Research
Computational Modelling: Understanding and Predicting Molecular Properties
Based within the Department of Chemistry at the University of Liverpool, the group uses computational modelling to solve problems in chemistry.
The group’s research activities employ molecular modelling to
i) Understand chemical systems more completely
ii) Propose new molecular candidates for synthesis and testing
iii) Predict the properties of molecules
Through this strategy we adopt a rational approach driving research through molecular design and understanding. We use and develop computational algorithms to achieve this.
There are four principle research areas
i) Medicinal Chemistry
ii) Materials Chemistry
iii) Reaction Mechanisms
iv) Chemoinformatics
Our research closely integrates modelling, synthesis and testing. We execute our highly collaborative programs both within the Department of Chemistry and at the chemistry:biology interface. Our group drives the modelling aspects of the research whilst collaborators provide the "synthesis" and "testing" aspects of the integrated research approach. We have active academic collaborations both within the University (e.g. Medicincal Chemistry Group, Centre for Drug Safety Science, Materials Chemistry and Reaction Mechanism) and externally (e.g. Liverpool School of Tropical Medicine and University of Washington,University of Glasgow and work closely with industry (e.g. GSK, Bayer, Biofocus (now Charles River) and Unilever).
We are extremely fortunate, and grateful, that our research is funded by research councils (Engineering and Physical Sciences Research Council, Medical Research Council, National Institute for Health Research), charities (Wellcome Trust, Leverhulme Trust, International Vector Control Consortium) and industry (GSK, Bayer and Unilever).
Modelling methods employed include:
Molecular Mechanics
Molecular Dynamics
Quantum Mechanics
Chemoinformatics
Machine Learning
Library Design
2D, 3D QSAR
ADMET
De novo design
Docking
Pharmacophore
Molecular alignment
Structural Biology
Data pipelining
Online Research Identities and Example Publications
Online Research Identities:
Google Scholar
ORCID
ResearchGate
Researcher ID
Scopus
Medicinal Chemistry
Identification of novel antimalarial chemotypes via chemoinformatic compound selection methods for a high-throughput screening program against the novel malarial target, PfNDH2: Increasing hit rate via virtual screening methods. Sharma, R., Lawrenson, A. S., Fisher, N. E., . . . Berry, N. G. (2012). Journal of Medicinal Chemistry, 55(7), 3144-3154.
Antimalarial 4(1H)-pyridones bind to the Q(i) site of cytochrome bc(1). Capper, M. J., O'Neill, P. M., Fisher, N., Strange, R. W., . . . Antonyuk, S. V. (2015). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112(3), 755-760.
Plasmodium IspD (2-C-Methyl- d -erythritol 4-Phosphate Cytidyltransferase), an Essential and Druggable Antimalarial Target. Imlay, L. S., Armstrong, C. M., Masters, . . . Odom, A. R. (2016). Plasmodium IspD (2-C-Methyl- d -erythritol 4-Phosphate Cytidyltransferase), an Essential and Druggable Antimalarial Target. ACS Infectious Diseases, 1(4), 157-167.
Small Molecule Inhibitors of Cyclophilin D to Protect Mitochondrial Function as a Potential Treatment for Acute Pancreatitis. Shore, E. R., Awais, M., Kershaw, N. M., . . . Sutton, R. (2016). Small Molecule Inhibitors of Cyclophilin D to Protect Mitochondrial Function as a Potential Treatment for Acute Pancreatitis. Journal of Medicinal Chemistry, 59(6), 2596-2611.
Materials Chemistry
An adaptable peptide-based porous material,J. Rabone, Y. F. Yue, S. Y. Chong, K. C. Stylianou, J. Bacsa, D. Bradshaw, G. R. Darling, N. G. Berry, Y. Z. Khimyak, A. Y. Ganin, P. Wiper, J. B. Claridge and M. J. Rosseinsky. Science, 2010, 329, 1053-1057.
Guest-Adaptable and Water-Stable Peptide-Based Porous Materials by Imidazolate Side Chain ControlA. P. Katsoulidis, K. S. Park, D. Antypov, C. Marti-Gastaldo, G. J. Miller, J. E. Warren, C. M. Robertson, F. Blanc, G. R. Darling, N. G. Berry, J. A. Purton, D. J. Adams and M. J. Rosseinsky. Angewandte Chemie-International Edition, 2014, 53, 193-198.
Will it gel? Successful computational prediction of peptide gelators using physicochemical properties and molecular fingerprints Gupta, J. K., Adams, D. J., & Berry, N. G. (2016). CHEMICAL SCIENCE, 7(7), 4713-4719.
Reaction Mechanisms
Cooperative Catalysis through Noncovalent Interactions W. Tang, S. Johnston, J. A. Iggo, N. G. Berry, M. Phelan, L. Lian, J. Bacsa and J. Xiao. Angewandte Chemie - International Edition, 2013, 52, 1668-1672.
The synthesis and structure of chiral enamine N-oxides O'Neil, I. A., McConville, M., Zhou, K., Brooke, C., Robertson, C. M., & Berry, N. G. (2014). The synthesis and structure of chiral enamine N-oxides. CHEMICAL COMMUNICATIONS, 50(55), 7336-7339.
Chiral bicyclic 2.2.2 octadiene ligands for Rh-catalysed catalytic asymmetric conjugate additions to acyclic enones: a quantitative structure-property relationship Luo, Y., Berry, N. G., & Carnell, A. J. (2012). CHEMICAL COMMUNICATIONS, 48(27), 3279-3281.
Alumni
Post-Doctoral Researchers
Nivya James (co-supervised with Prof. P. O’Neill)
Chris Woodley
Shirley Leung (co-supervised with Prof. P. O’Neill)
Jyoti Gupta (co-supervised with Prof. L. Hardwick)
David Hong (co-supervised with Prof. P. O’Neill)
Peter Gibbons (co-supervised with Prof. P. O’Neill)
Chandrakala Pidathala (co-supervised with Prof. P. O’Neill)
Shirley Leung (co-supervised with Prof. P. O’Neill)
Richard Amewu (co-supervised with Prof. P. O’Neill)
Jaclyn Bibby
Dmytro Antypov (co-supervised with Prof. M. Rosseinsky)
Alex Lawrenson
Raman Sharma
Jeremy Rabone (co-supervised with Prof. M. Rosseinsky)
PhD Students
Jack Simpson (co-supervised with Prof. D. Adams)
Liquin Guo (co-supervised with Prof. P. O’Neill)
Fazila Bunglawala (co-supervised with Dr M. Siccardi)
Charmaine Chu
Michael Rogers (co-supervised with Prof. P. O’Neill)
Matthew Pye (co-supervised with Prof. P. O’Neill)
Kathryn Price (co-supervised with Prof. P. O’Neill)
Teresa Almeida (co-supervised with Dr A. Carnell)
Natalie Roberts (co-supervised with Prof. P. O’Neill)
Emma Shore (co-supervised with Prof. P. O’Neill and Prof. R. Sutton)
Victoria Pedder (co-supervised with Dr A. Carnell)
Lee Taylor (co-supervised with Prof. P. O’Neill)
Steven Johnson (co-supervised with Prof. J. Xiao and Dr J. Iggo)
Alex Lawrenson
4th Year Project Students
Joshua Burgess-McCann (co-supervised with Prof. P. O’Neill)
Reshma Meah (co-supervised with Prof. J. Xiao and Dr J. Iggo)
Ella Mills (co-supervised with Prof. P. O’Neill)
Stephanie Gamble (co-supervised with Prof. P. O’Neill)
Eleanor Backhouse (co-supervised with Prof. P. O’Neill)
Nilema Rahman (co-supervised with Prof. P. O’Neill)
Lucy Grant
Elizabeth Farrington (co-supervised with Prof. P. O’Neill)
Francesca Lee (co-supervised with Prof. P. O’Neill)
Chris Woodley (co-supervised with Prof. P. O’Neill)
Heather Andrews (co-supervised with Prof. P. O’Neill)
Will Swindells (co-supervised with Dr J. Iggo)
Mateusz Wolf
Phil Kelsall (co-supervised with Prof. P. O’Neill)
Adam Byrne (co-supervised with Prof. P. O’Neill)
Kate Dunne (co-supervised with Dr A. Carnell)
Clare Gregson (co-supervised with Prof. P. O’Neill)
Jyoti Gupta (co-supervised with Prof. D. Adams)
Kathryn Price (co-supervised with Prof. P. O’Neill)
Kate Milburn (co-supervised with Prof. P. O’Neill)
Hannah Godfrey (co-supervised with Dr A. Carnell)
Vanessa Flynn (co-supervised with Prof. P. O’Neill)
Ben Alston (co-supervised with Dr D. Cooper)
David Holt (co-supervised with Prof. P. O’Neill)
3rd Year Project Students
Tyarna Smith
Jack Simpson
Chris Woodley
Sarah Livesley (co-supervised with Dr C. Aïssa)
Charmaine Chu
Mohammed Rahman
Josh Black
Jiyao Feng
Iain Aldous (co-supervised with Prof. N. Greeves)
Ajay Antichen (co-supervised with Prof. N. Greeves)
Nicola Hodgson (co-supervised with Prof. N. Greeves)
Lyndsey Vernon (co-supervised with Prof. N. Greeves)
Fiona Hatton (co-supervised with Dr C. Aïssa)
Summer Students
Jack Simpson
Chris Woodley
Benjamin Greeves
Naomi Ritchie (co-supervised with Prof. N. Greeves)
Alex Bretherton (co-supervised with Prof. N. Greeves)
Craig Wilson (co-supervised with Prof. N. Greeves)
Michael Rogers (co-supervised with Prof. N. Greeves)
Jyoti Gupta (co-supervised with Prof. N. Greeves)
Joshua Black (co-supervised with Dr G. Sedghi)
Kate Dunne (co-supervised with Prof. N. Greeves)
Emma Shore (co-supervised with Prof. N. Greeves)
Aled Roberts (co-supervised with Prof. N. Greeves)
Iain Aldous (co-supervised with Prof. N. Greeves)
Frances Potjewyd (co-supervised with Prof. N. Greeves)
Adam Byrne (co-supervised with Prof. N. Greeves)
Ajay Antichen (co-supervised with Dr G. Sedghi)
Lyndsey Vernon (co-supervised with Prof. N. Greeves)
Suzannah Hussain (co-supervised with Prof. N. Greeves)
Smaher Butt (co-supervised with Prof. N. Greeves)
Sze-Kie Ho (co-supervised with Prof. N. Greeves)
Research groups
Research grants
Lead Optimisation of a Series of Antimalarial Plasmepsin IX/X Betahydroxyethylamine Based Inhibitors
MEDICAL RESEARCH COUNCIL
February 2024 - January 2026
EPSRC Core Equipment Award 2022 - A multi-user XRD facility for Advanced Materials research
ENGINEERING & PHYSICAL SCIENCES RESEARCH COUNCIL
January 2023 - July 2024
Antivirulence treatment for microbial keratitis
FIGHT FOR SIGHT (UK)
May 2022 - June 2025
The role of chemosensory proteins in pyrethroid resistance
BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL
April 2021 - March 2024
Chemistry of open-shell correlated materials based on unsaturated hydrocarbons
ENGINEERING & PHYSICAL SCIENCES RESEARCH COUNCIL
October 2019 - September 2023
ISCF Wave 1: Earth-Abundant Metal-Air Batteries
ENGINEERING & PHYSICAL SCIENCES RESEARCH COUNCIL
October 2017 - September 2021
The Calcium-Air Battery
ENGINEERING & PHYSICAL SCIENCES RESEARCH COUNCIL
September 2017 - July 2019
Dynamic responsive porous crystals - Dynapore
EUROPEAN COMMISSION
October 2016 - September 2022
Rational Design, Synthesis and Biological Evaluation of Benzimidazoles Towards a Novel Therapy Selectively Targeting C. neoformans beta-tubulin
MEDICAL RESEARCH COUNCIL
July 2016 - December 2019
Lead Series Development & Optimisation af a New Drug Against Active and Latent Tuberculosis.
MEDICAL RESEARCH COUNCIL
October 2011 - March 2014
Sorption and reactivity in flexible amino acid-based nanoporous materials
ENGINEERING & PHYSICAL SCIENCES RESEARCH COUNCIL
April 2008 - October 2011
KEL09/13 - Molecular design and chemoinformatics: A combined approach to novel molecules
ENGINEERING & PHYSICAL SCIENCES RESEARCH COUNCIL
December 2010 - March 2012
Resistant Breaking Insecticides - Project New Pyrethroids
BAYER CORPORATION (USA)
December 2007 - December 2011
Impact Acceleration Account - University of Liverpool 2012
ENGINEERING & PHYSICAL SCIENCES RESEARCH COUNCIL
October 2012 - March 2017
Bridging and accelerating the translation of novel scientific findings for health and wealth gain
MEDICAL RESEARCH COUNCIL
March 2014 - August 2015
Metal-Bronsted Acid Cooperative Catalysis for Asymmetric Direct Reductive Amination
ENGINEERING & PHYSICAL SCIENCES RESEARCH COUNCIL
September 2009 - June 2013
A new drug target against Malaria
LEVERHULME TRUST (UK)
June 2006 - May 2009
Adaptable Porous Materials
ENGINEERING & PHYSICAL SCIENCES RESEARCH COUNCIL
July 2012 - March 2016
Positive Allosteric Modulators of Strychnine-Sensitive Glycine Receptors – A New Concept in Treating Chronic Pain
MEDICAL RESEARCH COUNCIL
September 2012 - February 2015
Research collaborations
Prof. Paul O'Neill
Covers a range of medicinal chemistry and chemical biology areas focused on malaria, TB and filariasis. https://www.liverpool.ac.uk/chemistry/research/medicinal-chemistry/
Prof. S. Ward
Liverpool School of Tropical Medicine
Covers a range of medicinal chemistry and chemical biology areas focused on malaria, TB and filariasis. https://www.liverpool.ac.uk/chemistry/research/medicinal-chemistry/
Prof. G. Biagini
Liverpool School of Tropical Medicine
Covers a range of medicinal chemistry and chemical biology areas focused on malaria and TB. https://www.liverpool.ac.uk/chemistry/research/medicinal-chemistry/
Prof. Nick Casewell
Liverpool School of Tropical Medicine
Discovery and early translation of small molecule toxin inhibitors for use as broadly effective, inexpensive, oral, prehospital snakebite treatments
Prof. Dave Adams
University of Glasgow
Predicting gelation properties
Prof. Matt Rossiensky
Protein inspired dynamic porous crystals
Prof. R. Sutton
Targeting Cyclophilin D to Treat Pancreatitis
Prof. Jianliang Xiao
Modelling reactions