Chemical Glycobiology: Glycans

• Chemical Glycobiology is a branch of study
• Glycans are complex carbohydrates, that consist of linked sugar units together
• Glycans attach to lipids and proteins
• Glycans facilitate cell signaling, immune response, and molecular recognition
• Glycans are not encoded by DNA directly
• Glycan synthases are enzymes
• Glycans are assembled by enzymes leading to regulation

Glycans

• "Glycosylated": sugar molecules (glycans) are attached to molecule, such as a lipid or protein
• Glycosylation impacts biological processes, function and stability
• Glycosylation is more complex than acetylation or phosphorylation
• N-glycan has hundreds of different variations

Common Sugars

• Most commonly found are a few sugars including:
  • D-glucose
  • D-galactose
  • D-mannose
• Modify by adding amines and and sulfates
• Colored shapes to simplify complex structures

Functions of Glycans

• Play key roles in immune response and communication
• Proteins exported from cell are glycosylated
• Glycoproteins are proteins with O-linked or N-linked glycans
• Proteoglycans have glycosaminoglycans, in extracellular matrix
• Glycolipids are lipids attached to cell membranes

Glycans Enzymes

• Not template from DNA
• Glycosidases remove sugars
• Glycosyltransferases add sugars
• Depends on cell type which leads to different tissues having differing profiles

Protein and Glycan Interactions

• Researchers observe proteins interacting with glycans instead of studying glycans directly
• Glycan synthesis is expressed in cells
• Absence of glycan affecting the cell can be understood by inhibiting glycosyltransferase
• Lack of glycan breakdown is found by blocking glycosidase

Glycan Mechanisms

• Glycosidases break glycans through
  • Retaining mechanism (enzyme-sugar bond formed)
  • Inverting mechanism (direct water attack)
  • Helpful to develop enzyme inhibitors

Inhibitors

• During reactions, sugar transition state resembles, oxocarbenium ion
• To block enzyme activity, mimic transition state with inhibitors
• "Trap" enzymes by attaching molecules to the transition state
• Used to layout enzyme inhibitors
• Sugars with Fluorine modification slow process by destabilizing reaction

Targeting Biomass

• Researchers used glycosylated cyclophellitol derivatives to locate cellulases
• Cellulases = Enzymes that break down the biomass component cellulose
• Specific visualized and pulled down fungal cellulases with biotinylated and fluorescent probes

Glycan Recognition

• Recognized by lectins
• Lectin/carbohydrate interactions affect immune response, cell signaling, and pathogen recognition
• Multiple binding sites needed for binding to occur powerfully
• Cell recognition is essential to the presence of sugars displayed outside cell
  • Trigger movement, adhesion and separation during development
• Trigger metastasis, degradation, aggregation, disease, auto-immune processes
• Glycosylation defines fate of proteins

Weak Sugar Binding Interactions

• Signaling relies on multivalent interactions
• Shape, hydrophobicity, metal chelation and hydrogen bonds

Cell Surface Mimicking

• Glycan profiles and fingerprints come from binding proteins and glycans in array

Tagging Cell Sugars

• Sugar metabolisms related
• Labeled:
  • Is hard to cross nucleotide sugar directly
  • Allows crossing labeled sugar that is protected
  • Become directly used after esterases removes
  • Pathway that goes into this is "salvage"

Visualizing Sugars

• Small reporters required
• Bio-orthogonal used to attach fluorophores
• Strain-promoted reactions of azides or cyclooctynes
• Inverse reactions with tetrazines

Glycan Arrays

• Examine diverse glycan/protein interactions and selectivity using synthetic and natural glycan arrays
• Profile protein-carbohydrate interactions

Lectins

• Researchers analyze a range of lectins and other proteins to test which bind carbohydrates
• Involve crude serum as well
• High throughput sugar investigations involve surface attachment
• By varying systematically researchers see connections

Enzymes

• Celluloses are analyzed
• Derivatives of glycosides show effects

Viruses

Viral RNA

• SARS viruses are positive-sense single stranded RNA
• Has around 30,000 bases for gene
• Use host machinery for virion creation

Replication

• Viral RNA enters
• Virus proteins synthesized
• Polyportiens made
• Copies made
• Structural modifications occurs
• New infection is ready

CoronaVirus

• Corona viruses bind to the ribosome
• RNA gets back transcribes
• DNA goes to the genome

Drug Targets

• Binds ACE2 protein and that stops cell
• Peptide prevents infection

Baltimore Classification

• Distinguishes classes by:
  • Nucleic acid used
  • dsDNA
  • ssDNA
  • RNA
• Retro: transcribing

Inhibitors

• Inhibitor binds to replication
• Disrupts function stopping multiplication
• Remdesivir for example stalls replication
• By product is toxic since enzyme uses it

Cell Viability

• Treating cell makes cell stop working and this kills it