Too sweet: cheminformatics for deglycosylation in natural products

An Effective Computational Strategy for UGTs Catalytic Function Prediction

The GT-B type glycosyltransferases play a crucial post-modification role in synthesizing natural products, such as triterpenoid and steroidal saponins, renowned for their diverse pharmacological activities. Despite phylogenetic analysis aiding in enzyme family classification, distinguishing substrate specificity between triterpenoid and steroidal saponins, with their highly similar cyclic scaffolds, remains a formidable challenge. Our studies unveil the potential transport tunnels for the glycosyl donor and acceptor in PpUGT73CR1, by molecular dynamics simulations. This revelation leads to a plausible substrate transport mechanism, highlighting the regulatory role of the N-terminal domain (NTD) in glycosyl acceptor binding and transport. Inspired by these structural and mechanistic insights, we further analyze the binding pockets of 44 plant-derived UGTs known to glycosylate triterpenes and sterols. Notably, sterol UGTs are found to harbor aromatic and hydrophobic residues with polar residues typically present at the bottom of the active pocket. Drawing inspiration from the substrate binding and product release mechanism revealed through structure-based molecular modeling, we devised a fast sequence-based method for classifying UGTs using the pre-trained ESM2 protein model. This method involved extracting the NTD features of UGTs and performing PCA clustering analysis, enabling accurate identification of enzyme function, and even differentiation of substrate specificity/promiscuity between structurally similar triterpenoid and steroidal substrates, which is further validated by experiments. This work not only deepens our understanding of substrate binding mechanisms but also provides an effective computational protocol for predicting the catalytic function of unknown UGTs.

Toward integration of glycan chemical databases: an algorithm and software tool for extracting sugars from chemical structures

Integration of glycan-related databases between different research fields is essential in glycoscience. It requires knowledge across the breadth of science because most glycans exist as glycoconjugates. On the other hand, especially between chemistry and biology, glycan data has not been easy to integrate due to the huge variety of glycan structure representations. We have developed WURCS (Web 3.0 Unique Representation of Carbohydrate Structures) as a notation for representing all glycan structures uniquely for the purpose of integrating data across scientific data resources. While the integration of glycan data in the field of biology has been greatly advanced, in the field of chemistry, progress has been hampered due to the lack of appropriate rules to extract sugars from chemical structures. Thus, we developed a unique algorithm to determine the range of structures allowed to be considered as sugars from the structural formulae of compounds, and we developed software to extract sugars in WURCS format according to this algorithm. In this manuscript, we show that our algorithm can extract sugars from glycoconjugate molecules represented at the molecular level and can distinguish them from other biomolecules, such as amino acids, nucleic acids, and lipids. Available as software, MolWURCS is freely available and downloadable ( https://gitlab.com/glycoinfo/molwurcs ).

COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database

The COCONUT (COlleCtion of Open Natural prodUcTs) database was launched in 2021 as an aggregation of openly available natural product datasets and has been one of the biggest open natural product databases since. Apart from the chemical structures of natural products, COCONUT contains information about names and synonyms, species and organism parts in which the natural product has been found, geographic information about where the respective sample has been collected and literature references, where available. COCONUT is openly accessible at https://coconut.naturalproducts.net. Users can search textual information and perform structure, substructure, and similarity searches. The data in COCONUT are available for bulk download as SDF, CSV and a database dump. The web application for accessing the data is open-source. Here, we describe COCONUT 2.0, for which the web application has been completely rewritten, and the data have been newly assembled and extensively curated. New features include data submissions by users and community curation facilitated in various ways.

Time-Dependent Comparison of the Structural Variations of Natural Products and Synthetic Compounds

The identification of natural products (NPs) has played a pivotal role in drug discovery and shaped the evolution of synthetic compounds (SCs). However, the extent to which NPs have historically influenced the structural characteristics of SCs remains unclear. In this study, we conducted a comprehensive, time-dependent chemoinformatic analysis to investigate the impact of NPs on the structural evolution of SCs. The physicochemical properties, molecular fragments, biological relevance, and chemical space of the molecules from the Dictionary of Natural Products were compared in a time series fashion with a synthetic compound collection sourced from 12 databases. Our findings reveal that NPs have become larger, more complex, and more hydrophobic over time, exhibiting increased structural diversity and uniqueness. Conversely, SCs exhibit a continuous shift in physicochemical properties, yet these changes are constrained within a defined range governed by drug-like constraints. SCs possess a broader range of synthetic pathways and structural diversity, albeit with a decline in biological relevance. The chemical space of NPs has become less concentrated compared to that of SCs. In conclusion, our study suggests that the structural evolution of SCs is influenced by NPs to some extent; however, SCs have not fully evolved in the direction of NPs.

A terpenoids database with the chemical content as a novel agronomic trait

Natural products play a pivotal role in drug discovery, and the richness of natural products, albeit significantly influenced by various environmental factors, is predominantly determined by intrinsic genetics of a series of enzymatic reactions and produced as secondary metabolites of organisms. Heretofore, few natural product-related databases take the chemical content into consideration as a prominent property. To gain unique insights into the quantitative diversity of natural products, we have developed the first TerPenoids database embedded with Content information (TPCN) with features such as compound browsing, structural search, scaffold analysis, similarity analysis and data download. This database can be accessed through a web-based computational toolkit available at http://www.tpcn.pro/. By conducting meticulous manual searches and analyzing over 10 000 reference papers, the TPCN database has successfully integrated 6383 terpenoids obtained from 1254 distinct plant species. The database encompasses exhaustive details including isolation parts, comprehensive molecule structures, chemical abstracts service registry number (CAS number) and 7508 content descriptions. The TPCN database accentuates both the qualitative and quantitative dimensions as invaluable phenotypic characteristics of natural products that have undergone genetic evolution. By acting as an indispensable criterion, the TPCN database facilitates the discovery of drug alternatives with high content and the selection of high-yield medicinal plant species or phylogenetic alternatives, thereby fostering sustainable, cost-effective and environmentally friendly drug discovery in pharmaceutical farming. Database URL: http://www.tpcn.pro/.

Cheminformatics Microservice: unifying access to open cheminformatics toolkits

In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management. In this work, we present the Cheminformatics Microservice. This open-source solution provides a unified interface for accessing commonly used functionalities of multiple cheminformatics toolkits, namely RDKit, Chemistry Development Kit (CDK), and Open Babel. In addition, more advanced functionalities like structure generation and Optical Chemical Structure Recognition (OCSR) are made available through the Cheminformatics Microservice based on pre-existing tools. The software service also enables developers to extend the functionalities easily and to seamlessly integrate them with existing workflows and applications. It is built on FastAPI and containerized using Docker, making it highly scalable. An instance of the microservice is publicly available at https://api.naturalproducts.net . The source code is publicly accessible on GitHub, accompanied by comprehensive documentation, version control, and continuous integration and deployment workflows. All resources can be found at the following link: https://github.com/Steinbeck-Lab/cheminformatics-microservice .

A chemoinformatic analysis on natural glycosides with respect to biological origin and structural class

Covering: up to 202216.19% of reported natural products (NPs) in the Dictionary of Natural Products (DNP) are glycosides. As one of the most important NPs' structural modifications, glycosylation can change the NPs' polarity, making the aglycones more amphipathic. However, until now, little is known about the general distribution profile of the natural glycosides in different biological sources or structural types. The reason, structural or species preferences of the natural glycosylation remain unclear. In this highlight, chemoinformatic methods were employed to analyze the natural glycosides from DNP, the most comprehensively annotated NP database. We found that the glycosylation ratios of NPs from plants, bacteria, animals and fungi decrease successively, which are 24.99%, 20.84%, 8.40% and 4.48%, respectively. Echinoderm-derived NPs (56.11%) are the most frequently glycosylated, while those produced by molluscs (1.55%), vertebrates (2.19%) and Rhodophyta (3.00%) are the opposite. Among the diverse structural types, a large proportion of steroids (45.19%), tannins (44.78%) and flavonoids (39.21%) are glycosides, yet aminoacids and peptides (5.16%), alkaloids (5.66%) are comparatively less glycosylated. Even within the same biological source or structural type, their glycosylation rates fluctuate drastically between sub- or cross-categories. The substitute patterns of flavonoid and terpenoid glycosides and the most frequently glycosylated scaffolds were identified. NPs with different glycosylation levels occupy different chemical spaces of physicochemical property and scaffold. These findings could help us to interpret the preference of NPs' glycosylation and investigate how NP glycosylation could aid NP-based drug discovery.

Antioxidant capacity of simplified oxygen heterocycles and proposed derivatives by theoretical calculations

CONTEXT

Some structural properties can be involved in the antioxidant capacity of several polyphenol derivatives, among them their simplified structures. This study examines the contribution of simplified structure for the antioxidant capacity of some natural and synthetic antioxidants. The resonance structures were related to the π-type electron system of carbon-carbon double bonds between both phenyl rings. Trans-resveratrol, phenyl-benzofuran, phenyl-indenone, and benzylidene-benzofuranone are the best basic antioxidant templates among the simplified derivatives studied here. Additionally, the stilbene moiety was found on the molecules with the best antioxidant capacity. Furthermore, our investigation suggests that these compounds can be used as antioxidant scaffold for designing and developing of new promising derivatives.

METHODS

To investigate the structure-antioxidant capacity for sixteen simplified natural and proposed derivatives we have employed density functional theory and used Gaussian 09. Our DFT calculations were performed using the B3LYP functional and the 6-31+G(d,p) basis set. All electron transfer mechanisms were investigated by using values of HOMO, ionization potential, energy affinity, stabilization energies, and spin density distributions.

Two years of explicit CiTO annotations

Citations are an essential aspect of research communication and have become the basis of many evaluation metrics in the academic world. Some see citation counts as a mark of scientific impact or even quality, but in reality the reasons for citing other work are manifold which makes the interpretation more complicated than a single citation count can reflect. Two years ago, the Journal of Cheminformatics proposed the CiTO Pilot for the adoption of a practice of annotating citations with their citation intentions. Basically, when you cite a journal article or dataset (or any other source), you also explain why specifically you cite that source. Particularly, the agreement and disagreement and reuse of methods and data are of interest. This article explores what happened after the launch of the pilot. We summarize how authors in the Journal of Cheminformatics used the pilot, shows citation annotations are distributed with Wikidata, visualized with Scholia, discusses adoption outside BMC, and finally present some thoughts on what needs to happen next.

MORTAR: a rich client application for in silico molecule fragmentation

Developing and implementing computational algorithms for the extraction of specific substructures from molecular graphs (in silico molecule fragmentation) is an iterative process. It involves repeated sequences of implementing a rule set, applying it to relevant structural data, checking the results, and adjusting the rules. This requires a computational workflow with data import, fragmentation algorithm integration, and result visualisation. The described workflow is normally unavailable for a new algorithm and must be set up individually. This work presents an open Java rich client Graphical User Interface (GUI) application to support the development of new in silico molecule fragmentation algorithms and make them readily available upon release. The MORTAR (MOlecule fRagmenTAtion fRamework) application visualises fragmentation results of a set of molecules in various ways and provides basic analysis features. Fragmentation algorithms can be integrated and developed within MORTAR by using a specific wrapper class. In addition, fragmentation pipelines with any combination of the available fragmentation methods can be executed. Upon release, three fragmentation algorithms are already integrated: ErtlFunctionalGroupsFinder, Sugar Removal Utility, and Scaffold Generator. These algorithms, as well as all cheminformatics functionalities in MORTAR, are implemented based on the Chemistry Development Kit (CDK).

Substituents of life: The most common substituent patterns present in natural products

Comparison of substituents present in natural products with the substituents found in average synthetic molecules reveals considerable differences between these two groups. The natural products substituents contain mostly oxygen heteroatoms, are structurally more complex, often containing double bonds and are rich in stereocenters. Substituents found in synthetic molecules contain nitrogen and sulfur heteroatoms, halogenes and more aromatic and particularly heteroaromatic rings. The characteristics of substituents typical for natural products identified here can be useful in the medicinal chemistry context, for example to guide the synthesis of natural product-like libraries and natural product-inspired fragment collections. The results may be used also to support compound derivatization strategies and the design of pseudo-natural natural products.

Pseudonatural Products Occur Frequently in Biologically Relevant Compounds

A new methodology for classifying fragment combinations and characterizing pseudonatural products (PNPs) is described. The source code is based on open-source tools and is organized as a Python package. Tasks can be executed individually or within the context of scalable, robust workflows. First, structures are standardized and duplicate entries are filtered out. Then, molecules are probed for the presence of predefined fragments. For molecules with more than one match, fragment combinations are classified. The algorithm considers the pairwise relative position of fragments within the molecule (fused atoms, linkers, intermediary rings), resulting in 18 different possible fragment combination categories. Finally, all combinations for a given molecule are assembled into a fragment combination graph, with fragments as nodes and combination types as edges. This workflow was applied to characterize PNPs in the ChEMBL database via comparison of fragment combination graphs with natural product (NP) references, represented by the Dictionary of Natural Products. The Murcko fragments extracted from 2000 structures previously described were used to define NP fragments. The results indicate that ca. 23% of the biologically relevant compounds listed in ChEMBL comply to the PNP definition and that, therefore, PNPs occur frequently among known biologically relevant small molecules. The majority (>95%) of PNPs contain two to four fragments, mainly (>95%) distributed in five different combination types. These findings may provide guidance for the design of new PNPs.

How different are marine microbial natural products compared to their terrestrial counterparts?

Covering: 1877 to 2020A key challenge in natural products research is the selection of biodiversity to yield novel chemistry. Recently, marine microorganisms have become a preferred source. But how novel are marine microorganism natural products compared to those reported from terrestrial microbes? Cluster analysis of chemical fingerprints and molecular scaffold analysis of 55 817 compounds reported from marine and terrestrial microorganisms, and marine macro-organisms showed that 76.7% of the compounds isolated from marine microorganisms are closely related to compounds isolated from terrestrial microorganisms. Only 14.3% of marine microorganism natural products are unique when marine macro-organism natural products are also considered. Studies targeting marine specific and understudied microbial phyla result in a higher likelihood of finding marine specific compounds, whereas the depth and geographic location of microorganism collection have little influence. We recommend marine targeted strain isolation, incorporating early use of genomic sequencing to guide strain selection, innovation in culture media and cultivation techniques and the application of cheminformatics tools to focus on unique natural product diversity, rather than the dereplication of known compounds.

New derivatives of the iridoid specioside from fungal biotransformation

Iridoids are widely found from species of Bignoniaceae family and exhibit several biological activities, such as anti-inflammatory, antimicrobial, antioxidant, and antitumor. Specioside is an iridoid found from Tabebuia species, mainly in Tabebuia aurea. Thus, here fungus-mediated biotransformation of the iridoid specioside was investigated by seven fungi. The fungus-mediated biotransformation reactions resulted in a total of nineteen different analogs by fungus Aspergillus niger, Aspergillus flavus, Aspergillus japonicus, Aspergillus terreus, Aspergillus niveus, Penicillium crustosum, and Thermoascus aurantiacus. Non-glycosylated specioside was the main metabolite observed. The other analogs were yielded from ester hydrolysis, hydroxylation, methylation, and hydrogenation reactions. The non-glycosylated specioside and coumaric acid were yielded by all fungi-mediated biotransformation. Thus, fungus applied in this study showed the ability to perform hydroxylation and glycosidic, as well as ester hydrolysis reactions from glycosylated iridoid. KEY POINTS: • The biotransformation of specioside by seven fungi yielded nineteen analogs. • The non-glycosylated specioside was the main analog obtained. • Ester hydrolysis, hydroxylation, methylation, and hydrogenation reactions were observe.

A Catalog of Natural Products Occurring in Watermelon-Citrullus lanatus

Sweet dessert watermelon (Citrullus lanatus) is one of the most important vegetable crops consumed throughout the world. The chemical composition of watermelon provides both high nutritional value and various health benefits. The present manuscript introduces a catalog of 1,679 small molecules occurring in the watermelon and their cheminformatics analysis for diverse features. In this catalog, the phytochemicals are associated with the literature describing their presence in the watermelon plant, and when possible, concentration values in various plant parts (flesh, seeds, leaves, roots, rind). Also cataloged are the chemical classes, molecular weight and formula, chemical structure, and certain physical and chemical properties for each phytochemical. In our view, knowing precisely what is in what we eat, as this catalog does for watermelon, supports both the rationale for certain controlled feeding studies in the field of precision nutrition, and plant breeding efforts for the development of new varieties with enhanced concentrations of specific phytochemicals. Additionally, improved and comprehensive collections of natural products accessible to the public will be especially useful to researchers in nutrition, cheminformatics, bioinformatics, and drug development, among other disciplines.

Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

We report the major conclusions of the online open-access workshop "Computational Applications in Secondary Metabolite Discovery (CAiSMD)" that took place from 08 to 10 March 2021. Invited speakers from academia and industry and about 200 registered participants from five continents (Africa, Asia, Europe, South America, and North America) took part in the workshop. The workshop highlighted the potential applications of computational methodologies in the search for secondary metabolites (SMs) or natural products (NPs) as potential drugs and drug leads. During 3 days, the participants of this online workshop received an overview of modern computer-based approaches for exploring NP discovery in the "omics" age. The invited experts gave keynote lectures, trained participants in hands-on sessions, and held round table discussions. This was followed by oral presentations with much interaction between the speakers and the audience. Selected applicants (early-career scientists) were offered the opportunity to give oral presentations (15 min) and present posters in the form of flash presentations (5 min) upon submission of an abstract. The final program available on the workshop website ( https://caismd.indiayouth.info/ ) comprised of 4 keynote lectures (KLs), 12 oral presentations (OPs), 2 round table discussions (RTDs), and 5 hands-on sessions (HSs). This meeting report also references internet resources for computational biology in the area of secondary metabolites that are of use outside of the workshop areas and will constitute a long-term valuable source for the community. The workshop concluded with an online survey form to be completed by speakers and participants for the goal of improving any subsequent editions.

NP Navigator: A New Look at the Natural Product Chemical Space

Natural products (NPs), being evolutionary selected over millions of years to bind to biological macromolecules, remained an important source of inspiration for medicinal chemists even after the advent of efficient drug discovery technologies such as combinatorial chemistry and high-throughput screening. Thus, there is a strong demand for efficient and user-friendly computational tools that allow to analyze large libraries of NPs. In this context, we introduce NP Navigator - a freely available intuitive online tool for visualization and navigation through the chemical space of NPs and NP-like molecules. It is based on the hierarchical ensemble of generative topographic maps, featuring NPs from the COlleCtion of Open NatUral producTs (COCONUT), bioactive compounds from ChEMBL and commercially available molecules from ZINC. NP Navigator allows to efficiently analyze different aspects of NPs - chemotype distribution, physicochemical properties, biological activity and commercial availability of NPs. The latter concerns not only purchasable NPs but also their close analogs that can be considered as synthetic mimetics of NPs or pseudo-NPs.

Machine Learning Methods to Predict the Terrestrial and Marine Origin of Natural Products

In recent years there has been a growing interest in studying the differences between the chemical and biological space represented by natural products (NPs) of terrestrial and marine origin. In order to learn more about these two chemical spaces, marine natural products (MNPs) and terrestrial natural products (TNPs), a machine learning (ML) approach was developed in the current work to predict three classes, MNPs, TNPs and a third class of NPs that appear in both the terrestrial and marine environments. In total 22,398 NPs were retrieved from the Reaxys® database, from those 10,790 molecules are recorded as MNPs, 10,857 as TNPs, and 761 NPs appear registered as both MNPs and TNPs. Several ML algorithms such as Random Forest, Support Vector Machines, and deep learning Multilayer Perceptron networks have been benchmarked. The best performance was achieved with a consensus classification model, which predicted the external test set with an overall predictive accuracy up to 81 %. As far as we know this approach has never been intended and therefore allow to be used to better understand the chemical space defined by MNPs, TNPs or both, but also in virtual screening to define the applicability domain of QSAR models of MNPs and TNPs.

Description and Analysis of Glycosidic Residues in the Largest Open Natural Products Database

Natural products (NPs), biomolecules produced by living organisms, inspire the pharmaceutical industry and research due to their structural characteristics and the substituents from which they derive their activities. Glycosidic residues are frequently present in NP structures and have particular pharmacokinetic and pharmacodynamic importance as they improve their solubility and are often involved in molecular transport, target specificity, ligand–target interactions, and receptor binding. The COlleCtion of Open Natural prodUcTs (COCONUT) is currently the largest open database of NPs, and therefore a suitable starting point for the detection and analysis of the diversity of glycosidic residues in NPs. In this work, we report and describe the presence of circular, linear, terminal, and non-terminal glycosidic units in NPs, together with their importance in drug discovery.

The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of Urceolina peruviana (C. Presl) J.F. Macbr. as a Preliminary Test Case

The role and importance of the identification of natural products are discussed in the perspective of the study of secondary metabolites. The rapid identification of already reported compounds, or structural dereplication, is recognized as a key element in natural product chemistry. The biological taxonomy of metabolite producing organisms, the knowledge of metabolite molecular structures, and the availability of metabolite spectroscopic signatures are considered as the three pillars of structural dereplication. The role and the construction of databases is illustrated by references to the KNApSAcK, UNPD, CSEARCH, and COCONUT databases, and by the importance of calculated taxonomic and spectroscopic data as substitutes for missing or lost original ones. Two NMR-based tools, the PNMRNP database that derives from UNPD, and KnapsackSearch, a database generator that provides taxonomically focused libraries of compounds, are proposed to the community of natural product chemists. The study of the alkaloids from Urceolina peruviana, a plant from the Andes used in traditional medicine for antibacterial and anticancer actions, has given the opportunity to test different approaches to dereplication, favoring the use of publicly available data sources.

COCONUT online: Collection of Open Natural Products database

Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in NP research around the world and in different application fields, therefore, over the years a multiplication of generalistic and thematic NP databases has been observed. However, there is, at this moment, no online resource regrouping all known NPs in just one place, which would greatly simplify NPs research and allow computational screening and other in silico applications. In this manuscript we present the online version of the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface to browse, search and easily and quickly download NPs. COCONUT web is freely available at https://coconut.naturalproducts.net .