Nature Inspired Solutions for Polymers: Will Cutinase Enzymes Make Polyesters and Polyamides Greener?

5siThe polymer and plastic sectors are under the urge of mitigating their environmental impact. The need for novel and more benign catalysts for polyester synthesis or targeted functionalization led, in recent years, to an increasing interest towards cutinases due to their natural ability to hydrolyze ester bonds in cutin, a natural polymer. In this review, the most recent advances in the synthesis and hydrolysis of various classes of polyesters and polyamides are discussed with a critical focus on the actual perspectives of applying enzymatic technologies for practical industrial purposes. More specifically, cutinase enzymes are compared to lipases and, in particular, to lipase B from Candida antarctica, the biocatalyst most widely employed in polymer chemistry so far. Computational and bioinformatics studies suggest that the natural role of cutinases in attacking natural polymers confer some essential features for processing also synthetic polyesters and polyamides.openopenFerrario, Valerio; Pellis, Alessandro; Cespugli, Marco; Guebitz, Georg; Gardossi, LuciaFerrario, Valerio; Pellis, Alessandro; Cespugli, Marco; Guebitz, Georg; Gardossi, Luci

A platform for target prediction of phenotypic screening hit molecules

Many drug discovery programmes, particularly for infectious diseases, are conducted phenotypically. Identifying the targets of phenotypic screening hits experimentally can be complex, time-consuming, and expensive. However, it would be valuable to know what the molecular target(s) is, as knowledge of the binding pose of the hit molecule in the binding site can facilitate the compound optimisation. Furthermore, knowing the target would allow de-prioritisation of less attractive chemical series or molecular targets. To generate target-hypotheses for phenotypic active compounds, an in silico platform was developed that utilises both ligand and protein-structure information to generate a ranked set of predicted molecular targets. As a result of the web-based workflow the user obtains a set of 3D structures of the predicted targets with the active molecule bound. The platform was exemplified using Mycobacterium tuberculosis, the causative organism of tuberculosis. In a test that we performed, the platform was able to predict the targets of 60% of compounds investigated, where there was some similarity to a ligand in the protein database.</p

Integration of bioinformatics analysis and experimental biocatalysis for a comprehensive approach to the synthesis of renewable polyesters

La crescente domanda di poliesteri funzionalizzabili ha accresciuto l\u2019interesse nello sviluppo di nuove strade per la sintesi biocatalizzata di polimeri, dove gli enzimi sono in grado di rispondere alla sfida di combinare condizioni di reazione sostenibili dal punto di vista ambientale con l\u2019alta selettivit\ue0 ed efficienza della catalisi. Gli enzimi sono un\u2019attrattiva sostenibile ai catalizzatori tossici usati nelle policondensazione, come quelli metallici, stagno in particolare. L\u2019obiettivo di questa tesi \ue8 quello di integrare approcci sperimentali e bioinformatici per lo studio di nuovi biocatalizzatori per le policondensazioni. Una valida alternativa \ue8 infatti rappresentata dagli enzimi, i quali consentono riciclabilit\ue0, assenza di contaminazione del prodotto grazie all\u2019immobilizzazione della proteina. Attualmente, i supporti per l\u2019immobilizzazione sono di natura non rinnovabile (metacrilici e stirenici). In questa tesi (Capitolo 3) si \ue8 esplorata la possibilit\ue0 di utilizzare la lolla di riso \u2013 un economico materiale di scarto lignocellulosico - a questo proposito. Verr\ue0 proposto un confronto tra metodi chemoenzimatici per la funzionalizzazione della lolla, con l\u2019obiettivo di ottenere un supporto di immobilizzazione rinnovabile capace di rispondere alle sfide della green chemistry. Il metodo enzimatico utilizza un sistema laccasi-mediatore con l\u2019inserimento di un linker diamminico. Questo approccio consente di evitare l\u2019utilizzo del periodato di sodio, che \ue8 responsabile di importanti alterazioni nella struttura morfologica della lolla, come dimostrato da microscopia SEM. Candida antarctica Lipasi B e due asparaginasi sono state immobilizzate e testate. La lipasi immobilizzata \ue8 stata utilizzata per sintetizzare un poliestere con l\u2019acido itaconico. Mentre le lipasi sono la pi\uf9 comune scelta per le reazioni di policondensazione, il nostro gruppo si \ue8 concentrato sullo studio di nuove serin idrolasi da utilizzare in questo campo, nello specifico, le cutinasi. Questa classe di enzimi \ue8 gi\ue0 stata utilizzata per catalizzare la sintesi efficiente di poliesteri con monomeri biobased, lavorando in condizioni sostenibili dal punto di vista ambientale. Uno studio bioinformatico approfondito delle cutinasi verr\ue0 proposto nel Capitolo 4 utilizzando i descrittori GRID-based di BioGPS. Il software ha consentito di proiettare una selezione di cutinasi su un modello UPCA (Unsupervised Pattern Cognition Analysis) precedentemente studiato da questo gruppo di ricerca, confermando che l\u2019ambiente chimico-fisico pre-organizzato di Cutinasi 1 da Thermobifida cellulosilytica \ue8 molto simile a quello di Candida antarctica Lipasi B ed \ue8 in grado di offrire ulteriori vantaggi in termini di tipologie di substrato accettati grazie al suo sito attivo molto superficiale. BioGPS \ue8 stato usato anche per generare il \u201ccataloforo\u201d di differenti sottoclassi di serin idrolasi, permettendo di estrarre le caratteristiche minime proprie di ciascuna di esse. Utilizzando il \u201ccataloforo\u201d e studi di dinamica molecolare \ue8 stato possibile chiarire le ragioni alla base delle caratteristiche vantaggiose delle cutinasi nella sintesi di poliesteri.The rising demand for advanced polyesters, displaying new functional properties, has boosted the development of new biocatalysed routes for polymer synthesis, where enzymes concretely respond to the challenge of combining benign conditions with high selectivity and efficient catalysis. Enzymes are attractive sustainable alternatives to toxic catalysts used in polycondensation, such as metal catalysts and tin in particular. Moreover, they enable the synthesis of functional polyesters that are otherwise not easily accessible by using traditional chemical routes. The aim of the present thesis is to integrate experimental and bioinformatics approaches in order to study new biocatalysts to be used in polycondensations. A valid alternative to metal catalysts is represented by enzymes. Biocatalyst recyclability and avoidance of product contamination are usually obtained via enzyme immobilization on solid carriers. Nowadays, non-renewable petrochemical-based supports are used for this purpose, namely methacrylic and styrenic resins. In this thesis (Chapter 3), rice husk - a waste product of rice milling available worldwide at a negligible price - has been explored as an innovative and fully renewable lignocellulosic carrier endowed with morphological complexity and chemical versatility that makes it prone to multiple and benign chemo-enzymatic modifications. A comparison of chemical and enzymatic methods for the functionalization of rice husk has been carried out, enabling the development of a renewable immobilization carrier suitable for responding to the looming challenge of green chemistry. The enzymatic method relies on laccase oxidation using laccase from Trametes spec. and TEMPO-radical mediator, followed by the insertion of a diamine spacer. As compared to the classical cellulose oxidation performed via sodium periodate, the enzymatic method offers the advantage of preserving the morphology of rice husk, as demonstrated by SEM microscopy. Laccase oxidation also assures benign operative conditions. Candida antarctica Lipase B, and two commercially available formulations of asparaginase, were immobilized and tested. In the first case, the lipase was successfully applied in the polycondensation of the biobased monomer dimethyl itaconate whereas the immobilized asparaginases were applied in the hydrolysis of asparagine, a precursor of the toxic acrylamide in food. In addition, lignin removal via alkaline hydrogen peroxide bleaching has been tested as a method for increasing the specific activity of the immobilized formulation. While lipases being the most common alternative for polycondensation reactions, our research group focused on the study of a novel class of serine hydrolases to be used in these kind of reactions, namely the cutinases. The cutinase class proved to catalyse the efficient polycondensation of biobased monomers working in mild conditions in terms of pressure and temperature. A thorough bioinformatics study was carried out based on GRID-based BioGPS descriptors (Chapter 4). BioGPS allowed to project a selection of cutinases on a Unsupervised Pattern Cognition Analysis (UPCA) model previously published by this research group, confirming that the pre-organized physicochemical environment in the active site of Cutinase 1 from Thermobifida cellulosilytica is very similar to the one of Candida antarctica Lipase B, while offering increased capabilities in terms of the size of the substrate accepted, thanks to a superficial and wide active site. The said software was used also to generate the \u201ccatalophor\u201d of different serine hydrolase subfamilies, enabling to extract the structural features that distinguish the various sub-families of serine hydrolases. Exploiting the \u201ccatalophor\u201d tool and molecular dynamics studies it was possible to shed light on the particular behaviour that makes cutinases an advantageous biocatalyst to be used in polycondensation reactions

Fully renewable polyesters via polycondensation catalyzed by Thermobifida cellulosilytica cutinase 1: an integrated approach

The present study addresses comprehensively the problem of producing polyesters through sustainable processes while using fully renewable raw materials and biocatalysts. Polycondensation of bio-based dimethyl adipate with different diols was catalyzed by cutinase 1 from Thermobifida cellulosilytica (Thc_cut1) under solvent free and thin-film conditions. The biocatalyst was immobilized efficiently on a fully renewable cheap carrier based on milled rice husk. A multivariate factorial design demonstrated that Thc_cut1 is less sensitive to the presence of water in the system and it works efficiently under milder conditions (50 \ub0C; 535 mbar) when compared to lipase B from Candida antarctica (CaLB), thus enabling energy savings. Experimental and computational investigations of cutinase 1 from Thermobifida cellulosilytica (Thc_cut1) disclosed structural and functional features that make this serine-hydrolase efficient in polycondensation reactions. Bioinformatic analysis performed with the BioGPS tool pointed out functional similarities with CaLB and provided guidelines for future engineering studies aiming, for instance, at introducing different promiscuous activities in the Thc_cut1 scaffold. The results set robust premises for a full exploitation of enzymes in environmentally and economically sustainable enzymatic polycondensation reactions

Criteria for Engineering Cutinases: Bioinformatics Analysis of Catalophores

Cutinases are bacterial and fungal enzymes that catalyze the hydrolysis of natural cutin, a three-dimensional inter-esterified polyester with epoxy-hydroxy fatty acids with chain lengths between 16 and 18 carbon atoms. Due to their ability to accept long chain substrates, cutinases are also effective in catalyzing in vitro both the degradation and synthesis of several synthetic polyesters and polyamides. Here, we present a bioinformatics study that intends to correlate the structural features of cutinases with their catalytic properties to provide rational basis for their effective exploitation, particularly in polymer synthesis and biodegradation. The bioinformatics study used the BioGPS method (Global Positioning System in Biological Space) that computed molecular descriptors based on Molecular Interaction Fields (MIFs) described in the GRID force field. The information was used to generate catalophores, spatial representations of the ability of each enzymatic active site to establish hydrophobic and electrostatic interactions. These tools were exploited for comparing cutinases to other serine-hydrolases enzymes, namely lipases, esterases, amidases and proteases, and for highlighting differences and similarities that might guide rational engineering strategies. Structural features of cutinases with their catalytic properties were correlated. The \u201ccatalophore\u201d of cutinases indicate shared features with lipases and esterases

Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential

: The steadily growing number of experimental G-protein-coupled receptor (GPCR) structures has revealed diverse locations of allosteric modulation, and yet few drugs target them. This gap highlights the need for a deeper understanding of allosteric modulation in GPCR drug discovery. The current work introduces a systematic annotation scheme to structurally classify GPCR binding sites based on receptor class, transmembrane helix contacts, and, for membrane-facing sites, membrane sublocation. This GPCR specific annotation scheme was applied to 107 GPCR structures bound by small molecules contributing to 24 distinct allosteric binding sites for comparative evaluation of three binding site detection methods (BioGPS, SiteMap, and FTMap). BioGPS identified the most in 22 of 24 sites. In addition, our property analysis showed that extrahelical allosteric ligands and binding sites represent a distinct chemical space characterized by shallow pockets with low volume, and the corresponding allosteric ligands showed an enrichment of halogens. Furthermore, we demonstrated that combining receptor and ligand similarity can be a viable method for ligandability assessment. One challenge regarding site prediction is the ligand shaping effect on the observed binding site, especially for extrahelical sites where the ligand-induced effect was most pronounced. To our knowledge, this is the first study presenting a binding site annotation scheme standardized for GPCRs, and it allows a comparison of allosteric binding sites across different receptors in an objective way. The insight from this study provides a framework for future GPCR binding site studies and highlights the potential of targeting allosteric sites for drug development

Detecting similar binding pockets to enable systems polypharmacology

In the era of systems biology, multi-target pharmacological strategies hold promise for tackling disease-related networks. In this regard, drug promiscuity may be leveraged to interfere with multiple receptors: the so-called polypharmacology of drugs can be anticipated by analyzing the similarity of binding sites across the proteome. Here, we perform a pairwise comparison of 90,000 putative binding pockets detected in 3,700 proteins, and find that 23,000 pairs of proteins have at least one similar cavity that could, in principle, accommodate similar ligands. By inspecting these pairs, we demonstrate how the detection of similar binding sites expands the space of opportunities for the rational design of drug polypharmacology. Finally, we illustrate how to leverage these opportunities in protein-protein interaction networks related to several therapeutic classes and tumor types, and in a genome-scale metabolic model of leukemia

Nanoinformatics: a new area of research in nanomedicine

Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and ?omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings

Selection of protein conformations for structure-based polypharmacology studies

Several drugs exert their therapeutic effect through the modulation of multiple targets. Structure-based approaches hold great promise for identifying compounds with the desired polypharmacological profiles. These methods use knowledge of the protein binding sites to identify stereoelectronically complementary ligands. The selection of the most suitable protein conformations to be used in the design process is vital, especially for multitarget drug design in which the same ligand has to be accommodated in multiple binding pockets. Herein, we focus on currently available techniques for the selection of the most suitable protein conformations for multitarget drug design, compare the potential advantages and limitations of each method, and comment on how their combination could help in polypharmacology drug design