Modification of Proteins Using Olefin Metathesis

Anionic Olefin Metathesis Catalysts Enable Modification of Unprotected Biomolecules in Water

Stability problems have limited the uptake of cationic olefin metathesis catalysts in chemical biology. Described herein are anionic catalysts that improve water-solubility, robustness, and compatibility with biomolecules such as DNA. A sulfonate tag is installed on the cyclic (alkyl)(amino) carbene (CAAC) ligand platform, chosen for resistance to degradation by nucleophiles, base, water, and β-elimination. Hoveyda-Grubbs catalysts bearing the sulfonated CAAC ligands deliver record productivity in metathesis of unprotected carbohydrates and nucleosides at neutral pH. Decomposed catalyst has negligible impact on metathesis selectivity, whereas N-heterocyclic carbene (NHC) catalysts degrade rapidly in water and cause extensive C=C migration.

How can biomaterial-conjugated antimicrobial peptides fight bacteria and be protected from degradation?

The emergence of antibiotic-resistant bacteria is a serious threat to public health. Antimicrobial peptides (AMP) are a powerful alternative to antibiotics due to their low propensity to induce bacterial resistance. However, cytotoxicity and short half-lives have limited their clinical translation. To overcome these problems, AMP conjugation has gained relevance in the biomaterials field. Nevertheless, few studies describe the influence of conjugation on enzymatic protection, mechanism of action and antimicrobial efficacy. This review addresses this gap by providing a detailed comparison between conjugated and soluble AMP. Additionally, commonly employed chemical reactions and factors to consider when promoting AMP conjugation are reviewed. The overall results suggested that AMP conjugated onto biomaterials are specifically protected from degradation by trypsin and/or pepsin. However, sometimes, their antimicrobial efficacy was reduced. Due to limited conformational freedom in conjugated AMP, compared to their soluble forms, they appear to act initially by creating small protuberances on bacterial membranes that may lead to the alteration of membrane potential and/or formation of holes, triggering cell death. Overall, AMP conjugation onto biomaterials is a promising strategy to fight infection, particularly associated to the use of medical devices. Nonetheless, some details need to be addressed before conjugated AMP reach clinical practice. STATEMENT OF SIGNIFICANCE: Covalent conjugation of antimicrobial peptides (AMP) has been one of the most widely used strategies by bioengineers, in an attempt to not only protect AMP from proteolytic degradation, but also to prolong their residence time at the target tissue. However, an explanation for the mode of action of conjugated AMP is still lacking. This review extensively gathers works on AMP conjugation and puts forward a mechanism of action for AMP when conjugated onto biomaterials. The implications of AMP conjugation on antimicrobial activity, cytotoxicity and resistance to proteases are all discussed. A thorough review of commonly employed chemical reactions for this conjugation is also provided. Finally, details that need to be addressed for conjugated AMP to reach clinical practice are discussed.

Biocompatible strategies for peptide macrocyclisation

Peptides are increasingly important drug candidates, offering numerous advantages over conventional small molecules. However, they face significant challenges related to stability, cellular uptake and overall bioavailability. While individual modifications may not address all these challenges, macrocyclisation stands out as a single modification capable of enhancing affinity, selectivity, proteolytic stability and membrane permeability. The recent successes of in situ peptide modifications during screening in combination with genetically encoded peptide libraries have increased the demand for peptide macrocyclisation reactions that can occur under biocompatible conditions. In this perspective, we aim to distinguish biocompatible conditions from those well-known examples that are fully bioorthogonal. We introduce key strategies for biocompatible peptide macrocyclisation and contextualise them within contemporary screening methods, providing an overview of available transformations.

Modular and diverse synthesis of amino acids via asymmetric decarboxylative protonation of aminomalonic acids

Stereoselective protonation is a challenge in asymmetric catalysis. The small size and high rate of transfer of protons mean that face-selective delivery to planar intermediates is hard to control, but it can unlock previously obscure asymmetric transformations. Particularly, when coupled with a preceding decarboxylation, enantioselective protonation can convert the abundant acid feedstocks into structurally diverse chiral molecules. Here an anchoring group strategy is demonstrated as a potential alternative and supplement to the conventional structural modification of catalysts by creating additional catalyst-substrate interactions. We show that a tailored benzamide group in aminomalonic acids can help build a coordinated network of non-covalent interactions, including hydrogen bonds, π-π interactions and dispersion forces, with a chiral acid catalyst. This allows enantioselective decarboxylative protonation to give α-amino acids. The malonate-based synthesis introduces side chains via a facile substitution of aminomalonic esters and thus can access structurally and functionally diverse amino acids.

Transition Metal Catalysis in Living Cells: Progress, Challenges, and Novel Supramolecular Solutions

The importance of transition metal catalysis is exemplified by its wide range of applications, for example in the synthesis of chemicals, natural products, and pharmaceuticals. However, one relatively new application is for carrying out new-to-nature reactions inside living cells. The complex environment of a living cell is not welcoming to transition metal catalysts, as a diverse range of biological components have the potential to inhibit or deactivate the catalyst. Here we review the current progress in the field of transition metal catalysis, and evaluation of catalysis efficiency in living cells and under biological (relevant) conditions. Catalyst poisoning is a ubiquitous problem in this field, and we propose that future research into the development of physical and kinetic protection strategies may provide a route to improve the reactivity of catalysts in cells.

Octreotide and Octreotide-derived delivery systems

Pharmaceutical peptide Octreotide is a somatostatin analog with targeting and therapeutic abilities. Over the last decades, Octreotide has been developed and approved to treat acromegaly and neuroendocrine tumours, and Octreotide-based radioactive conjugates have been leveraged clinically to detect small neuroendocrine tumour sites. Meanwhile, variety of Octreotide-derived delivery strategies have been proposed and explored for tumour targeted therapeutics or diagnostics in preclinical or clinical settings. In this review, we especially focus on the preclinical development and applications of Octreotide-derived drug delivery systems, diagnostic nanosystems, therapeutic nanosystems and multifunctional nanosystems, we also briefly discuss challenges and prospects of these Octreotide-derived delivery systems.

Influence of Substituents in a Six-Membered Chelate Ring of HG-Type Complexes Containing an N→Ru Bond on Their Stability and Catalytic Activity

An efficient approach to the synthesis of olefin metathesis HG-type catalysts containing an N→Ru bond in a six-membered chelate ring was proposed. For the most part, these ruthenium chelates can be prepared easily and in high yields based on the interaction between 2-vinylbenzylamines and Ind II (the common precursor for Ru-complex synthesis). It was demonstrated that the increase of the steric volume of substituents attached to the nitrogen atom and in the α-position of the benzylidene fragment leads to a dramatic decrease in the stability of the target ruthenium complexes. The bulkiest ⁱPr substituent bonded to the nitrogen atom or to the α-position does not allow the closing of the chelate cycle. N,N-Diethyl-1-(2-vinylphenyl)propan-1-amine is a limiting case; its interaction with Ind II makes it possible to isolate the corresponding ruthenium chelate in a low yield (5%). Catalytic activity of the synthesized complexes was tested in RCM reactions and compared with α-unsubstituted catalysts obtained previously. The structural peculiarities of the final ruthenium complexes were thoroughly investigated using XRD and NMR analysis, which allowed making a reliable correlation between the structure of the complexes and their catalytic properties.

Water-Accelerated Decomposition of Olefin Metathesis Catalysts

Water is ubiquitous in olefin metathesis, at levels ranging from contaminant to cosolvent. It is also non-benign. Water-promoted catalyst decomposition competes with metathesis, even for "robust" ruthenium catalysts. Metathesis is hence typically noncatalytic for demanding reactions in water-rich environments (e.g., chemical biology), a challenge as the Ru decomposition products promote unwanted reactions such as DNA degradation. To date, only the first step of the decomposition cascade is understood: catalyst aquation. Here we demonstrate that the aqua species dramatically accelerate both β-elimination of the metallacyclobutane intermediate and bimolecular decomposition of four-coordinate [RuCl(H₂O)_n(L)(=CHR)]Cl. Decomposition can be inhibited by blocking aquation and β-elimination.

Organometallic catalysis in aqueous and biological environments: harnessing the power of metal carbenes

Translating the power of transition metal catalysis to the native habitats of enzymes can significantly expand the possibilities of interrogating or manipulating natural biological systems, including living cells and organisms. This is especially relevant for organometallic reactions that have shown great potential in the field of organic synthesis, like the metal-catalyzed transfer of carbenes. While, at first sight, performing metal carbene chemistry in aqueous solvents, and especially in biologically relevant mixtures, does not seem obvious, in recent years there has been a growing number of reports demonstrating the feasibility of the task. Either using small molecule metal catalysts or artificial metalloenzymes, a number of carbene transfer reactions that tolerate aqueous and biorelevant media are being developed. This review intends to summarize the most relevant contributions, and establish the state of the art in this emerging research field.

The Janus face of high trans-effect carbenes in olefin metathesis: gateway to both productivity and decomposition

Ruthenium–cyclic(alkyl)(amino)carbene (CAAC) catalysts, used at ppm levels, can enable dramatically higher productivities in olefin metathesis than their N-heterocyclic carbene (NHC) predecessors. A key reason is the reduced susceptibility of the metallacyclobutane (MCB) intermediate to decomposition via β-H elimination. The factors responsible for promoting or inhibiting β-H elimination are explored via density functional theory (DFT) calculations, in metathesis of ethylene or styrene (a representative 1-olefin) by Ru–CAAC and Ru–NHC catalysts. Natural bond orbital analysis of the frontier orbitals confirms the greater strength of the orbital interactions for the CAAC species, and the consequent increase in the carbene trans influence and trans effect. The higher trans effect of the CAAC ligands inhibits β-H elimination by destabilizing the transition state (TS) for decomposition, in which an agostic MCB C_β–H bond is positioned trans to the carbene. Unproductive cycling with ethylene is also curbed, because ethylene is trans to the carbene ligand in the square pyramidal TS for ethylene metathesis. In contrast, metathesis of styrene proceeds via a ‘late’ TS with approximately trigonal bipyramidal geometry, in which carbene trans effects are reduced. Importantly, however, the positive impact of a strong trans-effect ligand in limiting β-H elimination is offset by its potent accelerating effect on bimolecular coupling, a major competing means of catalyst decomposition. These two decomposition pathways, known for decades to limit productivity in olefin metathesis, are revealed as distinct, antinomic, responses to a single underlying phenomenon. Reconciling these opposing effects emerges as a clear priority for design of robust, high-performing catalysts.

In ruthenium catalysts for olefin metathesis, carbene ligands of high trans influence/effect suppress decomposition via β-H elimination, but increase susceptibility to bimolecular decomposition.

An overview of chemo- and site-selectivity aspects in the chemical conjugation of proteins

The bioconjugation of proteins-that is, the creation of a covalent link between a protein and any other molecule-has been studied for decades, partly because of the numerous applications of protein conjugates, but also due to the technical challenge it represents. Indeed, proteins possess inner physico-chemical properties-they are sensitive and polynucleophilic macromolecules-that make them complex substrates in conjugation reactions. This complexity arises from the mild conditions imposed by their sensitivity but also from selectivity issues, viz the precise control of the conjugation site on the protein. After decades of research, strategies and reagents have been developed to address two aspects of this selectivity: chemoselectivity-harnessing the reacting chemical functionality-and site-selectivity-controlling the reacting amino acid residue-most notably thanks to the participation of synthetic chemistry in this effort. This review offers an overview of these chemical bioconjugation strategies, insisting on those employing native proteins as substrates, and shows that the field is active and exciting, especially for synthetic chemists seeking new challenges.

Ruthenium Olefin Metathesis Catalysts Featuring N-Heterocyclic Carbene Ligands Tagged with Isonicotinic and 4-(Dimethylamino)benzoic Acid Rests: Evaluation of a Modular Synthetic Strategy

A modular and flexible strategy towards the synthesis of N-heterocyclic carbene (NHC) ligands bearing Brønsted base tags has been proposed and then adopted in the preparation of two tagged NHC ligands bearing rests of isonicotinic and 4-(dimethylamino)benzoic acids. Such tagged NHC ligands represent an attractive starting point for the synthesis of olefin metathesis ruthenium catalysts tagged in non-dissociating ligands. The influence of the Brønsted basic tags on the activity of such obtained olefin metathesis catalysts has been studied.

Toward E-selective Olefin Metathesis: Computational Design and Experimental Realization of Ruthenium Thio-Indolate Catalysts

The selective transformation of 1-alkenes into E-olefins is a long-standing challenge in olefin metathesis. Density functional theory (DFT) calculations predict high E-selectivity for catalysts incorporating a bidentate, dianionic thio-indolate ligand within a RuXX’(NHC)(py)(= CHR) platform (NHC = N-heterocyclic carbene; py = pyridine). Such complexes are predicted to yield E-olefins by favoring anti-disposed substituents in the transition state expected to be rate-determining: specifically, that for cycloreversion of the metallacyclobutane intermediate. Three pyridine-stabilized catalysts Ru21a-c were synthesized, in which the thio-indolate ligand bears a H, Me, or Ph substituent at the C2 position, and the NHC ligand is the unsaturated imidazoline-2-ylidene Me2IMes (which bears N-mesityl groups and methyl groups on the C4,5 backbone). Single-crystal X-ray diffraction analysis of Ru21c confirms the ligand orientation required for E-selective metathesis, with the thio-indolate sulfur atom binding cis to the NHC, and the indolate nitrogen atom trans to the NHC. However, whereas the new complexes mediated metathetic exchange of their 2-thienylmethylidene ligand in the presence of the common metathesis substrates styrene and allylbenzene, no corresponding self-metathesis products were obtained. Only small amounts of 2-butene (73% (Z)-2-butene) were obtained in self-metathesis of propene using Ru21a. Detailed DFT analysis of this process revealed that product release is surprisingly slow, limiting the reaction rate and explaining the low metathesis activity. With the barrier to dissociation of (Z)-2-butene being lower than that of (E)-2-butene, the calculations also account for the observed Z-selectivity of Ru21a. These findings provide guidelines for catalyst redesign in pursuit of the ambitious goal of E-selective 1-alkene metathesis.

Graphic abstract

Weaving Enzymes with Polymeric Shells for Biomedical Applications

Enzyme therapeutics have received increasing attention due to their high biological specificity, outstanding catalytic efficiency, and impressive therapeutic outcomes. Protecting and delivering enzymes into target cells while retaining enzyme catalytic efficiency is a big challenge. Wrapping of enzymes with rational designed polymer shells, rather than trapping them into large nanoparticles such as liposomes, have been widely explored because they can protect the folded state of the enzyme and make post-functionalization easier. In this review, the methods for wrapping up enzymes with protective polymer shells are mainly focused on. It is aimed to provide a toolbox for the rational design of polymeric enzymes by introducing methods for the preparation of polymeric enzymes including physical adsorption and chemical conjugation with specific examples of these conjugates/hybrid applications. Finally, a conclusion is drawn and key points are emphasized.

Bimolecular Coupling in Olefin Metathesis: Correlating Structure and Decomposition for Leading and Emerging Ruthenium-Carbene Catalysts

Bimolecular catalyst decomposition is a fundamental, long-standing challenge in olefin metathesis. Emerging ruthenium-cyclic(alkyl)(amino)carbene (CAAC) catalysts, which enable breakthrough advances in productivity and general robustness, are now known to be extraordinarily susceptible to this pathway. The details of the process, however, have hitherto been obscure. The present study provides the first detailed mechanistic insights into the steric and electronic factors that govern bimolecular decomposition. Described is a combined experimental and theoretical study that probes decomposition of the key active species, RuCl2(L)(py)(═CH2) 1 (in which L is the N-heterocyclic carbene (NHC) H2IMes, or a CAAC ligand: the latter vary in the NAr group (NMes, N-2,6-Et2C6H3, or N-2-Me,6-iPrC6H3) and the substituents on the quaternary site flanking the carbene carbon (i.e., CMe2 or CMePh)). The transiently stabilized pyridine adducts 1 were isolated by cryogenic synthesis of the metallacyclobutanes, addition of pyridine, and precipitation. All are shown to decompose via second-order kinetics at -10 °C. The most vulnerable CAAC species, however, decompose more than 1000-fold faster than the H2IMes analogue. Computational studies reveal that the key factor underlying accelerated decomposition of the CAAC derivatives is their stronger trans influence, which weakens the Ru-py bond and increases the transient concentration of the 14-electron methylidene species, RuCl2(L)(═CH2) 2. Fast catalyst initiation, a major design goal in olefin metathesis, thus has the negative consequence of accelerating decomposition. Inhibiting bimolecular decomposition offers major opportunities to transform catalyst productivity and utility, and to realize the outstanding promise of olefin metathesis.

Routes to High-Performing Ruthenium-Iodide Catalysts for Olefin Metathesis: Ligand Lability Is Key to Efficient Halide Exchange

Clean, high-yielding routes are described to ruthenium-diiodide catalysts that were recently shown to enable high productivity in olefin metathesis. For the second-generation Grubbs and Hoveyda catalysts (GII: RuCl2(H2IMes)(PCy3)(=CHPh); HII: RuCl2(H2IMes)(=CHAr), Ar = C6H4-2-O i Pr), slow salt metathesis is shown to arise from the low lability of the ancillary PCy3 or ether ligands, which retards access to the four-coordinate intermediate required for efficient halide exchange. To exploit the lability of the first-generation catalysts, the diiodide complex RuI2(PCy3)(=CHAr) HI-I 2 was prepared by treating "Grubbs I" (RuCl2(PCy3)2(=CHPh), GI) with NaI, H2C=CHAr (1a), and a phosphine-scavenging Merrifield iodide (MF-I) resin. Subsequent installation of H2IMes or cyclic (alkyl)(amino)carbene (CAAC) ligands afforded the second-generation iodide catalysts in good to excellent yields. Given the incompatibility of the nitro group with a free carbene, the iodo-Grela catalyst RuI2(H2IMes)(=CHAr') (nG-I 2 : Ar' = C6H3-2-O i Pr-4-NO2) was instead accessed by sequential salt metathesis of GI with NaI, installation of H2IMes, and finally cross-metathesis with the nitrostyrenyl ether H2C=CHAr' (1b), with MF-I as the phosphine scavenger. The bulky iodide ligands improve the selectivity for macrocyclization in ring-closing metathesis.

Amphiphilic Biaryl Monophosphine Ligands by Regioselective Sulfonation

Amphiphilic ligands are valued for their ability to facilitate organometallic reactions in the presence of water. The regioselective sulfonation of a series of commercially available biaryl monophosphines to generate amphiphilic ligands is presented. In this one-step protocol, the temperature and addition of fuming sulfuric acid were carefully controlled to arrive at sulfonated biaryl monophosphine ligands in high yields with >95% regioselectivity without the need for chromatographic purification.

The Impact of Water on Ru-Catalyzed Olefin Metathesis: Potent Deactivating Effects Even at Low Water Concentrations

Ruthenium catalysts for olefin metathesis are widely viewed as water-tolerant. Evidence is presented, however, that even low concentrations of water cause catalyst decomposition, severely degrading yields. Of 11 catalysts studied, fast-initiating examples (e.g., the Grela catalyst RuCl2(H2IMes)(=CHC6H4-2-O i Pr-5-NO2) were most affected. Maximum water tolerance was exhibited by slowly initiating iodide and cyclic (alkyl)(amino)carbene (CAAC) derivatives. Computational investigations indicated that hydrogen bonding of water to substrate can also play a role, by retarding cyclization relative to decomposition. These results have important implications for olefin metathesis in organic media, where water is a ubiquitous contaminant, and for aqueous metathesis, which currently requires superstoichiometric "catalyst" for demanding reactions.

"Doubly Customizable" Unit for the Generation of Structural Diversity: From Pure Enantiomeric Amines to Peptide Derivatives

Readily available, low-cost 4R-hydroxy-l-proline (Hyp) is introduced as a "doubly customizable" unit for the generation of libraries of structurally diverse compounds. Hyp can be cleaved at two points, followed by the introduction of new functionalities. In the first cycle, the removal and replacement of the carboxylic group are carried out, followed (second cycle) by the scission of the 4,5-position and manipulation of the resulting chains. In this way, three new chains are generated and can be transformed independently to afford a diversity of products with tailored substituents, such as β-amino aldehydes, diamines, β-amino acid derivatives, including N-alkylated ones, or modified peptides. Many of these products are high-profit compounds but, in spite of their commercial value, are still scarce. Moreover, the process takes place with stereochemical control, and either pure R or S isomers can be obtained with small variations of the synthetic route.

Site-selective modification of peptide backbones

Exciting developments in the site-selective modification of peptide backbones are allowing an outstanding fine-tuning of peptide conformation, folding ability, and physico-chemical and biological properties.

Optimization of Ring-Opening Metathesis Polymerization (ROMP) under Physiologically Relevant Conditions

Ring opening metathesis polymerization (ROMP) is widely considered an excellent living polymerization technique that proceeds rapidly under ambient conditions and is highly functional group tolerant when performed in organic solvents. However, achieving the same level of success in aqueous media has proved to be challenging, often requiring an organic co-solvent or a very low pH to obtain fast initiation and high monomer conversion. The ability to efficiently conduct ROMP under neutral pH aqueous conditions would mark an important step towards utilizing aqueous ROMP with acid-sensitive functional groups or within a biological setting. Herein we describe our efforts to optimize ROMP in an aqueous environment under neutral pH conditions. Specifically, we found that the presence of excess chloride in solution as well as relatively small changes in pH near physiological conditions have a profound effect on molecular weight control, polymerization rate and overall monomer conversion. Additionally, we have applied our optimized conditions to polymerize a broad scope of water-soluble monomers and used this methodology to produce nanostructures via ring opening metathesis polymerization induced self-assembly (ROMPISA) under neutral pH aqueous conditions.