A real example:

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A real example
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Natural Product Peptides, Peptidomimetics
Peptide Analogues

• Natural Product Peptides (nonribosomal
  peptides)
• Product of secondary metabolism
• Synthesized on the NRPS
• Numerous pharmaceutically relevant peptides

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More Nonribosomal Peptides
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• Chemical synthesis demonstrated on solid support
• Synthesis weeks (soln) ? days (solid)
• Employ more and/or different protecting groups
• Unusual functional groups
• Cyclization on resin?
• Other modifications (i.e. sugar moiety)?
• Solid-supported synthesis has allowed the
  substitution and/or modification of AAs ?
  analogues
• AA, functional groups, stereochemistry,
  substitution, etc
• Study structure-activity relationships
• Potential therapeutics
• Note Industrial synthesis not performed on
  solid supported

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Peptide Analogues

• Recently, there have been developments in the
  modification of peptides, particularly AMPs
• AMPs Antimicrobial Peptides
• 15-30 AAs in length
• Produced by all animals (insects to frogs to
  humans)
• First line of defense against microbial organisms
• Answer to antibiotic resistance?
• Molecular diversity ? dependent on structure

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AMP Structure

• Large proportion of hydrophobic residues (
  50 )
• Also contain varying amounts of Lys, Arg His ?
  vely charged AAs
• These AAs vary in their arrangement within the
  peptide
• This arrangement of AAs allows disruption of
  bacterial membranes (anionic)

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Teflon? Peptide Fluorogainin-1

• Fluorous analogue of the AMP, magainin (isolated
  from the skin of frogs)
• Replaced hydrophobic residues (i.e., Val,
  Leu,etc) with fluorinated versions ? Teflon
  like
• Resulted in more stable peptides
• More resistant to unfolding by chemical
  denaturants heat
• NMR also showed higher structural integrity
• Results also indicated increased antimicrobial
  activity
• Likely due to the increased hydrophobicity of
  peptide
• This strong hydrophobic interaction may make the
  peptide less susceptible to proteases

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magainin series sites of fluorination Leu 6,
Ala 9, Gly 13, Val 17, and Ile 20
NMR structure of magainin 2
Other Analogues
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Peptidomimetics

• Peptide mimics
• Contain non-natural peptidic structural elements
  (i.e. peptide bonds or unusual functional groups)
• Molecules vary in size structure
• Commonly synthesized using Merrifield resin to
  study structure-activity relationships
• Possible drug candidates

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Examples of Peptidomimetics
Mimic ?-sheets
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Peptide Synthesis in the Prebiotic World

• Recall
• Murchison Meteorite
• Possible source of AAs (via the Strecker
  mechanism)
• Peptide (oligo) formation ?

• Selection of an enantiomer
• Selection by crystal faces
• Circularly polarized light from stars
• Enantioenrichment
• Via Serine octamer
• Enrichment by sublimation

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Peptide Synthesis in the Prebiotic World

• Also recall formation of peptides from
  monomers is energetically unfavorable (i.e.,
  ?Ggt0)
• Modern world ? enzymes
• Chemical synthesis ? activation strategies
• Prebiotic world ? some energy input needed?
• Possibilities?
• Synthesis with minerals!
• Clay has been shown to catalyze the condensation
  of Gly to peptides up to (Gly)6

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• The experiment
• Uses SFM (scanning force microscopy)

Apply gly to surface
Faults (cracks)
(at STP)

• No visible change in faults or layers
• HPLC showed no gly peptides

Hectorite (layered silicate) containing Mg2, Li
Cu2
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Experiment (cont)
Small glycine peptides (oligomers)
Apply gly to surface
Alternate cycles of heating to 90 C ddH2O
HPLC
Gly peptides of up to 6 AAs in length
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Other Similar Experiments
Varying the mineral can give different peptides!

• Another experiment
• Mixed NaCl Clay (mineral) heat
• NaCl alone gave only short peptides
• When clay was added, longer peptides were
  produced!

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• Hadean Beach the primary pump
• This resembles many of the features of chemical
  peptide synthesis
• Step 1 In aqueous phase (i.e., ocean), 25 C
• Similar to Wohler synthesis of urea
• Amino group is now less reactive (amide-like)

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• Step 2
• Tide moves out (i.e. AA is now in dry reaction
  conditions)
• Step 3

Likely present in primitive atmosphere
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• N is protected as a carbamate (recall BOC)
• CO2H activated as an anhydride

Loss of N2 is driving force for rxn
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• Step 4 5 Condensation
• Experimentally, this system generates
  oligo-peptides with diastereoselection
  preferred sequences (?)
• May have given rise to earliest protein catalysts

Drives rxn
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• Nucleic acid templated peptide synthesis
• Model for the transfer of RNA world into the
  protein world?
• Basic idea
• Modify DNA strands with activated amino acids
  (i.e., DNA-linked substrate)
• These DNA strands are specific in sequence in
  order to tune their hybridization abilities
• DNA acts a template for further reactions, such
  as peptide bond formation
• Reactions performed as one pot

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Nucleic Acid Template Synthesis

• Step 1
• Templates are loaded with an AA
• Attached to DNA as an N-hydroxysuccinimidyl ester
  (recall lab 6 ? NHS DCC)
• Each AA (i.e. R1) has a unique DNA sequence
  associated with it

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• Step 2
• Masking of portion of template (i.e., protect)
• Add other DNA-substrate molecules to the pot

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• Step 3
• Mixture is cooled to 4 C (for 20 mins) R1
  template selectively hybridizes
• Amine and activated carboxylate are now in close
  proximity can undergo intramolecular peptide
  bond formation

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• Step 4
• Temperature raised, causing dissociation of
  template
• DNA-R2 template hybridizes peptide bond
  formation occurs

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• Cycle repeats for the third AA (R3) until
  tripeptide is obtained

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• Model demonstrates that DNA can resemble an
  enzyme (i.e., ribozyme)
• Promotes coupling of 2 AAs through non-covalent
  interactions
• Specificity (template sequence ? one AA selected
  ? tRNA like)
• Could a similar model or sequence have given rise
  to peptides in the prebiotic world?

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• So far, we have looked at both amino acids
  peptides (peptide bond formation) in the
  prebiotic modern world
• Common themes were
• Selectivity
• Regioselectivity
• Stereoselectivity
• Protecting groups
• Overcoming ?G
• Activation of carboxylate to make a peptide bond
  (? E of starting material)
• Stabilization of TS (? E) (i.e., Lewis acid)
• What about an active site?

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• Peptide ? active site?
• Peptides may fold and/or associate to produce a
  simple active site
• Proteins/peptides have specific conformations due
  to intramolecular non-covalent forces
• H-bonding
• salt bridge
• Ionic
• Dipole-dipole
• Van der Waals
• The sum of many weak forces ? strong total
  binding force to restrict the conformation
• Folding has a ve ?S, but a ve ?H
• Also have covalent bonding disulphide bridge