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Tumour Selective Activation of Rotaxanated DNA-fork-binding Metallo-supramolecular Nano-cylinder Helicates

Lead Research Organisation: University of Birmingham
Department Name: School of Chemistry

Abstract

This proposal will develop at Birmingham a highly promising early career researcher, Dr Subhendu Karmakar, who has previous experience and skills from top labs in Jerusalem and India. He will gain advanced training at the interface of supramolecular and bioinorganic chemistry with biology, under the supervision of a leading bioinorganic chemist, Mike Hannon, that will develop him to a position where he will be ready to secure an academic position to launch his own independent research career in Bioinorganic Chemistry, supported by and further developing the European links and collaborations he will have formed. Alongside the new techniques and approaches in non-covalent DNA-binding and metallo-supramolecular and rotaxane drug designs, and the transferable skills training he will gain, he will transfer to Birmingham his expertise in activation of drugs in hypoxic tisues, enhancing the capabilities of the Birmingham team and enabling an exciting new project made possible only by interfacing their respective skill bases. The result will be a powerful and innovative new approach to agents that will bind and interfere with critical DNA fork structures essential to cancer cell replication and which will do so only in cancer cells and so minimise collateral damage to normal tissue and thus side-effects. The project will reveal and enable new horizons for metallo-supramolecular drug design and transform the state-of-the-art for metallo-therapeutics.

Publications

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Karmakar S (2025) Switching on Supramolecular DNA Junction Binding Using a Human Enzyme in Angewandte Chemie International Edition

 
Description Key Findings
WP1: Research Objectives RO1 and RO2, RO3, RO4 have been achieved as anticipated in the project timeline at Milestones M1 and M2 and M3: Metallo-cylinder drugs protected with tumour cell overexpressing enzyme responsive groups have been synthesized and characterized. These protected metallo-cylinders are inert and do not bind DNA. But following treatment with the enzyme, the protecting groups are removed and active metallo-cylinders are released which bind their DNA targets as demonstrated by gel electrophoresis and spectroscopies. Studies in cells show the same effect in cellulo. The work being written up for publication (D2 and D3) which are in revision.
The work has been presented in an oral presentation by the fellow Dr. Karmakar at major international conferences SABIC (Symposium on Advanced Biological Inorganic Chemistry, SABIC-2024, Kolkata, 7-11 January, Registration number: SABIC2024/OL/19) in India (Deliverable D1) an oral presentation and being a session chair at EuroBIC in Munster Germany (D4) and a Poster Presentation at the 2023 RSC Macrocyclic and Supramolecular Chemistry (MASC) Meeting (D5) on the timeline envisaged in the proposal. This has showcased the research accomplishments in designing tumour specific enzyme activable metallo-cylinder in front of a broad bioinorganic community. The responses were positive from the audience and in post-lecture interaction.
Alongside the research work packages and objectives the fellow has undertaken advanced training improving his skill base. He has attended taught courses on Safety, Presentation skills, and grant writing; has received bespoke research training on specific equipment/techniques (training objective TO1) including linear dichroism spectroscopy (a technique only available in a few labs worldwide), circular dichroism and gel electrophoresis; obtained new competent practical skills (TO2) in the design and synthesis & characterization of metallo-supramolecular agents, enzyme cleavage and techniques to study DNA binding; Developed good health and safety practices (TO4); Enhanced his multidisciplinary project management skills (TO3); and enhanced his presentation, leadership and communication skills with scientists and the public (TO 5,7,8).
Exploitation Route The fellow's training will be put to good use when he uses his new research skills for the next step in his career plan to become an independent researcher.
Sectors Chemicals

Healthcare

Pharmaceuticals and Medical Biotechnology

 
Title Raw Data Set for the publication: 'Switching On Supramolecular DNA Junction Binding Using a Human Enzyme' 
Description Data Set for a publication that has been submitted 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact none 
URL http://edata.bham.ac.uk/1178/
 
Description Collaboration with Bioscientist Dr Nik Hodges 
Organisation University of Birmingham
Department School of Biosciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Dr Karmakar has involved Dr Hodges in the research and together they have done cell line testing and the results have contributed to a paper that has been submitted
Collaborator Contribution Dr Hodges has enabled cell line testing and the results have contributed to a paper that has been submitted
Impact Multidisciplinary collaboration
Start Year 2023
 
Description collaboration with Alex Pothig TU Munich 
Organisation Technical University of Munich
Country Germany 
Sector Academic/University 
PI Contribution collaboration on crystallography of supramolecular complexes where we have prepared the samples
Collaborator Contribution collaboration on crystallography of supramolecular complexes where they have assisted with the crystallography
Impact paper submitted
Start Year 2023
 
Description International Conference Oral Presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Dr. Karmakar has participated an international conference and orally showcased his research accomplishments in designing tumour specific enzyme activable metallo-cylinder in front of a broad bioinorganic community (Symposium on Advanced Biological Inorganic Chemistry, SABIC-2024, Kolkata, 7-11 January, Registration number: SABIC2024/OL/19). The responses were positive from the audiences. Many of them have expressed interest on target selective nucleic acid junction binding during the post-presentation interaction.
Year(s) Of Engagement Activity 2024
URL https://www.indiabioinorganic.org/
 
Description Oral Presentation in EuroBIC-17 and Chaired a Scientific Session in the Same International Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Dr. Karmakar has participated an international conference and orally presented his research accomplishments in designing tumour specific enzyme activable metallo-cylinder in front of a broad bioinorganic community (17th European Biological Inorganic Chemistry Conference EuroBIC-17, Munster, 25-28 August'24). The responses were positive from the audiences. Many of them have expressed interest on target selective nucleic acid junction binding during the post-presentation interaction.
Dr. Karmakar also chaired a scientific session on personal request from the conference organizers.
Year(s) Of Engagement Activity 2024
URL https://www.uni-muenster.de/Chemie.ac/en/eurobic17/
 
Description Outreach Event for School Children 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Dr. Karmakar was part of a volunteer team for an outreach event organised by School of Chemistry, University of Birmingham (ChemBAM). 210 school students visited to the chemical labs of our newly made molecular science building on 18 June'24. In this event, Dr. Karmakar conducted a hands-on experiment demonstrating a light-driven chemical reaction through cyanotyping for the school children.
Year(s) Of Engagement Activity 2024
URL https://www.birmingham.ac.uk/schools/chemistry/services-schools
 
Description Poster Presentation at the 2023 RSC Macrocyclic and Supramolecular Chemistry (MASC) Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Dr. Karmakar has participated an international conference and presented a poster on his research accomplishments in designing tumour specific enzyme activable metallo-cylinder in front of a broad supramolecular community (2023 RSC Macrocyclic and Supramolecular Chemistry (MASC) Meeting, Birmingham, 18-19 December'23). The responses were positive from the audiences. Many of them have expressed interest on target selective nucleic acid junction binding during the post-presentation interaction.
Year(s) Of Engagement Activity 2023
URL https://x.com/masc_2023?lang=en