ProCarbDB: a database of carbohydrate-binding proteins

DIONYSUS: a database of protein-carbohydrate interfaces

Protein-carbohydrate interactions govern a wide variety of biological processes and play an essential role in the development of different diseases. Here, we present DIONYSUS, the first database of protein-carbohydrate interfaces annotated according to structural, chemical and functional properties of both proteins and carbohydrates. We provide exhaustive information on the nature of interactions, binding site composition, biological function and specific additional information retrieved from existing databases. The user can easily search the database using protein sequence and structure information or by carbohydrate binding site properties. Moreover, for a given interaction site, the user can perform its comparison with a representative subset of non-covalent protein-carbohydrate interactions to retrieve information on its potential function or specificity. Therefore, DIONYSUS is a source of valuable information both for a deeper understanding of general protein-carbohydrate interaction patterns, for annotation of the previously unannotated proteins and for such applications as carbohydrate-based drug design. DIONYSUS is freely available at www.dsimb.inserm.fr/DIONYSUS/.

Network pharmacology and experimental verification study on the mechanism of Hedyotis diffusa Willd in treating colorectal cancer

This study aimed to evaluate the pharmacological mechanism of Hedyotis diffusa Willd against CRC (colorectal cancer) using network pharmacological analysis combined with experimental validation. The active components and potential targets of Hedyotis diffusa Willd were screened from the tax compliance management program public database using network pharmacology. The core anti-CRC targets were screened using a protein-protein interaction (PPI) network. The mRNA and protein expression of core target genes in normal colon and CRC tissues and their relationship with overall CRC survival were evaluated using The Cancer Genome Atlas (TCGA), Human Protein Atlas (HPA), and Gene Expression Profiling Interactive Analysis (GEPIA) databases. Functional and pathway enrichment analyses of the potential targets were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The first six core targets with stable binding were molecular-docked with the active components quercetin and β-sitosterol. Finally, the results of network pharmacology were verified using in vitro experiments. In total, 149 potential targets were identified by searching for seven types of active components and the intersection of all potential and CRC targets. PPI network analysis showed that ten target genes, including tumor protein p53 (TP53) and recombinant cyclin D1 (CCND1), were pivotal genes. GO enrichment analysis involved 2043 biological processes, 52 cellular components, and 191 molecular functions. KEGG enrichment analysis indicated that the anticancer effects of H. alba were mediated by tumor necrosis factor, interleukin-17, and nuclear factor-κB (NF-κB) signaling pathways. Validation of key targets showed that the validation results for most core genes were consistent with those in this study. Molecular docking revealed that the ten core target proteins could be well combined with quercetin and β-sitosterol and the structure remained stable after binding. The results of the in vitro experiment showed that β-sitosterol inhibited proliferation and induced apoptosis in SW620 cells. This study identified a potential target plant for CRC through network pharmacology and in vitro validation.

Identification of the potential Pan-CDK antagonists: tracing the path of virtual screening and inhibitory activity on lung cancer cells

Cyclin-dependent kinases (CDKs) are overexpressed in tumor cells, and their aberrant activation can promote the progression of non-small-cell lung cancer (NSCLC). We utilized structure-based virtual screening and experimental validation to screen for potential CDKs antagonists among TargetMol natural products. Molecular docking and molecular dynamics simulation results indicate that Dolastatin 10 exhibits strong interactions with multiple subtypes of CDKs (CDK1, CDK2, CDK3, CDK4, and CDK6), forming stable CDKs-Dolastatin 10 complex compounds. Furthermore, in vitro experiments demonstrate that Dolastatin 10 significantly inhibits the viability, migration, and invasion of H1299 cells in a concentration-dependent manner, arresting the cell cycle at the G2/M phase by inducing cell senescence. These findings suggest that Dolastatin 10 may serve as a potential CDKs antagonist deserving further investigation.

Highly accurate carbohydrate-binding site prediction with DeepGlycanSite

As the most abundant organic substances in nature, carbohydrates are essential for life. Understanding how carbohydrates regulate proteins in the physiological and pathological processes presents opportunities to address crucial biological problems and develop new therapeutics. However, the diversity and complexity of carbohydrates pose a challenge in experimentally identifying the sites where carbohydrates bind to and act on proteins. Here, we introduce a deep learning model, DeepGlycanSite, capable of accurately predicting carbohydrate-binding sites on a given protein structure. Incorporating geometric and evolutionary features of proteins into a deep equivariant graph neural network with the transformer architecture, DeepGlycanSite remarkably outperforms previous state-of-the-art methods and effectively predicts binding sites for diverse carbohydrates. Integrating with a mutagenesis study, DeepGlycanSite reveals the guanosine-5'-diphosphate-sugar-recognition site of an important G-protein coupled receptor. These findings demonstrate DeepGlycanSite is invaluable for carbohydrate-binding site prediction and could provide insights into molecular mechanisms underlying carbohydrate-regulation of therapeutically important proteins.

CarbDisMut: database on neutral and disease-causing mutations in human carbohydrate-binding proteins

Protein-carbohydrate interactions are involved in several cellular and biological functions. Integrating structure and function of carbohydrate-binding proteins with disease-causing mutations help to understand the molecular basis of diseases. Although databases are available for protein-carbohydrate complexes based on structure, binding affinity and function, no specific database for mutations in human carbohydrate-binding proteins is reported in the literature. We have developed a novel database, CarbDisMut, a comprehensive integrated resource for disease-causing mutations with sequence and structural features. It has 1.17 million disease-associated mutations and 38,636 neutral mutations from 7,187 human carbohydrate-binding proteins. The database is freely available at https://web.iitm.ac.in/bioinfo2/carbdismut. The web-site is implemented using HTML, PHP and JavaScript and supports recent versions of all major browsers, such as Firefox, Chrome and Opera.

AI-Driven Enhancements in Drug Screening and Optimization

The greatest challenge in drug discovery remains the high rate of attrition across the different phases of the process, which cost the industry billions of dollars every year. While all phases remain crucial to ensure pharmaceutical-level safety, quality, and efficacy of the end product, streamlining these efforts toward compounds with success potential is pivotal for a more efficient and cost-effective process. The use of artificial intelligence (AI) within the pharmaceutical industry aims at just this, and has applications in preclinical screening for biological activity, optimization of pharmacokinetic properties for improved drug formulation, early toxicity prediction which reduces attrition, and pre-emptively screening for genetic changes in the biological target to improve therapeutic longevity. Here, we present a series of in silico tools that address these applications in small molecule development and describe how they can be embedded within the current pharmaceutical development pipeline.

Emergence of Cooperative Glucose-Binding Networks in Adaptive Peptide Systems

Minimalistic peptide-based systems that bind sugars in water are challenging to design due to the weakness of interactions and required cooperative contributions from specific amino-acid side chains. Here, we used a bottom-up approach to create peptide-based adaptive glucose-binding networks by mixing glucose with selected sets of input dipeptides (up to 4) in the presence of an amidase to enable in situ reversible peptide elongation, forming mixtures of up to 16 dynamically interacting tetrapeptides. The choice of input dipeptides was based on amino-acid abundance in glucose-binding sites found in the protein data bank, with side chains that can support hydrogen bonding and CH-π interactions. Tetrapeptide sequence amplification patterns, determined through LC-MS analysis, served as a readout for collective interactions and led to the identification of optimized binding networks. Systematic variation of dipeptide input revealed the emergence of two networks of non-covalent hydrogen bonding and CH-π interactions that can co-exist, are cooperative and context-dependent. A cooperative binding mode was determined by studying the binding of the most amplified tetrapeptide (AWAD) with glucose in isolation. Overall, these results demonstrate that the bottom-up design of complex systems can recreate emergent behaviors driven by covalent and non-covalent self-organization that are not observed in reductionist designs and lead to the identification of system-level cooperative binding motifs.

Using Graph-Based Signatures to Guide Rational Antibody Engineering

Antibodies are essential experimental and diagnostic tools and as biotherapeutics have significantly advanced our ability to treat a range of diseases. With recent innovations in computational tools to guide protein engineering, we can now rationally design better antibodies with improved efficacy, stability, and pharmacokinetics. Here, we describe the use of the mCSM web-based in silico suite, which uses graph-based signatures to rapidly identify the structural and functional consequences of mutations, to guide rational antibody engineering to improve stability, affinity, and specificity.

Multifaceted Computational Modeling in Glycoscience

Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.

GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA

The GrAfSS (Graph theoretical Applications for Substructure Searching) webserver is a platform to search for three-dimensional substructures of: (i) amino acid side chains in protein structures; and (ii) base arrangements in RNA structures. The webserver interfaces the functions of five different graph theoretical algorithms – ASSAM, SPRITE, IMAAAGINE, NASSAM and COGNAC – into a single substructure searching suite. Users will be able to identify whether a three-dimensional (3D) arrangement of interest, such as a ligand binding site or 3D motif, observed in a protein or RNA structure can be found in other structures available in the Protein Data Bank (PDB). The webserver also allows users to determine whether a protein or RNA structure of interest contains substructural arrangements that are similar to known motifs or 3D arrangements. These capabilities allow for the functional annotation of new structures that were either experimentally determined or computationally generated (such as the coordinates generated by AlphaFold2) and can provide further insights into the diversity or conservation of functional mechanisms of structures in the PDB. The computed substructural superpositions are visualized using integrated NGL viewers. The GrAfSS server is available at http://mfrlab.org/grafss/.

CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function

Protein-carbohydrate interactions are crucial for many cellular processes but can be challenging to biologically characterise. To improve our understanding and ability to model these molecular interactions, we used a carefully curated set of 370 protein-carbohydrate complexes with experimental structural and biophysical data in order to train and validate a new tool, cutoff scanning matrix (CSM)-carbohydrate, using machine learning algorithms to accurately predict their binding affinity and rank docking poses as a scoring function. Information on both protein and carbohydrate complementarity, in terms of shape and chemistry, was captured using graph-based structural signatures. Across both training and independent test sets, we achieved comparable Pearson's correlations of 0.72 under cross-validation [root mean square error (RMSE) of 1.58 Kcal/mol] and 0.67 on the independent test (RMSE of 1.72 Kcal/mol), providing confidence in the generalisability and robustness of the final model. Similar performance was obtained across mono-, di- and oligosaccharides, further highlighting the applicability of this approach to the study of larger complexes. We show CSM-carbohydrate significantly outperformed previous approaches and have implemented our method and make all data freely available through both a user-friendly web interface and application programming interface, to facilitate programmatic access at http://biosig.unimelb.edu.au/csm_carbohydrate/. We believe CSM-carbohydrate will be an invaluable tool for helping assess docking poses and the effects of mutations on protein-carbohydrate affinity, unravelling important aspects that drive binding recognition.

UniLectin, A One-Stop-Shop to Explore and Study Carbohydrate-Binding Proteins

All eukaryotic cells are covered with a dense layer of glycoconjugates, and the cell walls of bacteria are made of various polysaccharides, putting glycans in key locations for mediating protein-protein interactions at cell interfaces. Glycan function is therefore mainly defined as binding to other molecules, and lectins are proteins that specifically recognize and interact non-covalently with glycans. UniLectin was designed based on insight into the knowledge of lectins, their classification, and their biological role. This modular platform provides a curated and periodically updated classification of lectins along with a set of comparative and visualization tools, as well as structured results of screening comprehensive sequence datasets. UniLectin can be used to explore lectins, find precise information on glycan-protein interactions, and mine the results of predictive tools based on HMM profiles. This usage is illustrated here with two protocols. The first one highlights the fine-tuned role of the O blood group antigen in distinctive pathogen recognition, while the second compares the various bacterial lectin arsenals that clearly depend on living conditions of species even in the same genus. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Searching for the structural details of lectins binding the O blood group antigen Basic Protocol 2: Comparing the lectomes of related organisms in different environments.

Modernized uniform representation of carbohydrate molecules in the Protein Data Bank

Since 1971, the Protein Data Bank (PDB) has served as the single global archive for experimentally determined 3D structures of biological macromolecules made freely available to the global community according to the FAIR principles of Findability-Accessibility-Interoperability-Reusability. During the first 50 years of continuous PDB operations, standards for data representation have evolved to better represent rich and complex biological phenomena. Carbohydrate molecules present in more than 14,000 PDB structures have recently been reviewed and remediated to conform to a new standardized format. This machine-readable data representation for carbohydrates occurring in the PDB structures and the corresponding reference data improves the findability, accessibility, interoperability and reusability of structural information pertaining to these molecules. The PDB Exchange MacroMolecular Crystallographic Information File data dictionary now supports (i) standardized atom nomenclature that conforms to International Union of Pure and Applied Chemistry-International Union of Biochemistry and Molecular Biology (IUPAC-IUBMB) recommendations for carbohydrates, (ii) uniform representation of branched entities for oligosaccharides, (iii) commonly used linear descriptors of carbohydrates developed by the glycoscience community and (iv) annotation of glycosylation sites in proteins. For the first time, carbohydrates in PDB structures are consistently represented as collections of standardized monosaccharides, which precisely describe oligosaccharide structures and enable improved carbohydrate visualization, structure validation, robust quantitative and qualitative analyses, search for dendritic structures and classification. The uniform representation of carbohydrate molecules in the PDB described herein will facilitate broader usage of the resource by the glycoscience community and researchers studying glycoproteins.

Development and Evaluation of GlycanDock: A Protein-Glycoligand Docking Refinement Algorithm in Rosetta

Carbohydrate chains are ubiquitous in the complex molecular processes of life. These highly diverse chains are recognized by a variety of protein receptors, enabling glycans to regulate many biological functions. High-resolution structures of protein-glycoligand complexes reveal the atomic details necessary to understand this level of molecular recognition and inform application-focused scientific and engineering pursuits. When experimental challenges hinder high-throughput determination of quality structures, computational tools can, in principle, fill the gap. In this work, we introduce GlycanDock, a residue-centric protein-glycoligand docking refinement algorithm developed within the Rosetta macromolecular modeling and design software suite. We performed a benchmark docking assessment using a set of 109 experimentally determined protein-glycoligand complexes as well as 62 unbound protein structures. The GlycanDock algorithm can sample and discriminate among protein-glycoligand models of native-like structural accuracy with statistical reliability from starting structures of up to 7 Å root-mean-square deviation in the glycoligand ring atoms. We show that GlycanDock-refined models qualitatively replicated the known binding specificity of a bacterial carbohydrate-binding module. Finally, we present a protein-glycoligand docking pipeline for generating putative protein-glycoligand complexes when only the glycoligand sequence and unbound protein structure are known. In combination with other carbohydrate modeling tools, the GlycanDock docking refinement algorithm will accelerate research in the glycosciences.

LectomeXplore, an update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification

Lectins are non-covalent glycan-binding proteins mediating cellular interactions but their annotation in newly sequenced organisms is lacking. The limited size of functional domains and the low level of sequence similarity challenge usual bioinformatics tools. The identification of lectin domains in proteomes requires the manual curation of sequence alignments based on structural folds. A new lectin classification is proposed. It is built on three levels: (i) 35 lectin domain folds, (ii) 109 classes of lectins sharing at least 20% sequence similarity and (iii) 350 families of lectins sharing at least 70% sequence similarity. This information is compiled in the UniLectin platform that includes the previously described UniLectin3D database of curated lectin 3D structures. Since its first release, UniLectin3D has been updated with 485 additional 3D structures. The database is now complemented by two additional modules: PropLec containing predicted β-propeller lectins and LectomeXplore including predicted lectins from sequences of the NBCI-nr and UniProt for every curated lectin class. UniLectin is accessible at https://www.unilectin.eu/.

Prediction of protein-carbohydrate complex binding affinity using structural features

Protein-carbohydrate interactions play a major role in several cellular and biological processes. Elucidating the factors influencing the binding affinity of protein-carbohydrate complexes and predicting their free energy of binding provide deep insights for understanding the recognition mechanism. In this work, we have collected the experimental binding affinity data for a set of 389 protein-carbohydrate complexes and derived several structure-based features such as contact potentials, interaction energy, number of binding residues and contacts between different types of atoms. Our analysis on the relationship between binding affinity and structural features revealed that the important factors depend on the type of the complex based on number of carbohydrate and protein chains. Specifically, binding site residues, accessible surface area, interactions between various atoms and energy contributions are important to understand the binding affinity. Further, we have developed multiple regression equations for predicting the binding affinity of protein-carbohydrate complexes belonging to six categories of protein-carbohydrate complexes. Our method showed an average correlation and mean absolute error of 0.731 and 1.149 kcal/mol, respectively, between experimental and predicted binding affinities on a jackknife test. We have developed a web server PCA-Pred, Protein-Carbohydrate Affinity Predictor, for predicting the binding affinity of protein-carbohydrate complexes. The web server is freely accessible at https://web.iitm.ac.in/bioinfo2/pcapred/. The web server is implemented using HTML and Python and supports recent versions of major browsers such as Chrome, Firefox, IE10 and Opera.

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

Probabilistic identification of saccharide moieties in biomolecules and their protein complexes

The chemical composition of saccharide complexes underlies their biomedical activities as biomarkers for cardiometabolic disease, various types of cancer, and other conditions. However, because these molecules may undergo major structural modifications, distinguishing between compounds of saccharide and non-saccharide origin becomes a challenging computational problem that hinders the aggregation of information about their bioactive moieties. We have developed an algorithm and software package called "Cheminformatics Tool for Probabilistic Identification of Carbohydrates" (CTPIC) that analyzes the covalent structure of a compound to yield a probabilistic measure for distinguishing saccharides and saccharide-derivatives from non-saccharides. CTPIC analysis of the RCSB Ligand Expo (database of small molecules found to bind proteins in the Protein Data Bank) led to a substantial increase in the number of ligands characterized as saccharides. CTPIC analysis of Protein Data Bank identified 7.7% of the proteins as saccharide-binding. CTPIC is freely available as a webservice at (http://ctpic.nmrfam.wisc.edu).

ProCaff: protein–carbohydrate complex binding affinity database

Motivation

Protein–carbohydrate interactions perform several cellular and biological functions and their structure and function are mainly dictated by their binding affinity. Although plenty of experimental data on binding affinity are available, there is no reliable and comprehensive database in the literature.

Results

We have developed a database on binding affinity of protein–carbohydrate complexes, ProCaff, which contains 3122 entries on dissociation constant (Kd), Gibbs free energy change (ΔG), experimental conditions, sequence, structure and literature information. Additional features include the options to search, display, visualization, download and upload the data.

Availability and implementation

The database is freely available at http://web.iitm.ac.in/bioinfo2/procaff/. The website is implemented using HTML and PHP and supports recent versions of major browsers such as Chrome, Firefox, IE10 and Opera.

Contact

gromiha@iitm.ac.in

Supplementary information

Supplementary data are available at Bioinformatics online.

The terminal sialic acid of stage-specific embryonic antigen-4 has a crucial role in binding to a cancer-targeting antibody

Cancer remains a leading cause of morbidity and mortality worldwide, requiring ongoing development of targeted therapeutics such as monoclonal antibodies. Carbohydrates on embryonic cells are often highly expressed in cancer and are therefore attractive targets for antibodies. Stage-specific embryonic antigen-4 (SSEA-4) is one such glycolipid target expressed in many cancers, including breast and ovarian carcinomas. Here, we defined the structural basis for recognition of SSEA-4 by a novel monospecific chimeric antibody (ch28/11). Five X-ray structures of ch28/11 Fab complexes with the SSEA-4 glycan headgroup, determined at 1.5-2.7 Å resolutions, displayed highly similar three-dimensional structures indicating a stable binding mode. The structures also revealed that by adopting a horseshoe-shaped conformation in a deep groove, the glycan headgroup likely sits flat against the membrane to allow the antibody to interact with SSEA-4 on cancer cells. Moreover, we found that the terminal sialic acid of SSEA-4 plays a dominant role in dictating the exquisite specificity of the ch28/11 antibody. This observation was further supported by molecular dynamics simulations of the ch28/11-glycan complex, which show that SSEA-4 is stabilized by its terminal sialic acid, unlike SSEA-3, which lacks this sialic acid modification. These high-resolution views of how a glycolipid interacts with an antibody may help to advance a new class of cancer-targeting immunotherapy.