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Core 5 > Synthesis of biological molecules > Flashcards

Synthesis of biological molecules Flashcards

1
Q

Why are synthetic peptides and carbohydrates important?

A

Therapeutics:

drugs, vaccines, targetted drug delivery

Prove the structure of a natural product

Study of biological processes:

  • ligand receptor interactions
  • enzyme subrate interactions

enzyme reaction mechanisms

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2
Q

What are carbohydtrates used for?

A

cell recognition and adhesion

cell signalling

binding of pathogens

physical barriers

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3
Q

What is the structure of amino acids?

A

N terminus ion the left

C terminus on the right

Amino acids have three letter or one letter codes

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4
Q

How many amino acids constitute different titles of protein?

A

Peptide < 50 amino acids

Protein > 50 amino acids

Di peptide 2 amino acids

Oligopeptide 2-15 amino acids

Poly peptide 15-50 amino acids

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5
Q

What forms can a carbohydtrate exist in?

A

Open chain (acyclic)

Fischer form - the chain is bent round to look cyclic but is not bonded together

Chair form - anomeric hydroxyl is placed axial or equatorial

Axial = alpha

equatorial = beta

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6
Q

What are 3 examples of carbohydrates?

A

galactose, N-acetylgluosamine (GlcNac) and mannose

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7
Q

How is a glycosidic bond formed?

A

Formed in a condensation reaction between two hydroxyl groups on two separate sugars

Gal - α1, 6 - GlcNac = glycosidic bond between C1 on Gal and C6 on GlcNac

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8
Q

How do we achieve efficient and selective coupling of two amino acids?

A

Activate the C terminal carboxylic acid by turning the OH to a better leaving group

Avoid self-coupling by installing protecting groups

Avoid reaction with other functional groups by installing protecting groups

Use enantimeroically pure amino acids - want the S form

Avoid racemisation / lossof stereochemistry

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9
Q

How are amino acids activated in nature?

A

Activated through coupling to tRNA

Ribosome catalyses peptide nbond formation

Hydrogen bonding networks and orecise positioning of substrates promote reaction between the correct groups

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10
Q

How can we react amino acids synthetically?

A

Convert the hydroxyl of the carboxylic acid to an acyl chloride with COCl3 in DMF

Chlorine is a better leaving group than OH

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11
Q

What is the major problem with synthetic di peptide formation?

A

Side reactions:

Resonance delocalises the lone pair on N onto O

O- then reacts with acyl chlorideto form oxazolone

Oxazolone can tautomerise twice with a base

During tautomerisation the H can add from the top or bottom of the molecule - leads of loss of stereochemistry

Oxazolone can still react with the second amino acid which forms a mixture of products

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12
Q

How can we activate the hydroxyl?

A

DCC with a mild base that cannot act as a nucleophile - ensures the NH2 is not protonated

There is no internal cyclisation

The biproduct precipitates out of solution - easy to separate

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13
Q

What arethe most common protecting groups for the N terminus and C terminus?

A

N: Boc and F moc

C: methyl ester, t-butyl ester, benzyl ester,

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14
Q

What are the mechanism and conditions for installation and removal of Boc?

A

Installation: t-butyloxycarbonyl

Removal: TFA

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15
Q

What are the mechanism and conditions for installation and removal of Fmoc?

A

Installation: Fmoc-Cl and NaHCO3

Removal: piperidine

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16
Q

What are the mechanism and conditions for installation and removal of a methyl ester?

A

Installation: MeOH / H+ (HCL)

Removal: NaOH / H+

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17
Q

What are the mechanism and conditions for installation and removal of a t-Butyl ester?

A

Installation: 2-methyl propene / H+

Removal: TFA

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18
Q

What are the mechanism and conditions for installation and removal of a benzyl ester?

A

Installation: benzyl alcohol and H+

Removal: hydrogenatio: H2 / Pd/C catalyst

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19
Q

How can we protect side chains?

A

Carboxylic acids (aspartic, glutamic acid) - methyl esters, butyl esters, benzyl esters

amines (lysine): Boc and Cbz

Hydroxyl (serine, threonine, tyrosine) -

tert butyl ether

benzyl ether

silyl ether (TBDMS)

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20
Q

How do we instal and remove Cbz?

A

Installation: benzyloxycarbonyl (Cbz) + NaHCO3

Removal - H2 / Pd/C

Forms a carbamate

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21
Q

How do we instal and remove tert butyl and bezyl ethers?

A

Installation: Benzyl / tert butyl bromide + base

Removal catalytic hydrogenation - H2 / Pd/C

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22
Q

How do we instal and remove silyl ethers

A

Installation: silyl ether (TBDMS) + base

Removal: TBAF (source of F-)

TMS - least stable to acids and bases

TBDPS - selective for primary alcohols

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23
Q

What is the synthesis of a tripeptide?

A
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24
Q

What is a resin?

A

An insoluble polymer in bead form about 1mm in diamter

Also called: polymer bead, resin bead, solid phase, solid support

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25
Q

How do we attach an amino acid t the resin?

A

Usually the C terminus of the first amino acid is attched to the support.

OH attackes carbon and kicks out chloride

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26
Q

How do we attach the first amino acid to a Wang resin?

A

Use DCC / DIC to activate OH on the resin and do an esterification reaction

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27
Q

How do we attach the first amino acid to a Rink amide resin?

A

React COOH terminus with the NH2 of the resin to form an amide

28
Q

What are the advantages of the solid support?

A

No purification

No washing between steps

29
Q

What are the differences between protein assembly on solid support and in solution?

A

Boc cannot be used to protect N terminus on solid support

DCC cannot be used as activating agent as it precipitates out of solution which is undesirable using solid support - DIC has same mechanism

Side chain protecting groups are generally chosen for one step deprotonation and release from the support

30
Q

How do we cleave peptide from a Merrified resin?

A

Cleavage requires HF - very corrosive and toxic

31
Q

How do you cleave the peptide from the:

Wang resin

acid labile derivative Sasrin resin

A

Acid and TFA

0.5% TFA in DCM with acid

32
Q

What is the real synthesis of a tripeptide using Wang resin?

Why is Fmoc used to protect the N terminus and not Boc?

A

F moc is removed with piperidine whihc doesnt affect the rest of the synthesis

Boc is removed with TFA whuch cleaves the peptide from the resin and ends the synthesis

33
Q

What are the advantages and limitations of solid support peptide synthesis?

A

No work up required, Can be automated

No purification of intermediates possible - accumilation of impurities and incomplete coupling reactions lead to biproducts

Mixture of products can be diffuclt to separate

Limit on the amount of peptide that can be produced

34
Q

What are the terms used to descirbe carbohydrates?

A

Monosaccharide: single sugar unit

Disaccharide: two sugar units joined

Oligosccharide: more than two sugar units joined together

Carbohydrate: anything from mono —-> oligo sccharide

Glycoside: any carbohydrate molecules with anomeric substituent other than OH

Glycoconjugate: general term for a carbohydrate covalently linked to another biomolecule

35
Q

Why is the anomeric cnfiguration important?

A

anomeric OH axial = alpha

anomeric OH equatorial = beta

For many biological recognition events only one anomer will take part in the event

36
Q

How can we synthesise enantiomerically pure sugars?

A

Prevent mutarotation - fix equilibrium in one form (replace OH with OME)

Tune the experimental condition - choice of activating agent, protecting group, solvent

37
Q

What is the anomeric effect?

A

The effct that determines where the equilibrium between alpha and beta anomers lies

38
Q

What causes the anomeric effect?

A

hyperconjugation

dipole minimisation

39
Q

What is hyperconjugation?

A

For some anomeric substituents when in the axial position the antibonding orbital of the substituent lines up with the axial lone pair of the O in the ring (the non bonding orbital)

The non bonding orbital can donate eletron density into the anitbonding orbital which stabalises the complex.

This favours the alpha anomer

This cannopt happen in a beta anomer

40
Q

What is dipole minimisation?

A

In the alpha anomer the dipoles point away from each other

In the beta anomer they point in the same direction so there is a large dipole moment

This favours the alpha anomer

41
Q

What two things must be decided upon when synthesising carbohydrates?

A

What positions the sugars are going to be linked

e.g 1,3 or 1,6

The stereochemistry of the linkage

e.g - alpha or beta anomer

42
Q

How do we get efficient and selective coupling of two monomers?

A

Activate the donor anomeric hydroxyl to a better leaving group

Prevent loss of regio/stereochemistry with protecting groups

Achieve selecvtive formation of alpha or beta anomers with appropriate choice of solvent, activating agent

43
Q

What can we use to protect non anomeric hydroxyl groups on sugars?

A

Trityl

benzyl ether

acetic acid esters

benzyl or benzoyl esters

44
Q

How do we install / remove Trityl

A

Thus is a sterucally demanding group - used for primary hydroxyls

Installation: Trityl-Cl and base

Removal: mild acid (e.g AcOH)

45
Q

How do we instal and remove benzyl ethers?

A

Installation: BnBr/BnCl and base (NaH)

Removal: H2, Pd/C catalyst

46
Q

How dpo we instal and remove acetic acid esters?

A

Installation: AcO2, pyridine (acts as base and catalyst)

Removal: NaOMe, MeOH

47
Q

How do we instal and remove benzyl/benzoyl esters?

A

Installation: benzoyl chloride +pyridine

Removal MaOMe, MeOH

48
Q

How does nature acitivate the anomeric hydroxyl

A
  • activated through coupling to a nucleoside diphosphate group (e.g UDP)

Glycosyltransferases catalyse glycosidic bond formation with control over regio- and stereochemistry

49
Q

How can we activate the anomeric OH synthetically?

A

Actuvation with a good leaving group can lead to the formation of a carbocation (oxocarbenium ion). The nucleophile can then attack from above or below the face of the sugar

Due to the anomeric effect the alpha anomer is dominant

50
Q

What happens when Br is used as a leaving group in the activation of carbohystrates?

A

All OHs are protected with with AcO2 and pyridien then the anomeric OH is converted to Br with HBr

Only the beta product forms

51
Q

Why do we only observe the beta product when Br is a leaving group?

A

The lone pair on the C=O of the acetate attacks the electrophilic anomeric carbon to cyclise which blocks the bottom face and prevents the alpha anomer being formed

52
Q

How do we use trichloroacetimidate as an activating group?

A

Giid leaving group - must be activated by Lewis acid

installation: Cl3CCN + base (NaH)

TMS-OTf (imine attacks Si forming good leaving group)

Only beta product observed again

53
Q

How are thioethers used as activating groups?

A

Can be made into a good leaving group

anomeric OH is converte to Br with HBr and then to SPH with Ag2CO3 and HSPh or the anomeric OH is directly coverted to SPh with HSPh and BF3 . OEt

54
Q

How is SPh made into a good leaving group using acid?

A

NIS (N- iodo succunimide) + acid

55
Q

How is SPh made into a good leaving group with Tf2O?

A

mCPBA and Tf2O

56
Q

How can the stereochemistry of 1,2-trans glycosides be controlled?

A

neighbouring group participation

anomeric effect

solvent

57
Q

How can neighbouring group participation control the stereochemistry of the 1,2-trans glycosides?

A

A cyclic oxonium ion intermediate blocks one face of the ring so that the nucleophile of the second sugar can only attack on one face

When AcO in equatorial position beta anomer forms

When AcO in axial position alpha anomer forms

58
Q

In which situation does neighbouring group participation not work?

A

The use of HBr produces the alpha anomer despite the cyclic oxonium ion forming.

The beta anomer is the kinetic product and is formed initially but equiloibratuion happens quickly diue to the acidic conditions - equilibrium lies towards the alpha anomer

59
Q

How does the anomeric effect control the stereochemistry of the 1,2-trans glycosides?

A

In the absence of NGP the anomeric effect will drive formation of the alpha anomer

When the 2OH is protected by something other than Ac or Bz and in the equatorial position a 1,2-cis glycoside is produced

In mannose when the 2-OH is in the axial position a 1,2-trans glycoside is formed

60
Q

How does the solvent control the stereochemistry of 1,2-trans glycosides?

A

Nucleophilic solvents will participate in the reaction - follow same rules as other nucleophiles

The solvent nucleophile will mainly form the alpha anomer and block this face so the sugar can only attack at the equatorial position to form the beta anomer

In a non-nucleophilic solvent the anomeric effect drives formation of the alpha anomer

61
Q

How can we control the sterochemistry of 1,2-cis glycosides?

A

The anomeric effect

intramolecular tethering

62
Q

How does the anomeric effect influence the stereochemistry of 1,2-cis glycosides?

A

The anomeric effect is useful in forming 1,2-cis glycosides of gluscose or galactose where the 2-OH is pointing down (equatorial) - pushes towards the alpha anomer

In mannose when the 2-OH is pointing up the anomeric effect pushes towards the 1,2-trans glycoside

63
Q

How can intramolecular tethering be used to control the stereochemistry of 1,2-cis glycosides?

A

Intramolecular tethering can be used to form 1,2-cis glycosides of mannose

The 2-OH must be unprotected - SiMe2Cl2 and imidazole (base) is used to to couple to sugars

64
Q

What is the synthesis of a β(1,6) linked diasaccharide?

A
65
Q

Is it possible to automate oligosaccharide synthesis?

A

Varying degrees of success

Oligosaccharides are assembled on polystyrene Merrified resin

Must control stereo- and regioselectivity

Need close to 100% efficiency due to lack of purification of intermediates

The glyconeer 2.1 (2017) fully automated oligosaccharide synthesiser:

Mainly used to synthesis polymer of 1 sugar or repeating disaccharide

66
Q
A

Core 5 (6 decks)

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