Chemistry of RNA and peptides (from block synthesis to therapeutic applications). 3900-BT1-2
Two molecular classes that were considered undruggable in recent memory now account for a significant proportion of new drug approvals. Antisense oligonucleotides, small interfering RNA (siRNA), mRNA vaccines and a growing range of macrocyclic and modified peptides have all made it to the clinic because specific chemical issues were resolved, such as nuclease resistance, innate immune recognition, target affinity, membrane permeability, synthetic scale and tissue distribution. The organising principle of the course is that these are chemical problems, that their solutions can be seen in the structures of the approved drugs, and that students who understand the chemistry can predict the properties.
The course is structured as two parallel sections with a similar internal logic, enabling students to draw comparisons between them throughout.
Lectures 1 to 6: The starting point is that RNA function follows from structure and structural dynamics rather than sequence alone. This is why RNA is both a challenging drug target and a promising therapeutic option. Two lectures then address chemical modification: first, the epitranscriptome, where modification is a regulatory layer installed by cellular enzymes; then, the modifications of tRNA and rRNA, and the immunological consequence that made modified mRNA therapeutically possible. From Lecture 4 onwards, the focus turns to synthesis. This section covers the chemical properties of the nucleic acid backbone and sugar, as well as the analogues built on them, such as phosphorothioate, 2'-O-methyl and 2'-MOE, locked and bridged nucleic acids, morpholino and peptide nucleic acids. Each modification is examined in terms of its advantages and disadvantages. Lectures 5 and 6 explain how these molecules are synthesised, from phosphoramidite chemistry and the synthesis cycle to protecting group strategy for the 2'-hydroxyl and the arithmetic of coupling efficiency that limits achievable length. They also cover purification and characterisation, cap chemistry for mRNA and the manufacturing process and environmental issues at a tonne scale.
Lectures 7 to 10 cover the peptide and protein arc. Lecture 7 covers amino acid chemistry, the conformational basis of secondary and tertiary structure, and intrinsic disorder as a functional state rather than an inability to fold. Lectures 8 and 9 cover modification in the same order as the RNA arc. First, they address the biological post-translational modifications, their chemistry, and their functional logic. Then, they cover synthetic modifications for pharmacological purposes. In this section, the course addresses macrocyclisation, stapling, peptidomimetics, foldamers, lipidation, PEGylation, and half-life extension. Lecture 10 covers synthesis and functionalisation. Fmoc and Boc solid-phase peptide synthesis; native and expressed protein ligation; chemoselective bioconjugation; and genetic code expansion as a means of achieving site-specific modification of proteins that are too large to synthesise.
Lectures 11 and 12 cover convergence. The case study lecture works backwards from the label to the chemistry of approved drugs, including antisense oligonucleotides such as nusinersen, inotersen and tofersen, GalNAc-conjugated siRNA drugs such as patisiran, and SARS-CoV-2 mRNA vaccines. On the peptide side, GLP-1 receptor agonists are examined, where lipidation and albumin binding convert a peptide with a two-minute half-life into a weekly injection. The final lecture addresses the remaining issues. The central problem for oligonucleotides is delivery beyond the liver, and for peptides it is oral bioavailability. The course ends with a discussion of lipid nanoparticle chemistry, conjugate-based targeting, base and prime editing as therapeutic modalities, and the manufacturing and cost questions that determine which of these reach patients.
The assessment is designed around the central skill rather than recall, so the examination presents unseen structures.
Course coordinators
Type of course
Mode
Prerequisites (description)
Learning outcomes
Knowledge:
1. Can explain how RNA secondary and tertiary structure and its dynamics determine function; and can explain why this makes RNA both a difficult target and a viable therapeutic.
2. Describe the main chemical modifications of RNA, distinguishing between those installed by enzymes for regulatory purposes and those introduced synthetically for pharmacological purposes.
3. Explains the chemical properties of the phosphodiester backbone and ribose and details which properties are altered by each analogue class: nuclease stability, duplex affinity, RNase H competence, protein binding and immunogenicity.
4. Describes the phosphoramidite synthesis cycle, its protecting group strategy and the relationship between stepwise coupling yield and the maximum practical length of an oligonucleotide.
5. Explains the conformational basis of polypeptide structure, including intrinsic disorder, relating side-chain chemistry to reactivity and modification sites.
6. Describes major post-translational modifications, their chemistry and the synthetic strategies used to modify peptides for stability, permeability and affinity.
7. Compares solid-phase peptide synthesis, chemical ligation, bioconjugation, and genetic code expansion; selects an appropriate route for a given target.
8. Identifies the chemical modifications of a named, approved RNA or peptide drug and states what each modification contributes to its clinical properties.
Skills:
1. Can read an unfamiliar oligonucleotide or peptide structure and predict its stability, mechanism of action, and probable tissue distribution.
2. Proposes a synthetic route to a specified modified oligonucleotide or peptide and identifies the main difficulties involved.
3. Justifies a choice of chemical modification against a stated therapeutic requirement and states the associated cost.
4. Locates and reads the primary literature on a drug or modification class and distinguishes between mechanistic and correlative claims.
Social competences:
1. Discusses the clinical and economic consequences of chemical design decisions, including the cost of goods and access.
2. Recognises the limitations of a platform argument and avoids generalising from one successful drug to an entire class.
Assessment criteria
The exam takes the form of a multiple-choice test covering the material presented during the lectures. It lasts up to 90 minutes and consists of up to 30 questions or tasks, each scored individually, for a maximum total of 100 points.
The final grade is based on the percentage of points obtained out of the maximum possible score:
up to 50% – fail (2.0),
51–60% – satisfactory (3.0),
61–70% – satisfactory plus (3.5),
71–80% – good (4.0),
81–90% – good plus (4.5),
91–100% – very good (5.0).
A minimum of 51% of the total points is required to pass the course. A maximum of 2 absences is allowed.
Bibliography
Lecture 1. Overview of RNA structure and function
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Lectures 2 and 3. The importance of chemical modifications
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Lecture 4. Chemical properties of nucleic acid polymers and their analogs
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Lectures 5 and 6. Synthesis of nucleosides, nucleotides, oligonucleotides and analogs
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Lecture 7. Overview of amino acids and polypeptide structure and function
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Lectures 8 and 9. Peptide modifications
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Lecture 10. Methods for synthesis and functionalisation of peptides, proteins and conjugates
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Lecture 11. Case studies: approved RNA and peptide drugs
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Lecture 12. Emerging trends and challenges
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