amino acid building blocks. This transformation harnesses Boc-directed C-H metalation and demetalation to afford a wide range of C2-unsubstituted indole products in a redox-neutral fashion. This umpolung approach compared to the classic Larock indole synthesis offers a novel mechanism for heteroarene annulation and will be useful for the synthesis of natural products and drug molecules containing non-canonical tryptophan residues in a highly regioselective manner.

In Vivo Interactions of Nucleic Acid Nanostructures With Cells.

Nucleic acid nanostructures, derived from the assembly of nucleic acid building blocks (e.g., plasmids and oligonucleotides), are important intracellular carriers of therapeutic cargoes widely utilized in preclinical nanomedicine applications, yet their clinical translation remains scarce. In the era of "translational nucleic acid nanotechnology", a deeper mechanistic understanding of the interactions of nucleic acid nanostructures with cells in vivo will guide the development of more efficacious nanomedicines. This review showcases the recent progress in dissecting the in vivo interactions of four key types of nucleic acid nanostructures (i.e., tile-based, origami, spherical nucleic acid, and nucleic acid nanogel) with cells in rodents over the past five years. Emphasis lies on the cellular-level distribution of nucleic acid nanostructures in various organs and tissues and the cellular responses induced by their cellular entry. Next, in the spirit of preclinical translation, this review features the latest interactions of nucleic acid nanostructures with cells in large animals and humans. Finally, the review offers directions for studying the interactions of nucleic acid nanostructures with cells from both materials and biology perspectives and concludes with some regulatory updates.

Structure-Activity Relationship Studies of the Peptide Antibiotic Clovibactin.

Our laboratory reported the chemical synthesis and stereochemical assignment of the recently discovered peptide antibiotic clovibactin. The current paper reports an improved, gram-scale synthesis of the amino acid building block Fmoc-(2R,3R)-3-hydroxyasparagine-OH that enables structure-activity relationship studies of clovibactin. An alanine scan reveals that residues Phe1, d-Leu2, Ser4, Leu7, and Leu8 are important for antibiotic activity. The side-chain amide group of the rare d-Hyn5 residue is not essential to activity and can be replaced with a methyl group with a moderate loss of activity. An acyclic clovibactin analogue reveals that the macrolactone ring is essential to antibiotic activity. The enantiomer of clovibactin is active, albeit somewhat less so than clovibactin. A conformationally constrained clovibactin analogue retains moderate antibiotic activity, while a backbone N-methylated analogue is almost completely inactive. X-ray crystallography of these two analogues reveals that the macrolactone ring adopts a crown-like conformation that binds anions.

Single Cell MALDI-MSI Analysis of Lipids and Proteins within a Replicative Senescence Fibroblast Model.

In this study, we evaluate lipids and select proteins in human lung fibroblasts (hLFs) to interrogate changes occurring due to aging and senescence. To study single cell populations, a comparison of cells adhered onto slides using poly-D-lysine versus centrifugal force deposition was first analyzed to determine whether specific alterations were observed between preparations. The poly-D-lysine approach was than utilized to interrogate the lipidome of the cell populations and further evaluate potential applications of the MALDI-immunohistochemistry (IHC) platform for single-cell level analyses. Two protein markers of senescence, vimentin and p21, were both observed within the fibroblast populations and quantified. Lipidomic analysis of the fibroblasts found twelve lipids significantly altered because of replicative senescence, including fatty acids, such as stearic acid, and ceramide phosphoethanolamine species (CerPE). Similar to previous reports, alterations were detected in putative fatty acid building blocks, ceramides, among other lipid species. Altogether, our results reveal the ability to detect lipids implicated in senescence and show alterations to protein expression between normal and senescent fibroblast populations, including differences between young and aged cells. This report is the first time that the MALDI-IHC system has been utilized at a single-cell level to analyze both protein expression and lipid profiles in cultured cells, with a particular focus on changes associated with aging and senescence.

Hypervalent Iodine Amino Acid Building Blocks for Bioorthogonal Peptide Macrocyclization

AbstractEthynylbenziodoxol(on)es (EB(X)xs) reagents have emerged as useful reagents for peptide/protein modification due to their versatile reactivity and high selectivity. Herein, we report the successful introduction of ethynylbenziodoxoles (EBxs) on different amino acid building blocks (Lys/Orn/Dap), and show their compatibility with both solid phase peptide synthesis (SPPS) and solution phase peptide synthesis (SPS). The selective incorporation of the EBx core into peptide sequences enable efficient macrocyclizations under mild conditions for the synthesis of topologically unique cyclic and bicyclic peptides.

Hypervalent Iodine Amino Acid Building Blocks for Bioorthogonal Peptide Macrocyclization.

Ethynylbenziodoxol(on)es (EB(X)xs) reagents have emerged as useful reagents for peptide/protein modification due to their versatile reactivity and high selectivity. Herein, we report the successful introduction of ethynylbenziodoxoles (EBxs) on different amino acid building blocks (Lys/Orn/Dap), and show their compatibility with both solid phase peptide synthesis (SPPS) and solution phase peptide synthesis (SPS). The selective incorporation of the EBx core into peptide sequences enable efficient macrocyclizations under mild conditions for the synthesis of topologically unique cyclic and bicyclic peptides.

Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides

Peptide-like foldamers controlled by normal amide backbone hydrogen bonding have been extensively studied, and their folding patterns largely rely on configurational and conformational constraints induced by the steric properties of backbone substituents at appropriate positions. In contrast, opportunities to influence peptide secondary structure by functional groups forming individual hydrogen bond networks have not received much attention. Here, peptide-like foldamers consisting of alternating α,β,γ-triamino acids 3-amino-4-(aminomethyl)-2-methylpyrrolidine-3-carboxylate (AAMP) and natural amino acids glycine and alanine are reported, which were obtained by solution phase peptide synthesis. They form ordered secondary structures, which are dominated by a three-dimensional bridged triazaspiranoid-like hydrogen bond network involving the non-backbone amino groups, the backbone amide hydrogen bonds, and the relative configuration of the α,β,γ-triamino and α-amino acid building blocks. This additional stabilization leads to folding in both nonpolar organic as well as in aqueous environments. The three-dimensional arrangement of the individual foldamers is supported by X-ray crystallography, NMR spectroscopy, chiroptical methods, and molecular dynamics simulations.

Engineering supramolecular dynamics of self-assembly and turnover of oncogenic microRNAs to drive their synergistic destruction in tumor models

Rationally-engineered functional biomaterials offer the opportunity to interface with complex biology in a predictive, precise, yet dynamic way to reprogram their behaviour and correct shortcomings. Success here may lead to a desired therapeutic effect against life-threatening diseases, such as cancer. Here, we engineered “Crab”-like artificial ribonucleases through coupling of peptide and nucleic acid building blocks, capable of operating alongside and synergistically with intracellular enzymes (RNase H and AGO2) for potent destruction of oncogenic microRNAs. “Crab”-like configuration of two catalytic peptides (“pincers”) flanking the recognition oligonucleotide was instrumental here in providing increased catalytic turnover, leading to ≈30-fold decrease in miRNA half-life as compared with that for “single-pincer” conjugates. Dynamic modeling of miRNA cleavage illustrated how such design enabled “Crabs” to drive catalytic turnover through simultaneous attacks at different locations of the RNA-DNA heteroduplex, presumably by producing smaller cleavage products and by providing toeholds for competitive displacement by intact miRNA strands. miRNA cleavage at the 5′-site, spreading further into double-stranded region, likely provided a synergy for RNase H1 through demolition of its loading region, thus facilitating enzyme turnover. Such synergy was critical for sustaining persistent disposal of continually-emerging oncogenic miRNAs. A single exposure to the best structural variant (Crab-p-21) prior to transplantation into mice suppressed their malignant properties and reduced primary tumor volume (by 85 %) in MCF-7 murine xenograft models.

General Installation of (4H)-Imidazolone cis-Amide Bioisosteres Along the Peptide Backbone.

Imidazolones represent an important class of heterocycles present in a wide range of pharmaceuticals, metabolites, and bioactive natural products and serve as the active chromophore in green fluorescent protein. Recently, imidazolones have received attention for their ability to act as a nonaromatic amide bond bioisotere which improves pharmacological properties. Herein, we present a tandem amidine installation and cyclization with an adjacent ester to yield (4H)-imidazolone products. Using amino acid building blocks, we can access the first examples of α-chiral imidazolones that have been previously inaccessible. Additionally, our method is amenable to on-resin installation which can be seamlessly integrated into existing solid-phase peptide synthesis protocols. Finally, we show that peptide imidazolones are potent cis-amide bond surrogates that preorganize linear peptides for head-to-tail macrocyclization. This work represents the first general approach to the backbone and side-chain insertion of imidazolone bioisosteres at various positions in linear and cyclic peptides.

Evolution of the Manufacturing Route towards a Key Benzothiophen‐2‐yl‐Boronic Acid Building Block of Rogaratinib

AbstractThe evolution of the synthesis of a benzothiophene‐2‐yl‐boronic acid ‐ a key building block for the anti‐cancer agent Rogaratinib ‐ is reported from multi‐gram scale to industrialization. The pitfalls and learnings during process development are outlined, describing the optimization of the initial research synthesis route, investigation of an alternative approach based on a palladium‐catalyzed Newman‐Kwart rearrangement and finally changing the synthetic strategy from thiophene‐construction to benzene‐ring formation. Although the initial route was utilized to deliver material on kg‐scale, the requirements for market‐supply triggered the decision to pursue a new synthetic route. Catalyst costs, high purity‐requirements, and not the least technical practicality caused the change to a synthesis with indeed higher step‐count. However, this could be mitigated by repeated application of a telescoping approach. The free boronic acid was finally selected and manufactured as a stable isolated intermediate after challenges like proto‐deboronation and trimerization to boroxine upon drying could be solved by an optimized crystallization procedure.

Enabling C7 Methylation and Arylation of the Indolyl Core via P(III)‐Directed C−H Functionalization

AbstractPeripheral editing of complex molecules via C−H functionalization removes the pervasive retrosynthetic bias toward pre‐functionalization and taps into the innate, often subtle, stereoelectronic differences between C−H linkages. Using this approach, bioactive molecules and residues can be modified without being beholden to lengthy sequences, thus allowing biochemical hypotheses to be interrogated on accelerated timelines. Herein, the C−H functionalization paradigm is leveraged to tackle C7 C−H functionalization of the biologically important tryptophan core. The devised process, which was expanded to indolyl (and related) systems, utilizes an N‐bound unsymmetrical “designer” phosphine to direct C−H functionalization to the desired position while maintaining operational ease of directing group installation/removal. Quantum mechanically calculated steric properties and activation free energies suggest that this phosphine is hindered enough for favoring C−H functionalization over deactivation pathways but is still easily cleaved by nucleophiles. In addition, the process enables the direct C−H methylation, cyclopropanation, and arylation of tryptophan to yield unnatural amino acid (UAA) building blocks. As a testament to the versatility of this method, a solid phase peptide synthesis (SPPS)‐ready phosphinated tryptophan was incorporated into a pentapeptide and the C−H functionalization/dephosphination sequence was executed with ease. The utility of “on‐peptide” editing was exhibited through the late‐stage functionalization of several pentapeptides with a diverse set of C7 substituents on‐ and off‐resin.

Chemoenzymatic total synthesis of sorbicillactone A

The sorbicillinoid family is a large class of natural products known for their structural variety and strong, diverse biological activities. A special member of this family, sorbicillactone A, the first nitrogen-containing sorbicillinoid, exhibits potent anti-leukemic and anti-HIV activities and possesses a unique structure formed from sorbicillinol, alanine, and fumaric acid building blocks. To facilitate in-depth biological and structure-activity relationship studies of this promising natural product, we developed a chemoenzymatic approach that provides access to sorbicillactone A and several analogs with excellent yields under precise stereochemical control. The key steps of the highly convergent, stereoselective, and short route are the enantioselective oxidative dearomatization of sorbillin to sorbicillinol catalyzed by the enzyme SorbC and the subsequent Michael addition of a fumarylazlactone building block. Additionally, our synthetic findings and bioinformatic analysis suggest that sorbicillactone A is biosynthetically formed analogously.

Total chemical synthesis of PSMA-617: an API for prostate cancer endotherapeutic applications

Abstract Synthesis of PSMA-617, a peptide based ligand used in the preparation of nuclear medicine, 177Lu-PSMA-617, for the treatment of prostate cancer, is demonstrated in 6 steps, starting from appropriately protected amino acid building blocks. A solution phase Boc-strategy was adopted for the synthesis of peptide, wherein deprotection of carbamate group using HCl (g), was employed as the key step. The synthesis furnished PSMA-617 in purity >99.5 % as confirmed by HPLC analysis. ESI-MS and NMR analysis supported the structural integrity of the compound. The synthesized ligand was radiolabelled using 177Lu to generate the desired radiopharmaceutical, 177Lu-PSMA-617, in radiochemical purity >98 %, as revealed by radio HPLC and TLC analysis. This establishes its potential as a nuclear medicine for therapeutic application.

A General Approach to Optically Pure, α-Methyl Non-Natural Amino Acids: Enabling Unique Peptides as Drug Candidates.

An α-methyl, non-natural amino acid (NNAA) building block equipped with an alkyl halide tail that could be readily transformed into an organozinc was prepared. This single organometallic was cross-coupled to an array of heterocyclic electrophiles using the Pd-PEPPSI-IHeptCl catalyst to produce a wide selection of optically pure α-methyl NNAAs. With these in hand, non-natural peptides are being produced for evaluation in a variety of therapeutic areas in drug discovery.

Synthesis and self-assembly of dendritic-linear block copolymers containing poly(mandelic acid) with discrete molecular weights and stereochemical structures.

In this work, we present the synthesis of uniform PMAs, where the number of repeat units and their stereochemical arrangement are precisely defined. Utilizing an iterative convergent approach with orthogonally protected dimandelic acid building blocks, we achieved high molecular weight PMAs with the desired number of repeat units, extending up to 144 mandelic acids. Additionally, stereochemically defined poly(l-mandelic acid)s with up to 32 repeat units were successfully synthesized. These uniform PMAs were subsequently coupled with uniform branched poly(ethylene glycol) blocks to create uniform dendritic-linear block copolymers. The self-assembly of these block copolymers in solution was systematically investigated. In solution self-assembly, the synthesized block copolymers showed multiple phases from cylinder to inverse cubic as the molecular weight of PMA increased. In the case of solvent diffusion-evaporation-mediated self-assembly, the block copolymers underwent a phase transition as the rate of water addition decreased.

Acid-Modulated Peptide Synthesis for Application on Oxide Biosensor Interfaces.

In this paper we report an acid-modulated strategy for novel peptide microarray production on biosensor interfaces. We initially selected a controlled pore glass (CPG) as a support for solid-phase peptide synthesis (SPPS) to implement a chemistry that can be performed at the interface of multiple field effect transistor (FET) sensors, eventually to generate label-free peptide microarrays for protein screening. Our chemistry uses a temporary protection of the N-terminal amino function of each amino acid building block with a tert-butyloxycarbonyl (Boc) group that can be removed after each SPPS cycle, in combination with semi-permanent protection of the side chains of trifunctional amino acid residues. Such a protection scheme with a well-proven record of application in conventional, batchwise SPPS has been fine-tuned for optimal performance on CPG and, from there, translated to SPR chips that allow layer-by-layer monitoring of amino acid coupling. Our results validate this acid-modulated synthesis as a feasible approach for producing peptides in high yields and purity on flat glass surfaces, such as those in bio-FETs.

Cover Picture: Optimized Stereoselective and Scalable Synthesis of Five‐Membered Cyclic trans‐β‐Amino Acid Building Blocks via Reductive Amination (BKCS 12/2023) Jungwoo Hong, Wonchul Lee, Hee‐Seung Lee

Unnatural β‐amino acids play pivotal roles in organic synthesis, drug development, and peptide chemistry. Highlighting their significance, the study by Jungwoo Hong, Wonchul Lee, and Hee‐Seung Lee presents an optimized, scalable method for producing enantiopure five‐membered cyclic trans‐β‐amino acid building blocks. More details are available in the article by Jungwoo Hong, Wonchul Lee, Hee‐Seung Lee image

Lewis Acid-Base Adducts of α-Amino Acid-Derived Silaheterocycles and N-Methylimidazole

In chloroform solution, the reaction of bis(tert-butylamino)dimethylsilane ((tBuNH)2SiMe2) and an α-amino acid (α-amino isobutyric acid, H2Aib; D-phenylglycine, H2Phg; L-valine, H2Val) in the presence of N-methylimidazole (NMI) gave rise to the formation of the pentacoordinate silicon complexes (Aib)SiMe2-NMI, (Phg)SiMe2-NMI and (Val)SiMe2-NMI, respectively. Therein, the amino acid building block was a di-anionic bidentate chelator at the silicon atom. In solution, the complexes were involved in rapid coordination–dissociation equilibria between the pentacoordinate Si complex (e.g., (Aib)SiMe2-NMI) and its constituents NMI and a five-membered silaheterocycle (e.g., (Aib)SiMe2), as shown by 29Si NMR spectroscopy. The energetics of the Lewis acid-base adduct formation and the competing solvation of the NMI molecule by chloroform were assessed with the aid of computational methods. In CDCl3 solution, deuteration of the silaheterocycle NH group proceeded rapidly, with more than 50% conversion within two days. Upon cooling to −44 °C, the chloroform solvates of the adducts (Aib)SiMe2-NMI and (Phg)SiMe2-NMI crystallized from their parent solutions and allowed for their single-crystal X-ray diffraction analyses. In both cases, the Si atom was situated in a distorted trigonal bipyramidal coordination sphere with equatorial Si–C bonds and an equatorial Si–N bond (the one of the silaheterocycle). The axial positions were occupied by a carboxylate O atom of the silaheterocycle and the NMI ligand’s donor-N-atom.

Optimized stereoselective and scalable synthesis of five‐membered cyclic trans‐β‐amino acid building blocks via reductive amination

AbstractWe present an optimized method for the stereoselective synthesis of five‐membered alicyclic and heterocyclic trans‐β‐amino acid derivatives. The process involves a reductive amination of β‐keto esters using chiral auxiliary amines, with formic acid acting as a facilitator for rapid, diastereoselective reductions under gentle conditions. Our approach notably enhances isolated yields and permits the scalable production of trans‐2‐aminocyclopentanecarboxylic acid (trans‐ACPC), 4‐aminopyrrolidine‐3‐carboxylic acid (trans‐APC), 4‐aminotetrahydrofuran‐3‐carboxylic acid (trans‐ATFC), and 4‐aminotetrahydrothiophene‐3‐carboxylic acid (trans‐ATTC) building blocks.

Synergistic Combination of Antimicrobial Peptides and Cationic Polyitaconates in Multifunctional PLA Fibers.

Combining different antimicrobial agents has emerged as a promising strategy to enhance efficacy and address resistance evolution. In this study, we investigated the synergistic antimicrobial effect of a cationic biobased polymer and the antimicrobial peptide (AMP) temporin L, with the goal of developing multifunctional electrospun fibers for potential biomedical applications, particularly in wound dressing. A clickable polymer with pendent alkyne groups was synthesized by using a biobased itaconic acid building block. Subsequently, the polymer was functionalized through click chemistry with thiazolium groups derived from vitamin B1 (PTTIQ), as well as a combination of thiazolium and AMP temporin L, resulting in a conjugate polymer-peptide (PTTIQ-AMP). The individual and combined effects of the cationic PTTIQ, Temporin L, and PTTIQ-AMP were evaluated against Gram-positive and Gram-negative bacteria as well as Candida species. The results demonstrated that most combinations exhibited an indifferent effect, whereas the covalently conjugated PTTIQ-AMP displayed an antagonistic effect, potentially attributed to the aggregation process. Both antimicrobial compounds, PTTIQ and temporin L, were incorporated into poly(lactic acid) electrospun fibers using the supercritical solvent impregnation method. This approach yielded fibers with improved antibacterial performance, as a result of the potent activity exerted by the AMP and the nonleaching nature of the cationic polymer, thereby enhancing long-term effectiveness.