Polypeptoids synthesis based on Ugi reaction: Advances and perspectives

Curation and cheminformatics analysis of a Ugi-reaction derived library (URDL) of synthetically tractable small molecules for virtual screening application

Virtual screening (VS) is an important approach in drug discovery and relies on the availability of a virtual library of synthetically tractable molecules. Ugi reaction (UR) represents an important multi-component reaction (MCR) that reliably produces a peptidomimetic scaffold. Recent literature shows that a tactically assembled Ugi adduct can be subjected to further chemical modifications to yield a variety of rings and scaffolds, thus, renewing the interest in this old reaction. Given the reliability and efficiency of UR, we collated an UR derived library (URDL) of small molecules (total = 5773) for VS. The synthesis of the majority of URDL molecules may be carried out in 1-2 pots in a time and cost-effective manner. The detailed analysis of the average property and chemical space of URDL was also carried out using the open-source Datawarrior program. The comparison with FDA-approved oral drugs and inhibitors of protein-protein interactions (iPPIs) suggests URDL molecules are 'clean', drug-like, and conform to a structurally distinct space from the other two categories. The average physicochemical properties of compounds in the URDL library lie closer to iPPI molecules than oral drugs thus suggesting that the URDL resource can be applied to discover novel iPPI molecules. The URDL molecules consist of diverse ring systems, many of which have not been exploited yet for drug design. Thus, URDL represents a small virtual library of drug-like molecules with unexplored chemical space designed for VS. The structures of all molecules of URDL, oral drugs, and iPPI compounds are being made freely accessible as supplementary information for broader application.

Stepping Further from Coupling Tools: Development of Functional Polymers via the Biginelli Reaction

Multicomponent reactions (MCRs) have been used to prepare polymers with appealing functions. The Biginelli reaction, one of the oldest and most famous MCRs, has sparked new scientific discoveries in polymer chemistry since 2013. Recent years have seen the Biginelli reaction stepping further from simple coupling tools; for example, the functions of the Biginelli product 3,4-dihydropyrimidin-2(1H)-(thi)ones (DHPM(T)) have been gradually exploited to develop new functional polymers. In this mini-review, we mainly summarize the recent progress of using the Biginelli reaction to identify polymers for biomedical applications. These polymers have been documented as antioxidants, anticancer agents, and bio-imaging probes. Moreover, we also provide a brief introduction to some emerging applications of the Biginelli reaction in materials and polymer science. Finally, we present our perspectives for the further development of the Biginelli reaction in polymer chemistry.

A Field Guide to Optimizing Peptoid Synthesis

N-Substituted glycines (peptoids) are a class of peptidomimetic molecules used as materials for health, environmental, and drug delivery applications. Automated solid-phase synthesis is the most widely used approach for preparing polypeptoids, with a range of published protocols and modifications for selected synthetic targets. Simultaneously, emerging solution-phase syntheses are being leveraged to overcome limitations in solid-phase synthesis and access high-molecular weight polypeptoids. This Perspective aims to outline strategies for the optimization of both solid- and solution-phase synthesis, provide technical considerations for robotic synthesizers, and offer an outlook on advances in synthetic methodologies. The solid-phase synthesis sections explore steps for protocol optimization, accessing complex side chains, and adaptation to robotic synthesizers; the sections on solution-phase synthesis cover the selection of initiators, side chain compatibility, and strategies for controlling polymerization efficiency and scale. This text acts as a "field guide" for researchers aiming to leverage the flexibility and adaptability of peptoids in their research.

Introducing the aza-Michael addition reaction between acrylate and dihydropyrimidin-2(1H)-thione into polymer chemistry

The aza-Michael addition reaction between dihydropyrimidin-2(1H)-thione and acrylate has been used to fabricate new polymers through different synthesis routes.

Bio-instructive materials on-demand - combinatorial chemistry of peptoids, foldamers, and beyond

Combinatorial chemistry allows for the rapid synthesis of large compound libraries for high throughput screenings in biology, medicinal chemistry, or materials science. Especially compounds from a highly modular design are interesting for the proper investigation of structure-to-activity relationships. Permutations of building blocks result in many similar but unique compounds. The influence of certain structural features on the entire structure can then be monitored and serve as a starting point for the rational design of potent molecules for various applications. Peptoids, a highly diverse class of bioinspired oligomers, suit perfectly for combinatorial chemistry. Their straightforward synthesis on a solid support using repetitive reaction steps ensures easy handling and high throughput. Applying this modular approach, peptoids are readily accessible, and their interchangeable side-chains allow for various structures. Thus, peptoids can easily be tuned in their solubility, their spatial structure, and, consequently, their applicability in various fields of research. Since their discovery, peptoids have been applied as antimicrobial agents, artificial membranes, molecular transporters, and much more. Studying their three-dimensional structure, various foldamers with fascinating, unique properties were discovered. This non-comprehensive review will state the most interesting discoveries made over the past years and arouse curiosity about what may come.

An Inspection into Multifarious Ways to Synthesize Poly(Amino Acid)s

Poly(α-amino acid)s (PAAs) attract growing attention due to their essential role in the application as biomaterials. To synthesize PAAs with desired structures and properties, scientists have developed various synthetic techniques with respective advantages. Here, different approaches to preparing PAAs are inspected. Basic features and recent progresses of these methods are summarized, including polymerizations of amino acid N-carboxyanhydrides (NCAs), amino acid N-thiocarboxyanhydrides (NTAs), and N-phenoxycarbonyl amino acids (NPCs), as well as other synthetic routes. NCA is the most classical monomer to prepare PAAs with high molecular weights (MWs). NTA polymerizations are promising alternative pathways to produce PAAs, which can tolerate nucleophiles including alcohols, mercaptans, carboxyl acids, and water. By various techniques including choosing appropriate solvents or using organic acids as promoters, NTAs polymerize to produce polypeptoids and polypeptides with narrow dispersities and designed MWs up to 55.0 and 57.0 kg mol^-1 , respectively. NPC polymerizations are phosgene-free ways to synthesize polypeptides and polypeptoids. For the future prospects, detail investigations into polymerization mechanisms of NTA and NPC are expected. The synthesis of PAAs with designed topologies and assembly structures is another intriguing topic. The advantages and unsettled problems in various synthetic ways are discussed for readers to choose appropriate approaches for PAAs.

Recent Advances in Thermoresponsive OEGylated Poly(amino acid)s

Thermoresponsive polymers have been widely studied in the past decades due to their potential applications in biomedicine, nanotechnology, and so on. As is known, poly(N-isopropylacrylamide) (PNIPAM) and poly(oligo(ethylene glycol)methacrylates) (POEGMAs) are the most popular thermoresponsive polymers, and have been studied extensively. However, more advanced thermoresponsive polymers with excellent biocompatibility, biodegradability, and bioactivity also need to be developed for biomedical applications. OEGylated poly(amino acid)s are a kind of novel polymer which are synthesized by attaching one or multiple oligo(ethylene glycol) (OEG) chains to poly(amino acid) (PAA).These polymers combine the great solubility of OEG, and the excellent biocompatibility, biodegradability and well defined secondary structures of PAA. These advantages allow them to have great application prospects in the field of biomedicine. Therefore, the study of OEGylated poly(amino acid)s has attracted more attention recently. In this review, we summarized the development of thermoresponsive OEGylated poly(amino acid)s in recent years, including the synthesis method (such as ring-opening polymerization, post-polymerization modification, and Ugi reaction), stimuli-response behavior study, and secondary structure study. We hope that this periodical summary will be more conducive to design, synthesis and application of OEGylated poly(amino acid)s in the future.

Understanding Acid-Promoted Polymerization of the N-Substituted Glycine N-Thiocarboxyanhydride in Polar Solvents

Polymerization of N-substituted glycine N-thiocarboxyanhydrides (NNTAs) is a promising pathway to prepare functional polypeptoids benefiting from their tolerance to nucleophilic impurities. However, controlled NNTA polymerization is hard to achieve in amide polar solvents, including N,N-dimethylacetamide (DMAc), N,N-dimethylformamide (DMF), and N-methyl pyrrolidone (NMP), the only aprotic solvents for many biomacromolecules and polypeptoids. In the present work, we successfully achieve controlled NNTA polymerization in amide polar solvents by adding acetic acid as a promoter. The promotion is applied to the polymerization of sarcosine NTA, N-ethyl glycine NTA, and N-butyl glycine NTA. DMAc, DMF, and NMP are suitable solvents to prepare polypeptoids with designable molecular weights and low dispersities (1.06-1.21). The polysarcosines with high molecular weights are prepared up to 35.2 kg/mol. A kinetic investigation quantitatively reveals that the presence of acetic acid not only accelerates the polymerization, but also suppresses H₂S-catalyzed decomposition of NNTAs by decreasing the concentration of H₂S dissolved in polar solvents. Benzoic acid is also able to promote the polymerization, while trifluoroacetic acid, phosphoric acid, and phenol are not appropriate promoters. The moderate acidity of acids is essential. l-Methionine, l-tryptophan, and l-phenylalanine, which are dissolved in DMF, initiate the controlled polymerization of sarcosine-NTA in the presence of acetic acid and introduce functional end groups to polysarcosines quantitatively. In DMAc, hydrophilic vancomycin is grafted by poly(N-butyl glycine). The amphiphilic product dissolves in dichloromethane and stabilizes water-in-oil emulsion.

Ugi four-component polymerization of amino acid derivatives: a combinatorial tool for the design of polypeptoids

The combinatorial Ugi-4C polymerization of amino acid derivatives is attractive for the future development of polypeptoids and resulting applications.

Poly(ε-lysine) and its derivatives via ring-opening polymerization of biorenewable cyclic lysine

Minireview focused on poly(ε-lysine) and its derivatives via ring-opening polymerization of biorenewable cyclic lysine.

Ugi Reaction of Amino Acids: From Facile Synthesis of Polypeptoids to Sequence-Defined Macromolecules

Polypeptoids have been prepared and researched for more than 20 years. However, the efficient generation of polypeptoids and sequence-defined polypeptoids faces many challenges and difficulties. The Ugi reaction of amino acids has recently been introduced into polypeptoid chemistry as a new and powerful method to furnish polypeptoids. In the following mini review, the recent progress on the application of the Ugi reaction of amino acids in polypeptoid science, including polypeptoid from sustainable furfural, sequence-defined polypeptoids, and more is summarized. Moreover, the future development of the Ugi reaction of amino acids in polypeptoid science is discussed.

Multicomponent Reactions for Integrating Multiple Functional Groups into an Antioxidant

A large number of convincing evidences has revealed the correlation of the pathogeny of diseases with the oxidative damages of DNA, protein, biomembrane, and other biological species, while supplementation of antioxidants is demonstrated to be a promising way to avoid, at least, rectify the unbalance redox status in vivo. Although many endeavors have focused on synthesis of antioxidants, a main hurdle still hinders the wide usages of synthetic antioxidants because of low bioavailability and potential cytotoxicity. The search for antioxidants with multiple functional groups being recognized by different receptors becomes a much sought by researchers, and multicomponent reactions (MCRs) provide with powerful tools for the construction of multifunctional antioxidants. Presented herein is a personal account on the application of MCRs for the synthesis of multifunctional antioxidants, while radical-induced oxidation of DNA acts as the experimental system for evaluating antioxidative effect. Concretely, the Biginelli three-component reaction (3CR) affords such a dihydropyrimidine scaffold that the tautomerization between C=S and C-SH leads to antioxidative effect. The Povarov 3CR is able to integrate multiple antioxidative groups, i. e., ferrocenyl and -N(CH₃ )₂ , into a quinoline scaffold, while the Groebke 3CR provides with imidazo[1,2-a]pyridine skeleton for inhibiting DNA oxidation. Additionally, the Knoevenagel-related MCRs also become efficient strategies for achieving radical-scavengers. On the other hand, the Ugi 4CR and Passerini 3CR result in the dipeptide and α-acyloxycarboxamide, respectively, with the benefit for the integration of antioxidative features by aliphatic chains. Therefore, MCRs have emerged as efficient tools for integrating multiple antioxidative features into one molecule in order to meet with complicated requirements from various biological surroundings.

Shear-Induced Adhesion of Alternating Peptides Prepared by Ugi Four-Center Three-Component Reaction

The development of new peptide-based glues has been strongly urged from the viewpoints of industrial applications and biomedical engineering. However, the large-scale synthesis of polypeptides with an ordered sequence is highly challenging, which strictly restricts materials resources for the research and development of polypeptides. In this work, the framework of adhesive alternating peptides has been designed to be glycine (Gly)-N-substituted valine (Val) as the dipeptide repeating sequence, considering the peptapeptide repeating sequence of viscoelastic natural elastin as a motif. The alternating peptides are prepared via three-component polymerization exploiting Ugi four-center three-component reaction as the elemental polymerization reaction. The adhesive strength (S_Adh ) values of the polymers are evaluated by a shear adhesive test method using two glass plates. Alternating peptides with Gly-N-benzylated Val dipeptide repeating units exhibit the optimal adhesive properties such as much higher S_Adh than that of conventional fibrin glue and a unique readhesion capability. It is indicated that the remarkably high S_Adh would be attributed to the shear-induced structural change of single polymer chain, the slow relaxation of extended structure, and the weak interchain interactions. Due to the favorable adhesive properties of alternating peptides, these adhesives may be highly suitable for real-world applications.

Self-Assembly of Minimal Peptoid Sequences

Peptoids are biofunctional N-substituted glycine peptidomimics. Their self-assembly is of fundamental interest because they demonstrate alternatives to conventional peptide structures based on backbone chirality and beta-sheet hydrogen bonding. The search for self-assembling, water-soluble "minimal" sequences, be they peptide or peptidomimic, is a further challenge. Such sequences are highly desired for their compatibility with biomacromolecules and convenient synthesis for broader application. We report the self-assembly of a set of trimeric, water-soluble α-peptoids that exhibit a relatively low critical aggregation concentration (CAC ∼ 0.3 wt %). Cryo-EM and angle-resolved DLS show different sequence-dependent morphologies, namely uniform ca. 6 nm wide nanofibers, sheets, and clusters of globular assemblies. Absorbance and fluorescence spectroscopies indicate unique phenyl environments for π-interactions in the highly ordered nanofibers. Assembly of our peptoids takes place when the sequences are fully ionized, representing a departure from superficially similar amyloid-type hydrogen-bonded peptide nanostructures and expanding the horizons of assembly for sequence-specific bio- and biomimetic macromolecules.

Multicomponent Radziszewski Emulsion Polymerization toward Macroporous Poly(ionic liquid) Catalysts

Interconnected macroporous imidazolium-based monoliths are produced via the modified Radziszewski multicomponent reaction (MCR) applied to triamines under high internal phase emulsion (HIPE) conditions. This straightforward one-pot synthesis combines the efficiency and versatility of MCRs with the ease of implementation of the emulsion templating polymerization process. The characterization of the chemical structure and morphology of the resulting materials confirms the formation of the expected macroporous poly(ionic liquid)s (PILs) networks. The promising catalytic activity and recyclability of these porous PIL monoliths are illustrated for the transesterification reaction and the decarboxylation of caffeic acid. In these cases, almost complete conversion is reached while benefiting from the advantages associated with a heterogeneous catalyst.