The document discusses solid phase peptide synthesis (SPPS) methods using different protecting groups. It describes the t-Boc and Fmoc protecting group strategies, comparing their advantages and disadvantages. The t-Boc strategy uses acid-labile protecting groups removed by TFA, while the Fmoc strategy uses a base-labile Fmoc group and acid-labile side chain protecting groups, allowing milder acidic conditions. The document outlines the different protocols used in SPPS, including resin attachment, amino acid coupling and protecting group removal steps. It also discusses side reactions that can occur and strategies to minimize them, such as using orthogonal protecting groups or modified amino acid derivatives.
SIDE REACTION OCCUR IN PEPTIDE YNTJESIS ARE DISCUSSED HERE WITH ITTATED PROTON, PROTONATIONS RACEMIZATION, INITIATED ACTIVITY, ACYLATION, ALKYLATION, OVERACTIVATION
CHEMISTRY OF PEPTIDES [M.PHARM, M.SC, BSC, B.PHARM]Shikha Popali
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SIDE REACTION OCCUR IN PEPTIDE YNTJESIS ARE DISCUSSED HERE WITH ITTATED PROTON, PROTONATIONS RACEMIZATION, INITIATED ACTIVITY, ACYLATION, ALKYLATION, OVERACTIVATION
CHEMISTRY OF PEPTIDES [M.PHARM, M.SC, BSC, B.PHARM]Shikha Popali
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Chemistry of peptide (BPHARM,MPHARM,MSC,BSC)Shikha Popali
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Microwave assisted reactions prepared by Dhanashree Kavhale. M. Pharm. II semester (Pharmaceutical Chemistry).
The microwave chemistry is also called as Green Chemistry.
Presented by Shikha Popali and Harshpal singh Wahi students from Gurunanak college of pharmacy, Nagpur in Department of pharmaceutical Chemistry. The explained topic is seful for every chemistry student and for others too
Process chemistry AS PER PCI SYLLABUS FOR M.PHARMShikha Popali
pharmaceutical process chemistry is process WHERE FROM THE RESEARCH TO FINISH PRODUCT INCLUDING THE PRODUCT DEVELOPMENT AT LABORATORY LEVEL THAN PILOT PLANT WHERE THE PRODUCT IS MANUFACTURED IN 10X THAN FINAL AT 100X THAT IS SCALE UP PLANT.
When there are two functional groups of unequal reactivity within a molecule, the more reactive group can be made to react alone, but it may not be possible to react the less reactive functional group selectively.
A group the use of which makes possible to react a less reactive functional group selectively in presence of a more reactive group is known as protecting group.
A protecting group blocks the reactivity of a functional group by converting it into a different group which is inert to the conditions of some reaction(s) that is to be carried out as part of a synthetic route
Asymmetric synthesis (As per new syllabus of PCI)
Methods of asymmetric synthesis using chiral pool
Chiral auxiliaries and catalytic asymmetric synthesis
Enantiopure seperation
Stereoselective synthesis
Recent advances
References
THE SOLID PHASE PEPTIDE SYNTHESIS IS SLIGHTLY DIFFRENT FROM PEPTIDE SYNTHESIS WHICH IS DISCUSSED HERE, ITS SYNTHESIS WITH STRUCTURE ANS BASICS ARE DISCUSSED WHICH WILL BE VERY USEFUL FOR READERS.
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Photochemical reaction is included in the syllabus Advance Organic Chrmitry M Pharm (Pharmaceutical Chemistry) which discribes thode chemical reactions which are takes place by the help of light
Microwave assisted reactions prepared by Dhanashree Kavhale. M. Pharm. II semester (Pharmaceutical Chemistry).
The microwave chemistry is also called as Green Chemistry.
Presented by Shikha Popali and Harshpal singh Wahi students from Gurunanak college of pharmacy, Nagpur in Department of pharmaceutical Chemistry. The explained topic is seful for every chemistry student and for others too
Process chemistry AS PER PCI SYLLABUS FOR M.PHARMShikha Popali
pharmaceutical process chemistry is process WHERE FROM THE RESEARCH TO FINISH PRODUCT INCLUDING THE PRODUCT DEVELOPMENT AT LABORATORY LEVEL THAN PILOT PLANT WHERE THE PRODUCT IS MANUFACTURED IN 10X THAN FINAL AT 100X THAT IS SCALE UP PLANT.
When there are two functional groups of unequal reactivity within a molecule, the more reactive group can be made to react alone, but it may not be possible to react the less reactive functional group selectively.
A group the use of which makes possible to react a less reactive functional group selectively in presence of a more reactive group is known as protecting group.
A protecting group blocks the reactivity of a functional group by converting it into a different group which is inert to the conditions of some reaction(s) that is to be carried out as part of a synthetic route
Asymmetric synthesis (As per new syllabus of PCI)
Methods of asymmetric synthesis using chiral pool
Chiral auxiliaries and catalytic asymmetric synthesis
Enantiopure seperation
Stereoselective synthesis
Recent advances
References
THE SOLID PHASE PEPTIDE SYNTHESIS IS SLIGHTLY DIFFRENT FROM PEPTIDE SYNTHESIS WHICH IS DISCUSSED HERE, ITS SYNTHESIS WITH STRUCTURE ANS BASICS ARE DISCUSSED WHICH WILL BE VERY USEFUL FOR READERS.
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Guided by a specific monoclonal antibody (mAb), antibody drug conjugates or ADC are a new, emerging, class of drugs able to deliver a drug payload directly to an intended target. This approach has recently been boosted by the U.S. Food and Drug Administration approval of brentuximab vedotin (Adcetris®; Seattle Genetics) to treat Hodgkin’s lymphoma and ado-trastuzumab emtansine (Kadcyla®; Genentech) for metastatic breast cancer. These new biotherapeutic drugs will bring many regulatory issues to the forefront regarding the ADME (Absorption, Distribution, Metabolism and Excretion) profile of each ADC. In this article, the authors discuss this and other important aspects of antibody-drug conjugates.
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Improved Stability of Formate Dehydrogenase by Coating with Didodecyldimethyl...researchinventy
Hydrophilic formate dehydrogenase (FDH) from candida boidinii was chemically modified by coating it with didodecyldimethylammonium bromide (DDAB). This coating changed the phase behavior of the enzyme, making it highly soluble in hydrophobic solvents and thereby offering the chance for biphasic enzyme recycling from hydrophilic substrates and products. Different coating procedures of FDH with DDAB were investigated and all proved suitable for efficient coating of the enzyme’s outer surface. A 50 mM Tris- (hydroxymethyl)-amminomethan (tris) buffer at pH 8 was chosen to make DDAB soluble and avoid aggregation. The reaction of NAD+ with uncoated and coated FDH to NADH and CO2 was monitored by UV-vis spectroscopy and kinetic parameters (rmax, Km, KI , EA) for the the FDH were determined. The coated enzyme resulted in a lower relative initial activity between 40-60% compared to the uncoated one. The stability of the coated enzyme (FDH*) was improved significantly and remained stable in long-term experiments, resulting in a deactivation rate kD smaller than 3% per day and a half-life time t1/2largerthan 23 days, while the deactivation rate of the uncoated enzyme was 260% per daywitha t1/2of 0.3 days. Both activation energies were similar, with 42 kJ mol-1 for the coated and 48 kJ mol-1 for the uncoated enzyme.This result suggests that there is not significant transport resistance originating from the DDAB coating layer. The reason for the significantly lower activity of the coated FDH probably stems from accumulation of formed CO2 in the coating layer, thereby preventing high equilibrium conversions
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Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
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4. Transient protecting groups
for amino groups that
form the peptide bond
Permanent protecting groups
for functional groups within
the amino acid side chains
tBoc Fmoc
1963: Merrifield
acid labile, Nα-protecting group
1970: Carpino & Han
a base labile Nα-protecting group
Synthesis, 1979, 955.Biochemistry, 1964, 3, 1385.
Protecting groups
11/13/2016 4niper_H
Transient protecting groups
tBoc Protection
6. 11/13/2016 6
Fmoc
protection
Fmoc deprotection
Based upon the graduated acid lability of
the side-chain protecting groups.
In this approach,
• Boc group is removed by neat TFA or TFA in DCM
• Side-chain protecting groups
• peptide–resin linkages
tBoc/ Bzl Fmoc/tBu
Removed by strong
acid like HF
•Use of highly toxic HF
•Need for PTFE-lined apparatus
•Specialists job
•Use of strongly acidic conditions
can damage peptides
In this approach,
•Base labile Fmoc group is used for protection
•Acid labile side-chain protecting groups
•Acid labile linkers that constitute the C-terminal
amino acid protecting group
Advantage:
Temporary / permanent orthogonal protections
are removed by different mechanisms allowing the
use of milder acidic conditions for final deprotection
and cleavage of the peptide from the resin.
For all these reasons, Fmoc-based SPPS
Method is now the method of choice for
the routine synthesis of peptides
Based upon an orthogonal
protecting group strategy
But not generally used, Why?
Strategies
Mol. Biotech., 2006, 33, 239-54.
7. 11/13/2016 7
Boc / Bn → Based upon the graduated acid
lability of the side-chain protecting groups.
Fmoc / tBu → Based upon an orthogonal
protecting group strategy
niper_H
Strategies
9. 11/13/2016 niper_H 9
Resin + BOC AA (Cs/ TEA salt)
Carboxamide resin by DCC/DMAP
Benzoylation / acetylation of
unreacted –OH group of PAM
BOC deprotection by TFA / DCM
+ Dithioerythritol (DTE)
scavenger for Cys, Met, Trp
Washing DCM, IPA
AA as Trifluoro acetate
+ TEA / DCM neutralization
Washing DCM, IPA
Coupling of activated BOC AA
Deprotection, Neutralization, coupling
Dinytrophenylethyl (DNPE)
PG of His, Formyl PG of Trp
removed by Piperidine / DMF
Cleavage from resin by HF
Anisole, Thiocresol, Dimethyl
sulfide as Scavenger for side
chain PG alkylating agent
BOC-SPPS
10. 11/13/2016 niper_H 10
PAM resin
Phenyl acetamido
methyl linker
BHA resin MBHA resinMerrifield resin
Partial cleavage during
deprotection of BOC
Balances Stability to TFA, lability to HF
Acid catalyzed acyl
NO migration
Side Reactions for BOC-PSSP
Resins BOC-SPPS
Diketopiperazine
Formation
Protonated N → Less prone
Reversed by Base
Aspartamide Formation
Peptide having
Asp-Gly
Asp-Ala
Asp-Ser
11. 11/13/2016 niper_H 11
Asp-Pro cleavage with HF
Homoserine Lactone Formation
C-terminal Met
cyclize to
homoserine lactone
γ-COOH lose water in acid
↓
acylium ion
↓
cyclization
Side chain involving Glu
12. 11/13/2016 niper_H 12
Resins for peptide amide synthesis.
Resins for peptide acid synthesis.
(Wang) resin:
Fmoc-Aaa(X)-OH:DIC:DMAP 2:2:0.2
equiv to the resin OH content) in DMF
diketopiperazine formation side reaction
SASRIN (Super Acid Sensitive ResIN)
Peptide is cleavable with
0.5-1.0% TFA in DCM
1 g ClTrt-resin + 2 mmol Fmoc-Aaa(X)-OH
+ 8 mmol DIEA in 3-5 mL DCM, for 1.5 h
0.8 mL MeOH to block unreacted groups
washing with DCM, iPrOH, MeOH, ether
prevents the diketopiperazine formation
Attachment of Cys and His derivative
to the resin is free from enantiomerisation
Rink Amide-AM (Aminomethyl) and
Rink Amide-MBHA (4-methylbenz
hydrylamine) resins.
Fmoc-SPPS
13. 11/13/2016 niper_H 13
Linkers are bifunctional molecules anchoring the
growing peptide to the insoluble carrier. Linkers may
be coupled to any carrier suitable for SPPS, an
important option if alternatives to polystyrene-based
resins (PS-DVB) have to be considered.
Ramage linker
Rink linker
HMP linker
4-Formyl-3-methoxy
Phenoxyacetic acid
LinkersFmoc-SPPS
14. 11/13/2016 niper_H 14
Mechanism of base-catalyzed
racemization during activation.
More potent coupling reagents such as HATU or very active Fmoc
amino acid derivatives such as the acid fluorides may drive the
coupling to completion.
Coupling Reagents
18. Resin beads + DCM filtration
under vacuum Wash reaction vessel, resin with
DMF → MeOH → DCM→ DMF
Desired Fmoc-amino-acid in dry DCM
+ DMAP in DMF
↓
Cap the remaining hydroxyl groups
by adding benzoic or acetic anhydride
And pyridine in DMF.
Mol. Biotech., 2006, 33, 239-54.
11/13/2016 18niper_H
Protocol 1: Resin swelling
Protocol 3: Attachment to hydroxy
methyl based resin
Protocol 2: Standard
washing procedures
Fmoc amino acid + DIPEA in dry DCM
↓
Wash the resin with DMF
↓
+ DCM/MeOH/ DIPEA (80:15:5) to cap
remaining reactive chloride group.
↓
Wash with DMF and DCM
After drying in vacuum, the
Substitution can be measured from
Fmoc release.
Protocol 4: Attachment to
trityl based resin
Fmoc-SPPS
21. wash the resin with DMF + N-α Fmoc protected amino acid
↓
+ HBTU / HCTU coupling → filtration → Wash the resin.
11/13/2016 21niper_H
Protocol 5: Standard coupling procedure
Activating amino acid
Coupling amino acid
Swell the resin in DCM → filtration+ 50/50
DCM/acetic anhydride solution Remove
the capping solution by filtration → Wash
with DCM Check the disappearance of free
amino groups by colorimetry
Resin is washed once with DMF
↓
80/20 DMF/piperidine solution
↓
Filtration → Wash the resin.
Protocol 6: Capping Protocol 7: Removal of
Nα Fmoc protection
22. (Scavengers) Trifluoroacetic acid/water/triisopropyl silane 95/2.5/2.5
per 100 mg of resin Filter + MTBE to precipitate the peptide. Solubilize the
peptide in acetonitrile/water/ TFA 50/50/0.1 and lyophilize.
Dissolve the lyophilized peptide in a 5% acetic acid solution
+ 10% volume of DMSO pre-adjusted pH to 6.0 - 7.0 with a 0.5 M NH4OAc
Disulfide bridge formation should be monitored by reverse phase HPLC.
Dissolve linear peptide in buffer (0.1–0.2 M Tris-HCl, pH 7.7–8.7)
+ 1 mM EDTA and reduced (1–10 mM) and oxidized (0.1–1 mM) glutathione
Lyophilize the solution after acidification with a TFA solution (pH 2.0)
11/13/2016 22niper_H
Protocol 8: Standard TFA cleavage
Protocol 9: Standard formation of disulfide bridges by air oxidation
Protocol 10: Formation of disulfide bridges using oxidative folding in redox buffer
23. 11/13/2016 niper_H 23
Cleaving a side-chain protected peptide form
2- chlorotrityl chloride resin with HFIP
Formation of disulde bond with DMSO.
25. Diketopiperazine formation after
deprotection of the penultimate amino acid
N-Terminal guanidinylation
by the coupling reagent
11/13/2016 25niper_H
Reaction occurs during couplings
mediated by uronium/ aminium
reagents or carbodiimides. Avoided
by preactivation of the amino acid
(i.e. the coupling reagent is
consumed). The side reaction can’t
occur when activating with
phosphonium salts (Bop, PyBop).
By using 2-chlorotrityl chloride
resin or other bulky resins such
as DHPP-Resin.
By coupling the appropriate
Fmoc-dipeptide in lieu of the
penultimate amino acid.
By coupling the appropiate
Trt-amino acid → Deblocking
with dilute TFA yields the
protonated dipeptide
Fmoc-SPPS – Side chain reactions
27. 11/13/2016 niper_H 27
Application of other cleavage reagents (DBU, TBAF, DEA, morpholine)
eliminate the piperidide formation, but not the succinimide formation.
Addition of HOBt to the cleavage mixture can reduce the succinimide
ring closure. But the best results may get with the use of Fmoc-(Hmb)-
amino acid derivatives:
Hmb: 2-hydroxy-4-methoxybenzyl (removable with TFA)
NH CH C
O
N CH2 C
O
CH2
C OtBu
O
(Hmb)amino acid derivatives are
secundary amines:
Removal of Fmoc group and the
attachement of the next Asp
derivative is difficult, needs
longer time.
Ninhydrin test can’t detect the
efficacy of the coupling.
Fmoc-(Fmoc-Hmb)Gly-OH
The increasing of the solubility of protected peptide fragments
as well as preventing of aggregation of ”difficult” sequences can
be reach by the application of Hmb groups.
28. N-O shift involving
serine or threonine
Base-induced β-elimination
of C- terminal cysteine
J. Pept. Sci., 2005, 11, 441.11/13/2016 28niper_H
Reversal is induced by
bases, e.g. aq. NH3.
This side reaction is minimized (but not
avoided!) when trityl is used for the
protection of the C-terminal Cys.
Deguanidination side reaction on Arg
If the guanidino moiety from Arg side chain is acylated by amino
acid derivatives, it could be decomposed into Orn side product.
29. 11/13/2016 niper_H 29
Boc Fmoc
It is better for avoiding DKP formation;
There is no problem with the Boc
cleavage, so it is better in case of
peptides that aggregate easily.
Aggregates are destroyed in every
TFA cleavage step;
Because of the extra neutralisation
step, the synthetic cycle takes longer
time;
Resins for Boc-strategy are available
for Fmoc-chemistry, too. Two steps
cleavage procedure may results in
better crude product. First step TFA
cleavage (side chain protecting groups)
then HF (peptide-resin bond). More
suitable for preparation of branched
peptides.
ClTrt resin must be used to
prevent DKP formation;
Incomplete Fmoc deprotection
in case of aggregating peptides;
It is better for acid sensitive
peptides (Trp, Met), oxidation,
alkylation can be avoided. Asp-Pro
bond is highly acid sensitive.
especially recommended for
O-glycosylated or sulfated
peptides;
Because of the orthogonality of
Na and side chain protecting groups
fully protected sequences can be
prepared.
Comparision