MSci in Chemistry with study in continental Europe (University of Bristol, 2002)
PhD in Chemistry (University of Bristol, 2006)
I am an experienced post-doctoral researcher in computational enzymology, first becoming interested in the area as an undergraduate student. I have worked on many projects employing QM/MM techniques to explore aspects of enzyme reaction mechanisms and catalysis.
“Innovative routes to monoterpene hydrocarbons and their high value derivatives”
Terpenes and their derivatives form the largest and most diverse class of natural products. Monoterpenes are industrially important in the production of flavours and fragrances and there is considerable interest in producing these compounds by biocatalysis. We are working as part of a mutidisciplinary synthetic biology project with the groups of Prof. Nigel Scrutton and Prof. David Leys at the University of Manchester to investigate these compounds.
Phosphite dehydrogenase (PTDH)
Working with the group of Prof. Wilfred van der Donk at the University of Illinois at Urbana-Champaign, we identified a catalytic role for Met53 in catalysis in PTDH. The important interaction between Met53 and His292 is not present in the crystal structure of the ternary complex, highlighting the important role computation can play in the identification of important transient species during a reaction.
Aromatic amine dehydrogenase (AADH) and methylamine dehydrogenase (MADH)
Working with the groups of Prof. Nigel Scrutton and Prof. David Leys at the University of Manchester we used a combination of crystallography, enzyme kinetics and computation to investigate the role of quantum tunnelling in the rate-limiting proton transfer step in both AADH and MADH.
Chorismate mutase has been the centre of much debate about enzyme catalysis over the past few decades, with computational techniques playing an important role in identifying the source of the enzyme’s catalytic power.
Ahmad S, Ranaghan KE, Azam SS. Combating tigecycline resistant Acinetobacter
baumannii: A leap forward towards multi-epitope based vaccine discovery. Eur J
Pharm Sci. 2019; pii: S0928-0987(19)30084-3. doi:10.1016/j.ejps.2019.02.023.
Ranaghan KE, Shchepanovska D, Bennie SJ, Lawan N, Macrae S, Zurek J, Manby FR,
Mulholland AJ. Projector-based embedding eliminates density functional dependence
for QM/MM calculations of reactions in enzymes and solution. J Chem Inf Model.
2019; doi: 10.1021/acs.jcim.8b00940.
Leferink NGH, Ranaghan KE, Karrupiah V, Currin A, van der Kamp MW, Mulholland AJ, and Scrutton NS. Experiment and simulation reveal how mutations in functional plasticity regions guide plant monoterpene product outcome. ACS Catal 2018; 8 (5), 3780-3791. doi: 10.1021/acscatal.8b00692
Callegari D, Ranaghan KE, Woods CJ, Minari R, Tiseo M, Mor M, Mulholland AJ,
Lodola A. L718Q mutant EGFR escapes covalent inhibition by stabilizing a
non-reactive conformation of the lung cancer drug osimertinib. Chem Sci. 2018; 9(10):2740-2749. doi: 10.1039/c7sc04761d.
Asad Y, Ahmad S, Rungrotmongkol T, Ranaghan KE, Azam SS. Immuno-informatics
driven proteome-wide investigation revealed novel peptide-based vaccine targets
against emerging multiple drug resistant Providencia stuartii. J Mol Graph Model.
2018;80:238-250. doi: 10.1016/j.jmgm.2018.01.010.
Karuppiah V, Ranaghan KE, Leferink NGH, Johannissen LO, Shanmugam M, Ní
Cheallaigh A, Bennett NJ, Kearsey LJ, Takano E, Gardiner JM, van der Kamp MW, Hay S, Mulholland AJ, Leys D, Scrutton NS. Structural Basis of Catalysis in the
Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase. ACS
Catal. 2017;7(9):6268-6282. doi: 10.1021/acscatal.7b01924.
Ranaghan KE, Morris WG, Masgrau L, Senthilkumar K, Johannissen LO, Scrutton
NS, Harvey JN, Manby FR, Mulholland AJ. Ab Initio QM/MM Modeling of the
Rate-Limiting Proton Transfer Step in the Deamination of Tryptamine by Aromatic
Amine Dehydrogenase. J Phys Chem B. 2017;121(42):9785-9798. doi:
Baseer S, Ahmad S, Ranaghan KE, Azam SS. Towards a peptide-based vaccine
against Shigella sonnei: A subtractive reverse vaccinology based approach.
Biologicals. 2017; 50:87-99. doi: 10.1016/j.biologicals.2017.08.004.