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New Vistas in Fragment-Based Drug Discovery: Development of a Modular Synthetic Platform for Fragment Elaboration in 3-D and Fragment-Based Lead Generation of Small Molecule Inhibitors of the Nsp3 Macrodomain in SARS-CoV-2

   Department of Chemistry

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  Prof P O'Brien  No more applications being accepted  Funded PhD Project (UK Students Only)

About the Project

Background: Fragment-based methods are now well established for the identification of lead compounds in drug discovery.[1] Fragments are small molecules (molecular weight ~150-300) which bind weakly to proteins. However, especially with X-ray crystal structures of protein-fragment complexes, the elaboration of a fragment to designed lead compounds (MW ~400-500) which are strong protein binders, can be achieved. The synthetic chemistry needed to optimise a fragment hit to a lead compound remains a bottleneck in fragment-based drug discovery, as highlighted by Astex recently.[2] This is especially true when optimising along 3-D vectors. Building on our ongoing interest in the exploration of 3-D pharmaceutical space,[3,4] in this project, we will develop a modular synthetic platform that will enable fragments in current libraries[5] to be elaborated into 3-D lead compounds with functionality in defined 3-D vectors (sub-project 1). In a separate part of the project (sub-project 2), based on preliminary findings,[6,7] an interdisciplinary team (molecular biology, synthetic and medicinal chemistry, biophysics, X-ray crystallography) will use fragment-based lead generation[1] to discover small molecule inhibitors of the Nsp3 macrodomain, a novel enzyme target that is present in SARS-CoV-2. Ultimately, the results could underpin the development of a new treatment of COVID-19 (and future CoV-related diseases).


Sub-project 1: Modular Synthetic Platform for Fragment Elaboration in 3-D:

1. Design and synthesis of cyclopropyl and cyclobutyl bifunctional 3-D building blocks – and development of fragment elaboration methodology (Year 1-2)

2. Development of hit compounds against different proteins including the Nsp3 macrodomainin SARS-CoV-2 (Years 2-3)

 Sub-project 2: Fragment-Based Lead Generation of Small Molecule Inhibitors of the Nsp3 Macrodomain in SARS-CoV-2

1. Design, synthesis and analysis of Nsp3 macrodomain binders with IC50 <5 mM activity (Years 1-3)

2. Mapping out structure-activity relationships for the macrodomain (Years 2-3)

Experimental approach:

Sub-project 1: Initially, a set of cyclopropyl and cyclobutyl bifunctional 3-D building blocks will be designed to include common functionality for further elaboration. The 3-D building blocks will comprise a protected amine and a cross-coupling handle on different 3-D bicyclic, fused or spirocyclic scaffolds. Then, each of the 3-D building blocks will be synthesised on a multi-gram scale, addressing issues of diastereo- and enantioselectivity. Next, it will be necessary to demonstrate that robust and orthogonal synthetic chemistry can be used to attach the 3-D building blocks to common fragments. It will also be necessary to explore methodology for further functionalisation of the fragment-building block hybrid to explore lead-like space. Finally, through collaborations, the elaboration of fragment hits against different proteins to lead-like compounds will also be explored.

Sub-project 2: The O’Brien group has ongoing collaboration with Ivan Ahel (Sir William Dunn School of Pathology, University of Oxford) and Frank von Delft (Diamond Light Source, XChem screening facility and Centre for Medicines Discovery, University of Oxford). This interdisciplinary team (molecular biology, synthetic and medicinal chemistry, biophysics, X-ray crystallography) have obtained preliminary fragment hits (234 structures) from an X-ray crystallographic screen of the Nsp3 macrodomain, some of which have been validated in an in vitro biochemical assay.[6,7] To progress to lead compounds, iterative rounds of “design, test, make” will be carried out. The design (structure-based, computational docking) and synthesis parts will be carried out in the O’Brien group at York, with the Ahel and von Delft groups providing read-outs of activity and binding via the biochemical assay and X-ray crystallography respectively. Initial synthetic efforts will be focused on progressing the O’Brien group fragment hits. Different series of elaborated fragments will be designed and new synthetic routes and methodology will be developed as required.

 Novelty: The concept of developing a synthetic platform to facilitate the elaboration of fragments to lead-like compounds is novel. It builds effectively on several hot topics in the synthesis and fragment medicinal chemistry arenas. The macrodomain is a 150 amino acid protein module with (ADP-ribosyl)-hydrolase activity that is a part of the SARS-CoV-2 multidomain protein Nsp3. ADP-ribosylation is a reversible post-translational modification of proteins synthesised by the PARP family of enzymes, and regulates many pathways in human cells, including antiviral defences. Several of the human PARPs (e.g. PARP14) act as antiviral proteins to prevent virus replication. In contrast, the viral macrodomain removes the ADP-ribosylation modifications, thereby enabling the virus to counteract the PARP-induced innate immunity. Thus, the macrodomain enzyme represents a promising and novel drug target for the treatment of coronavirus infections. Well-behaved inhibitors for this domain have not been developed to date.

Training: This project will provide state-of-the-art training in modern synthetic methodology and medicinal chemistry. The graduating PhD student will be fully equipped for a future career in the pharmaceutical industry. All Chemistry research students have access to our innovative Doctoral Training in Chemistry (iDTC): cohort-based training to support the development of scientific, transferable and employability skills:

The Department of Chemistry holds an Athena SWAN Gold Award and is committed to supporting equality and diversity for all staff and students. The Department strives to provide a working environment which allows all staff and students to contribute fully, to flourish, and to excel:

For more information about the project, click on the supervisor's name above to email the supervisor. For more information about the application process or funding, please click on email institution

This PhD will formally start on 1 October 2022. Induction activities may start a few days earlier.

To apply for this project, submit an online PhD in Chemistry application:

You should hold or expect to achieve the equivalent of at least a UK upper second class degree in Chemistry or a related subject.  

Funding Notes

Fully funded for 3 years by AstraZeneca and the Department of Chemistry and covers: (i) a tax-free annual stipend at the standard Research Council rate (£15,609 for 2021-22), (ii) tuition fees at the Home rate, (iii) funding for consumables. See guidance for further details:
Studentships are available to any student who is eligible to pay tuition fees at the home rate:


[1] D. A. Erlanson, S. W. Fesik, R. E. Hubbard, W. Jahnke and H. Jhoti, Nat Rev Drug Discov, 2016, 15, 605.
[2] C. W. Murray and D. C. Rees, Angew. Chem. Int. Ed., 2016, 55, 488.
[3] A. R. Gomez-Angel, J. R. Donald, J. D. Firth, C. De Fusco, R. I. Storer, D. J. Cox and P. O’Brien, Tetrahedron, 2021, 81, 131961.
[4] T. D. Downes et al., Chem. Eur. J., 2020, 26, 89.
[5] M. J. Waring et al., J. Med. Chem. 2019, 62, 3741.
[6] M. Schuller et al., Sci. Adv., 2021, 7, eabf8711

Candidate selection process:
• You should hold or expect to receive at least an upper second class degree in chemistry or a chemical sciences related subject
• Applicants should submit a PhD application to the University of York by the closing date
• Supervisors may contact candidates either by email, telephone or web-chat
• Supervisors can nominate up to 2 candidates to be interviewed for the project
• The interview panel will shortlist candidates for interview from all those nominated
• Shortlisted candidates will be invited to a panel interview on 30th or 31st March or 1st April
• The awarding committee will award studentships following the panel interviews
• Candidates will be notified of the outcome of the panel’s decision by email

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