Related Experiment Video
Updated: Jun 19, 2026
10:58
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
17.0K
Bayesian optimization of glycopolymer structures for the interaction with cholera toxin B subunit
Masanori Nagao1, Osuke Nakahara1, Xincheng Zhou1
1Department of Chemical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan. miuray@chem-eng.kyushu-u.ac.jp.
Nanoscale
|May 31, 2024
Summary
Researchers optimized synthetic glycopolymers to mimic GM1 structures. The best-performing glycopolymers showed strong binding to cholera toxin B subunit (CTB), indicating potential for therapeutic applications.
Area of Science:
- Carbohydrate Chemistry
- Biomaterials Science
- Computational Chemistry
Background:
- Ganglioside GM1 plays a crucial role in cellular processes and pathogen interactions.
- Synthetic glycopolymers offer a versatile platform for mimicking natural carbohydrate structures.
- Cholera toxin B subunit (CTB) is a key target for developing inhibitors due to its role in cholera pathogenesis.
Purpose of the Study:
- To determine the optimal composition of synthetic glycopolymers for mimicking GM1.
- To identify glycopolymers with enhanced binding affinity to cholera toxin B subunit (CTB).
Main Methods:
- Bayesian optimization was employed to efficiently explore the structural space of glycopolymers.
- Enzyme-linked immunosorbent assay (ELISA) was used to quantify the binding interactions between glycopolymers and CTB.
- Gaussian process regression was utilized to predict optimal glycopolymer compositions based on experimental data.
Main Results:
- The optimal glycopolymer composition was found to be 60 mol% galactose and 25 mol% neuraminic acid.
- This optimized glycopolymer demonstrated a low IC50 value of 75 μM for CTB inhibition.
- The study successfully identified a synthetic glycopolymer with significantly enhanced binding to CTB.
Conclusions:
- Synthetic glycopolymers can be effectively optimized to mimic GM1 structures.
- The identified glycopolymer composition shows high affinity for CTB, suggesting potential as a therapeutic agent.
- Bayesian optimization is a powerful tool for accelerating the design of functional glycoconjugates.
More Related Videos
Related Concept Videos
02:34Structural Isomerism
Isomerism in Complexes
Isomers are different chemical species that have the same chemical formula. Structural isomerism of coordination compounds can be divided into two subcategories, the linkage isomers and coordination-sphere isomers.
Linkage isomers occur when the coordination compound contains a ligand that can bind to the transition metal center through two different atoms. For example, the CN− ligand can bind through the carbon atom or through the nitrogen atom. Similarly, SCN− can be...
Isomers are different chemical species that have the same chemical formula. Structural isomerism of coordination compounds can be divided into two subcategories, the linkage isomers and coordination-sphere isomers.
Linkage isomers occur when the coordination compound contains a ligand that can bind to the transition metal center through two different atoms. For example, the CN− ligand can bind through the carbon atom or through the nitrogen atom. Similarly, SCN− can be...
02:15Protein and Protein Structure
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...
02:35Noncovalent Attractions in Biomolecules
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
01:25Drug-Receptor Bonds
Drug-receptor bonds are formed through various chemical forces when drugs interact with target cells. Covalent bonds, strong and irreversible, are exemplified by DNA-alkylating anticancer agents that inhibit cell division. However, such irreversible drug binding lacks selectivity and can modify the DNA of the surrounding healthy cells. Covalent binding often contributes to tissue toxicity, as seen with chloroform and paracetamol metabolites binding to the liver, causing hepatotoxicity.
In...
In...
01:16Adrenergic Agonists: Chemistry and Structure-Activity Relationship
Adrenergic agonists' structure-activity relationship (SAR) determines their selectivity and efficacy. These agonists comprise a phenylethylamine moiety with an aromatic ring and an ethylamine side chain.
Aromatic ring substitutions: Substituting the aromatic ring with –OH groups at positions 3 and 4 yields catecholamines (e.g., epinephrine), which have a high affinity for adrenoceptors. Hydrogen bonding between –OH groups and receptors enhances adrenergic activity.
Separation of the aromatic...
Aromatic ring substitutions: Substituting the aromatic ring with –OH groups at positions 3 and 4 yields catecholamines (e.g., epinephrine), which have a high affinity for adrenoceptors. Hydrogen bonding between –OH groups and receptors enhances adrenergic activity.
Separation of the aromatic...
01:28Structure-Activity Relationships and Drug Design
Drug design is a dynamic field that involves discovering and developing new medications based on specific biological targets. This process heavily relies on structure-activity relationships (SAR) and quantitative structure-activity relationships (QSAR) to guide the design and optimization of efficient drugs.
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence its...
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence its...