The Chemistry of Peptides and Proteins: Basic Principles and Recent Advances
Lecturer: Professor Ashraf Brik
Course duration: 13 weeks
Weekly lecture: 2 hr
Course pre-requirements: Organic chemistry 1m and 2m, Biochemistry, Organic for engineering and life sciences. (
Peptide and protein chemistries are incredibly exciting topics not only from the chemical point of view but also for their broad utilities in various research areas such as drug discovery, nanotechnology and catalysis. Despite over hundred years of knowledge in peptide chemistry, highlighted by two Nobel Prizes, the field is still of great interest for many organic chemists who are trying to develop novel and greener chemical approaches to prepare polypeptides and cope with the challenges of the current century. Moreover, their ease of tunability and diverse chemical and three-dimensional structures make them an attractive scaffold in many research areas. On the other hand, protein synthesis and selective protein modifications applying state of the art chemical methods are relatively newer fields and are expected to influence greatly our molecular understanding of health and disease.
This course aims to give the student the basic knowledge and understanding of the chemistry behind peptide and protein synthesis and expose the students to the diverse approaches to prepare these interesting macromolecules, including the use of classic solution and solid phase approaches and modern new strategies to construct peptide bonds. The student will be exposed to the challenges and opportunities in all these approaches from the synthetic point of view.
The other goal of the course is to expose the students to how protein chemistry is greatly influencing our understanding of the structure and function of proteins in general and how chemical transformations applied to small molecules (e.g. metathesis) can be challenged when exercised in the protein context. This part will include an overview of protein structure and composition, followed by studying early and modern approaches to chemical and semi-synthetically prepare proteins targets.
Finally the course will cover the different approaches for selective protein modifications, which include the use of classical reagents and new ones that are based on diverse chemical structures including organometallic complexes and chemoenzymatic approaches. The application of all these approaches in chemical biology with various examples will be covered.
The specific topics include:
Peptide Synthesis
1) Historical perspective of peptide synthesis and early development
2) Principles of peptide synthesis
3) Solution phase synthesis
4) Solid phase synthesis
- Resins, linkers, coupling reagents, cleavage conditions
- Side reactions
- Fmoc vs Boc chemistry
5) New developments in amide bond formation (e.g. umpolung reaction, KAHA based amide formation, organometallic complexes, thioacid and azide coupling)
Chemical protein synthesis
6) Overview of protein structure
7) The concept of chemoselective ligation
8) Native chemical ligation (NCL)
- Principles
- Peptide thioester preparation (Boc vs Fmoc—via NBZ, hydrazide intermediate, N-S acyl transfer methods, anchoring strategy)
- Limitations of NCL and selected examples of expanding ligation methods (e.g. NCL coupled with desulfurization, axillary mediated ligation)
- Selected example of protein synthesis via NCL
9) Application of protein synthesis
- Selected examples of posttranslationally modified proteins (e.g. glycosylated and ubiquitinated proteins)
- D-proteins
- Labeled proteins
10) Protein semi-synthesis
- Intein based approaches
- Expression of polypeptide with N-terminal Cys
11) Non-NCL based ligation approaches
- KAHA ligation
- Staudinger ligation
- Thioacide and azide based ligation
- New non-native amide bond ligation e.g. Click chemistry based approaches
12) Selective Protein modification (why and how)
- Classical methods for protein modifications (e.g. maleimide chemistry)
- Recent development in metal and organo-reagents for protein modifications
- Unnatural amino acid incorporation for post protein modifications
- Applications (e.g. drug discovery, understanding protein function)
13) Chemoenzymatic methods for protein synthesis and modifications.
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Course requirements: Attendance of at least 80% of lectures
Grading: Final exam from class notes and papers discussed during the course.
Sources: 1) Papers and reviews published in various journals; 2) Books
1) Chemical approaches and the synthesis of peptides and proteins (Paul Lloyd-Wiiliams, Frenando Albericio, Ernest Giralt)
2) Chemistry of peptide synthesis (N Leo Benoiton)
3) Methods in Enzymology Volume 289, Solid Phase Peptide Synthesis (Gregg B. Fields)
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