Enzymatic polyethylene biorecycling: Confronting challenges and shaping the future.

Polyethylene (PE) is a widely used plastic known for its resistance to biodegradation, posing a significant environmental challenge. Recent advances have shed light on microorganisms and insects capable of breaking down PE and identified potential PE-degrading enzymes (PEases), hinting at the possibility of PE biorecycling. Research on enzymatic PE degradation is still in its early stages, especially compared to the progress made with polyethylene terephthalate (PET). While PET hydrolases have been extensively studied and engineered for improved performance, even the products of PEases remain mostly undefined. This Perspective analyzes the current state of enzymatic PE degradation research, highlighting obstacles in the search for bona fide PEases and suggesting areas for future exploration. A critical challenge impeding progress in this field stems from the inert nature of the C-C and C-H bonds of PE. Furthermore, breaking down PE into small molecules using only one monofunctional enzyme is theoretically impossible. Overcoming these obstacles requires identifying enzymatic pathways, which can be facilitated using emerging technologies like omics, structure-based design, and computer-assisted engineering of enzymes. Understanding the mechanisms underlying PE enzymatic biodegradation is crucial for research progress and for identifying potential solutions to the global plastic pollution crisis.

1,5,7-Triazabicyclo[4.4.0]dec-5-ene: An Effective Catalyst for Amide Formation by Lactone Aminolysis.

The amide is one of the most prevalent functional groups throughout natural and engineered chemical space. Among various methods of constructing amide bonds, lactone aminolysis remains one of the most atom economical. Herein, we report 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) as an effective catalyst for lactone aminolysis under mild conditions. This methodology is compatible with a wide range of lactones and amines (>50 examples), including various natural products and pharmaceuticals, and applicable to the synthesis of bioactive molecules. Detailed mechanistic studies under synthetically relevant conditions, including reaction progress kinetic analysis and variable time normalization analysis, reveal a likely mechanism for this reaction involving acyl-TBD as the reactive intermediate.

Deuteration for Metabolic Stabilization of SARS-CoV-2 Inhibitors GC373 and Nirmatrelvir.

Nirmatrelvir and GC373 inhibit the SARS-CoV-2 3CL protease and hinder viral replication in COVID-19. As nirmatrelvir in Paxlovid is oxidized by cytochrome P450 3A4, ritonavir is coadministered to block this. However, ritonavir undesirably alters the metabolism of other drugs. Hydrogens can be replaced with deuterium in nirmatrelvir and GC373 to slow oxidation. Results show that deuterium slows oxidation of nirmatrelvir adjacent to nitrogen by ∼40% and that the type of warhead can switch the site of oxidative metabolism.

Solid-State Enzymatic Hydrolysis of Mixed PET/Cotton Textiles.

Waste polyester textiles are not recycled due to separation challenges and partial structural degradation during use and recycling. Chemical recycling of polyethylene terephthalate (PET) textiles through depolymerization can provide a feedstock of recycled monomers to make "as-new" polymers. While enzymatic PET recycling is a more selective and more sustainable approach, methods in development, however, have thus far been limited to clean, high-quality PET feedstocks, and require an energy-intensive melt-amorphization step ahead of enzymatic treatment. Here, high-crystallinity PET in mixed PET/cotton textiles could be directly and selectively depolymerized to terephthalic acid (TPA) by using a commercial cutinase from Humicola insolens under moist-solid reaction conditions, affording up to 30±2 % yield of TPA. The process was readily combined with cotton depolymerization through simultaneous or sequential application of the cellulase enzymes CTec2®, providing up to 83±4 % yield of glucose without any negative influence on the TPA yield.

Semisynthetic transformation of banana peel to enhance the conversion of sugars to 5-hydroxymethylfurfural.

This study aimed to efficiently convert banana peels (BP) into 5-hydroxymethylfurfural (HMF) by using an integrated mechanoenzymatic/catalytic approach. There is no report on HMF production using mechanoenzymatic hydrolysis. Moreover, this method enables saccharification of lignocellulose without bulk solvents or pretreatment. The effects of the reaction volume, milling time, and reactive aging (RAging) on the mechanoenzymatic hydrolysis of BP were studied. The solvent-free enzymatic hydrolysis of BP under RAging conditions was found to provide higher glucose (40.5 wt%) and fructose (17.2 wt%) yields than chemical hydrolysis. Next, the conversion of the resulting monosaccharides into HMF in the presence of the AlCl3·H2O/HCl-DMSO/H2O system resulted in 71.9 mol% yield, which is so far the highest HMF yield obtained from cellulosic food wastes. Under identical reaction conditions, direct conversion of untreated BP to HMF yielded 22.7 mol% HMF, suggesting that mechanoenzymatic hydrolysis greatly promotes the release of sugars from BP to improve HMF yield.

Mechanoenzymatic Reactions Involving Polymeric Substrates or Products.

Mechanoenzymology is an emerging field in which mechanical mixing is used to sustain enzymatic reactions in low-solvent or solvent-free mixtures. Many enzymes have been reported that thrive under such conditions. Considering the central role of biopolymers and synthetic polymers in our society, this minireview highlights the use of mechanoenzymology for the synthesis or depolymerization of oligomeric or polymeric materials. In contrast to traditional in-solution reactions, solvent-free mechanoenzymology has the advantages of avoiding solubility issues, proceeding in a minimal volume, and reducing solvent waste while potentially improving the reaction efficiency and accessing new reactivity. It is expected that this strategy will continue to gain popularity and find more applications.

Enzymatic depolymerization of highly crystalline polyethylene terephthalate enabled in moist-solid reaction mixtures.

Less than 9% of the plastic produced is recycled after use, contributing to the global plastic pollution problem. While polyethylene terephthalate (PET) is one of the most common plastics, its thermomechanical recycling generates a material of lesser quality. Enzymes are highly selective, renewable catalysts active at mild temperatures; however, they lack activity toward the more crystalline forms of PET commonly found in consumer plastics, requiring the energy-expensive melt-amorphization step of PET before enzymatic depolymerization. We report here that, when used in moist-solid reaction mixtures instead of the typical dilute aqueous solutions or slurries, the cutinase from Humicola insolens can directly depolymerize amorphous and crystalline regions of PET equally, without any pretreatment, with a 13-fold higher space-time yield and a 15-fold higher enzyme efficiency than reported in prior studies with high-crystallinity material. Further, this process shows a 26-fold selectivity for terephthalic acid over other hydrolysis products.

Structural Dynamics of Cytochrome P450 3A4 in the Presence of Substrates and Cytochrome P450 Reductase.

Cytochrome P450 3A4 (CYP3A4) is the most important drug-metabolizing enzyme in humans and has been associated with harmful drug interactions. The activity of CYP3A4 is known to be modulated by several compounds and by the electron transfer partner, cytochrome P450 reductase (CPR). The underlying mechanism of these effects, however, is poorly understood. We have used hydrogen-deuterium exchange mass spectrometry to investigate the impact of binding of CPR and of three different substrates (7-benzyloxy-4-trifluoromethyl-coumarin, testosterone, and progesterone) on the conformational dynamics of CYP3A4. Here, we report that interaction of CYP3A4 with substrates or with the oxidized or reduced forms of CPR leads to a global rigidification of the CYP3A4 structure. This was evident from the suppression of deuterium exchange in several regions of CYP3A4, including regions known to be involved in protein-protein interactions (helix C) and substrate binding and specificity (helices B' and E, and loop K/ß1). Furthermore, the bimodal isotopic distributions observed for some CYP3A4-derived peptides were drastically impacted upon binding to CPR and/or substrates, suggesting the existence of stable CYP3A4 conformational populations that are perturbed by ligand/CPR binding. The results have implications for understanding the mechanisms of ligand binding, allostery, and catalysis in CYP enzymes.

Effect of pH on the antimicrobial activity of the macrophage metabolite itaconate.

The production of itaconate by macrophages was only discovered in 2011. An increasing number of studies have since revealed essential biological functions for this small molecule, ranging from antimicrobial to immunomodulator. The antibacterial role of itaconate has however been questioned because the estimated concentration of itaconate in macrophages (low-millimolar) is lower than the minimum inhibitory concentration (MIC) of itaconate reported for several bacterial strains (low-to-mid-millimolar). We note that some of these investigations have tended to ignore the high acidity of this small diacid (pKas 3.85 and 5.45), thereby potentially biassing activity measurements. We measured the MIC of itaconate in Escherichia coli (not known to metabolize itaconate) and in Salmonella enterica serovar Typhimurium (known to metabolize itaconate) at varying pH values to probe the effect that pH has on itaconate toxicity. Herein, we demonstrate that the antimicrobial effect of itaconate is dependent upon the pH of the media and that itaconate does have antimicrobial activity at biologically relevant pH and concentrations. Under nutrient-poor conditions, the antimicrobial activity of itaconate in both E. coli and S. Typhimurium increased approximately 200-fold when the pH was dropped by one unit, whereas itaconate was not found to be toxic under nutrient rich conditions. Our results also reveal that the activity of itaconate is synergistic with acidity, yet is not a function of increased permeability with protonation. Similar experiments performed with succinate (a pKa-matched diacid) yielded drastically different results, consistent with a target-based mechanism of action for itaconate. Overall, our work shows the importance of controlling the pH when performing experiments with itaconic acid.

Exploring Heteroaromatic Rings as a Replacement for the Labile Amide of Antiplasmodial Pantothenamides.

Malaria-causing Plasmodium parasites are developing resistance to antimalarial drugs, providing the impetus for new antiplasmodials. Although pantothenamides show potent antiplasmodial activity, hydrolysis by pantetheinases/vanins present in blood rapidly inactivates them. We herein report the facile synthesis and biological activity of a small library of pantothenamide analogues in which the labile amide group is replaced with a heteroaromatic ring. Several of these analogues display nanomolar antiplasmodial activity against Plasmodium falciparum and/or Plasmodium knowlesi, and are stable in the presence of pantetheinase. Both a known triazole and a novel isoxazole derivative were further characterized and found to possess high selectivity indices, medium or high Caco-2 permeability, and medium or low microsomal clearance in vitro. Although they fail to suppress Plasmodium berghei proliferation in vivo, the pharmacokinetic and contact time data presented provide a benchmark for the compound profile likely required to achieve antiplasmodial activity in mice and should facilitate lead optimization.

Combining Small-Molecule Bioconjugation and Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) to Expose Allostery: the Case of Human Cytochrome P450 3A4.

We report a novel approach to study allostery which combines the use of carefully selected bioconjugates and hydrogen-deuterium exchange mass spectrometry (HDX-MS). This strategy avoids issues related to weak substrate binding and ligand relocalization. The utility of our method is demonstrated using human cytochrome P450 3A4 (CYP3A4), the most important drug-metabolizing enzyme. Allosteric activation and inhibition of CYP3A4 by pharmaceuticals is an important mechanism of drug interactions. We performed HDX-MS analysis on several CYP3A4-effector bioconjugates, some of which mimic the allosteric effect of positive effectors, while others show activity enhancement even though the label does not occupy the allosteric pocket (agonistic) or do not show activation while still blocking the allosteric site (antagonistic). This allowed us to better define the position of the allosteric site, the protein structural dynamics associated with allosteric activation, and the presence of coexisting conformers.

Comparative evaluation of itaconate and its derivatives reveals divergent inflammasome and type I interferon regulation in macrophages.

Following activation, macrophages undergo extensive metabolic rewiring1,2. Production of itaconate through the inducible enzyme IRG1 is a key hallmark of this process3. Itaconate inhibits succinate dehydrogenase4,5, has electrophilic properties6 and is associated with a change in cytokine production4. Here, we compare the metabolic, electrophilic and immunologic profiles of macrophages treated with unmodified itaconate and a panel of commonly used itaconate derivatives to examine its role. Using wild-type and Irg1-/- macrophages, we show that neither dimethyl itaconate, 4-octyl itaconate nor 4-monoethyl itaconate are converted to intracellular itaconate, while exogenous itaconic acid readily enters macrophages. We find that only dimethyl itaconate and 4-octyl itaconate induce a strong electrophilic stress response, in contrast to itaconate and 4-monoethyl itaconate. This correlates with their immunosuppressive phenotype: dimethyl itaconate and 4-octyl itaconate inhibited IκBζ and pro-interleukin (IL)-1ß induction, as well as IL-6, IL-10 and interferon-ß secretion, in an NRF2-independent manner. In contrast, itaconate treatment suppressed IL-1ß secretion but not pro-IL-1ß levels and, surprisingly, strongly enhanced lipopolysaccharide-induced interferon-ß secretion. Consistently, Irg1-/- macrophages produced lower levels of interferon and reduced transcriptional activation of this pathway. Our work establishes itaconate as an immunoregulatory, rather than strictly immunosuppressive, metabolite and highlights the importance of using unmodified itaconate in future studies.

Towards Controlling the Reactivity of Enzymes in Mechanochemistry: Inert Surfaces Protect ß-Glucosidase Activity During Ball Milling.

The activity of ß-glucosidases-the enzymes responsible for the final step in the enzymatic conversion of cellulose to glucose-can be maintained and manipulated under mechanochemical conditions in the absence of bulk solvent, either through an unexpected stabilization effect of inert surfaces, or by altering the enzymatic equilibrium. The reported results illustrate unique aspects of mechanoenzymatic reactions that are not observable in conventional aqueous solutions. They also represent the first reported strategies to enhance activity and favor either direction of the reaction under mechanochemical conditions.

Mechanoenzymatic Transformations in the Absence of Bulk Water: A More Natural Way of Using Enzymes.

Mechanochemical enzymatic reactions without bulk water have emerged as a low-waste and efficient method to access useful chemicals and to depolymerize biomass components in a single step. This emergent mechanoenzymatic reaction strategy is able to take advantage of the stereospecificity, regio- and stereoselectivity, as well as renewability of enzymes, while avoiding bulk solvents, offering the opportunity to control the direction of the reaction, bypassing reactant solubility issues, and enabling reactions with water-sensitive substrates or products. Enzymes are traditionally used in dilute aqueous solution, which is quite different from their crowded, water-depleted natural environment. This review outlines recent work which demonstrates that enzymes can be equally or even more efficient under mechanochemical conditions, without bulk aqueous or organic solvent.

Efficient Enzymatic Hydrolysis of Biomass Hemicellulose in the Absence of Bulk Water.

Current enzymatic methods for hemicellulosic biomass depolymerization are solution-based, typically require a harsh chemical pre-treatment of the material and large volumes of water, yet lack in efficiency. In our study, xylanase (E.C. 3.2.1.8) from Thermomyces lanuginosus is used to hydrolyze xylans from different sources. We report an innovative enzymatic process which avoids the use of bulk aqueous, organic or inorganic solvent, and enables hydrolysis of hemicellulose directly from chemically untreated biomass, to low-weight, soluble oligoxylosaccharides in >70% yields.

Inhibition and Activation of Kinases by Reaction Products: A Reporter-Free Assay.

Kinases are widely distributed in nature and are implicated in many human diseases. Thus, an understanding of their activity and regulation is of fundamental importance. Several kinases are known to be inhibited by ADP. However, thorough investigation of this phenomenon is hampered by the lack of a simple and effective assay for studying this inhibition. We now present a quick, general approach for measuring the effects of reaction products on kinase activity. The method, based on isothermal titration calorimetry, is the first universal, reporter-free, continuous assay for probing kinase inhibition or activation by ADP. In applications to an aminoglycoside phosphotransferase [APH(3')-IIIa] and pantothenate kinases from Escherichia coli (EcPanK) and Pseudomonas aeruginosa (PaPanK), we found ADP to be an efficient inhibitor of all three kinases, with inhibition constant (Ki) values similar to or lower than the Michaelis-Menten constant (Km) values of ATP. Interestingly, ADP was an activator at low concentrations and an inhibitor at high concentrations for EcPanK. This unusual effect was quantitatively modeled and attributed to cooperative interactions between the two subunits of the dimeric enzyme. Importantly, our results suggest that, at typical bacterial intracellular concentrations of ATP and ADP (approximately 1.5 mM and 180 µM, respectively), all three kinases are partially inhibited by ADP, allowing enzyme activity to rapidly respond to changes in the levels of both metabolites.

The coenzyme A biosynthetic pathway: A new tool for prodrug bioactivation.

Prodrugs account for more than 5% of pharmaceuticals approved worldwide. Over the past decades several prodrug design strategies have been firmly established; however, only a few functional groups remain amenable to this approach. The aim of this overview is to highlight the use of coenzyme A (CoA) biosynthetic enzymes as a recently explored bioactivation scheme and provide information about its scope of utility. This emerging tool is likely to have a strong impact on future medicinal and biological studies as it offers promiscuity, orthogonal selectivity, and the capability of assembling exceptionally large molecules.

Mechanoenzymatic Breakdown of Chitinous Material to N-Acetylglucosamine: The Benefits of a Solventless Environment.

Chitin is not only the most abundant nitrogen-containing biopolymer on the planet, but also a renewable feedstock that is often treated as a waste. Current chemical methods to break down chitin typically employ harsh conditions, large volumes of solvent, and generate a mixture of products. Although enzymatic methods have been reported, they require a harsh chemical pretreatment of the chitinous substrate and rely on dilute solution conditions that are remote from the natural environment of microbial chitinase enzymes, which typically consists of surfaces exposed to air and moisture. We report an innovative and efficient mechanoenzymatic method to hydrolyze chitin to the N-acetylglucosamine monomer by using chitinases under the recently developed reactive aging (RAging) methodology, based on repeating cycles of brief ball-milling followed by aging, in the absence of bulk solvent. Our results demonstrate that the activity of chitinases increases several times by switching from traditional solution-based conditions of enzymatic catalysis to solventless RAging, which operates on moist solid substrates. Importantly, RAging is also highly efficient for the production of N-acetylglucosamine directly from shrimp and crab shell biomass without any other processing except for a gentle wash with aqueous acetic acid.

A Covalently Attached Progesterone Molecule Outcompetes the Binding of Free Progesterone at an Allosteric Site of Cytochrome P450 3A4.

Because of its exceptional substrate promiscuity, human P450 3A4 (CYP3A4) is arguably the most important drug-metabolizing enzyme. CYP3A4 also has the particularity of binding multiple ligands simultaneously, which is associated with heterotropic or homotropic, positive or negative, cooperativity or allostery. Solving the kinetics of such complex systems remains challenging, and so is identifying the binding pockets involved. Progesterone (PRG) is a known allosteric activator of CYP3A4-catalyzed 7-benzyloxy-4-trifluoromethylcoumarin (BFC) debenzylation. We report herein the use of bioconjugation as a successful strategy to identify this PRG allosteric site. A progesterone analogue (PGM) was covalently attached, separately at several locations, near a peripheral binding pocket previously proposed to be an allosteric site. Studies of BFC debenzylation in the presence of free PRG revealed that two of the bioconjugates successfully positioned the covalently attached PGM moiety in a way that mimics the allosteric activation observed with free PRG. Interestingly, the PGM bioconjugate with the better fit yielded a higher permanent activation of the enzyme.

Probing the ligand preferences of the three types of bacterial pantothenate kinase.

Pantothenate kinase (PanK) catalyzes the transformation of pantothenate to 4'-phosphopantothenate, the first committed step in coenzyme A biosynthesis. While numerous pantothenate antimetabolites and PanK inhibitors have been reported for bacterial type I and type II PanKs, only a few weak inhibitors are known for bacterial type III PanK enzymes. Here, a series of pantothenate analogues were synthesized using convenient synthetic methodology. The compounds were exploited as small organic probes to compare the ligand preferences of the three different types of bacterial PanK. Overall, several new inhibitors and substrates were identified for each type of PanK.