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Dr Arianna Fornili

Arianna

Reader in Computational Chemistry | Director of the Artificial Intelligence for Drug Discovery MSc programme

Email: a.fornili@qmul.ac.uk
Room Number: G. O. Jones Building, Room 219

Profile

Dr Arianna Fornili is Reader in Computational Chemistry and former Intermediate Basic Science Research Fellow of the British Heart Foundation. She joined QMUL after holding postdoctoral research associate positions at the Randall Division of Cell and Molecular Biophysics (King’s College London) and the DIBIT San Raffaele Scientific Institute in Milan. Her research group (https://afornililab.wordpress.com/) focuses on the computational modelling of protein dynamics to understand protein function, elucidate the molecular basis of disease and develop small molecules with therapeutic applications.

Undergraduate Teaching

  • Essential Skills for Chemists (Tutorials) (CHE100)
  • Essential Skills for Chemists II (CHE210)

Past modules:

  • Pharmaceutical Chemistry (CHE206A) 
  • Pharmaceutical Chemistry (CHE206B)
  • Introductory Programming for Chemists (CHE209)
  • Chemistry Research Project (CHE600)
  • Chemistry Investigative Project (CHE601)
  • Chemistry MSci Research Project (CHE700)

Postgraduate Teaching

  • Introductory programming for drug discovery (CHE709P)
  • Computational ligand-based drug discovery (CHE703P)
  • Data-driven drug discovery (CHE704P)

Director of the Artificial Intelligence for Drug Discovery MSc

 

Research

Research Interests:

My research activity is focused on the computational study of protein dynamics and its relationship to protein function.

The main interest of the group is the study of structural, dynamical and mechanical properties of proteins from the cardiac muscle. Heart contraction arises from a complex interplay of precisely timed molecular motions and the identification of new therapeutic targets for cardiomyopathies relies on a deep understanding of these mechanisms. Combining Molecular Modelling, Molecular Dynamics simulation and Bioinformatics techniques, we investigate how post-translational modifications and cardiomyopathy-related mutations affect the protein motion and stability.

The group is also involved in the development of computational methods for the study of conformational transitions in proteins. In addition to promoting the motion of molecular motors, conformational changes can be essential for many protein functions and they are often required for protein-protein interaction and allosteric regulation. The group aims at improving both the sampling and the detection of biologically relevant conformational transitions, which are usually beyond the timescale of traditional molecular simulations.

Research Department

Publications

Selected Publications

Christos Matsingos*, Lesley A Howell, Peter J McCormick, Arianna Fornili* (2024) Elucidating the activation mechanism of the proton-sensing GPR68 receptor. Journal of Molecular Biology 436:168688. doi: https://doi.org/10.1016/j.jmb.2024.168688

Saima Rehman, Anna Katarina Antonovic, Ian E McIntire, Huaixin Zheng, Leanne Cleaver, Maria Baczynska, Carlton O Adams, Theo Portlock, Katherine Richardson, Rosie Shaw, Alain Oregioni, Giulia Mastroianni, Sara BM Whittaker, Geoff Kelly, Christian D Lorenz, Arianna Fornili*, Nicholas P Cianciotto*, James A Garnett* (2024) The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans. Nature Communications 15:4912. doi: https://doi.org/10.1038/s41467-024-49255-4

Katarzyna W Kliza*, Wei Song, Irene Pinzuti, Simone Schaubeck, Simone Kunzelmann, David Kuntin, Arianna Fornili, Alessandro Pandini, Kay Hofmann, James A Garnett, Benjamin Stieglitz*, Koraljka Husnjak* (2024) N4BP1 functions as a dimerization-dependent linear ubiquitin reader which regulates TNF signalling. Cell Death Discovery 10:183. doi: https://doi.org/10.1038/s41420-024-01913-8

Alexander Sonne,  Anna Katarina Antonovic,  Elise Melhedegaard,  Fariha Akter,  Jesper L. Andersen,  Heinz Jungbluth,  Nanna Witting,  John Vissing,  Edmar Zanoteli,  Arianna Fornili,  Julien Ochala* (2023). Abnormal myosin post-translational modifications and ATP turnover time associated with human congenital myopathy-related RYR1 mutations. Acta Physiologica 00:e14035. doi: 10.1111/apha.14035

Fariha Akter, Julien Ochala, Arianna Fornili* (2023). Binding pocket dynamics along the recovery stroke of human β-cardiac myosin. PLoS Computational Biology 19(5): e1011099. 10.1371/journal.pcbi.1011099

Anna Katarina Antonovic, Julien Ochala, Arianna Fornili* (2023). Comparative study of binding pocket structure and dynamics in cardiac and skeletal myosin. Biophysical Journal. 10.1016/j.bpj.2022.11.2942

Audrey Colomba, Jeroen Claus, Forson Gao, Roger George, Arianna Fornili, Angus J.M. Cameron* (2022). Targeting the HER3 pseudokinase domain with small molecule inhibitors. Methods in Enzymology. 10.1016/bs.mie.2022.03.044

Stefano Motta, Alessandro Pandini*, Arianna Fornili, Laura Bonati* (2021). Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks. Journal of Chemical Theory and Computation. https://doi.org/10.1021/acs.jctc.0c01308

S. Hashem, W. G. Davies, A. Fornili* (2020). Heart Failure Drug Modifies the Intrinsic Dynamics of the Pre-Power Stroke State of Cardiac Myosin. Journal of Chemical Information and Modeling. 10.1021/acs.jcim.0c00953. PDF of accepted version.

S. Rehman, L. S. Grigoryeva, K. H. Richardson, P. Corsini, R. C. White, R. Shaw, T. J. Portlock, B. Dorgan, Z. S. Zanjani, A. Fornili, N. P. Cianciotto*, J. A. Garnett* (2020). Structure and functional analysis of the Legionella pneumophila chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradation. PLOS Pathogens, 10.1371/journal.ppat.1008342

M. Tiberti, B.-D. Lechner, A. Fornili* (2019). Binding Pockets in Proteins Induced by Mechanical Stress. Journal of Chemical Theory and Computation.10.1021/acs.jctc.8b00755

M. Tiberti*, A. Pandini, F. Fraternali, A. Fornili* (2018). In silico identification of rescue sites by double force scanning. Bioinformatics. 34:207-214.  10.1093/bioinformatics/btx515

S. Hashem, M. Tiberti, A. Fornili* (2017). Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil. PLoS Computational Biology 13: e1005826. 10.1371/journal.pcbi.1005826

A. Pandini and A. Fornili* (2016). Using Local States To Drive the Sampling of Global Conformations in Proteins. Journal of Chemical Theory and Computation. 12:1368–1379. 10.1021/acs.jctc.5b00992

C Carluccio, F Fraternali*, F Salvatore, A Fornili, A Zagari* (2015). Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase. Journal of Biomolecular Structure and Dynamics, 10.1080/07391102.2015.1052016.

H Lu, S Chung, A Fornili, F Fraternali* (2015). Anatomy of protein disorder, flexibility and disease-related mutations. Frontiers in Molecular Biosciences 2:47. 10.3389/fmolb.2015.00047

A Fornili, E Rostkova, F Fraternali, M Pfuhl (2014). Phosphorylation Modulates the Dynamics of the N-Terminal Tail in Cardiac RLC. Biophysical Journal vol. 106, (2) 33A-33A. 10.1016/j.bpj.2013.11.253

C Carluccio, F Fraternali, F Salvatore*, A Fornili*, A Zagari (2013). Structural features of the regulatory ACT domain of phenylalanine hydroxylase. PLoS ONE vol. 8, (11) 10.1371/journal.pone.0079482

A Fornili*, A Pandini, HC Lu, F Fraternali* (2013). Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles. Journal of Chemical Theory and Computation vol. 9, (11) 5127-5147. 10.1021/ct400486p

A Pandini*, A Fornili, F Fraternali, J Kleinjung* (2013). GSATools: Analysis of allosteric communication and functional local motions using a structural alphabet. Bioinformatics vol. 29, (16) 2053-2055. 10.1093/bioinformatics/btt326

S Vavassori, M Cortini, S Masui, S Sannino, T Anelli, IR Caserta, C Fagioli, MF Mossuto, A Fornili, E van Anken, M Degano, K Inaba, R Sitia* (2013). A pH-Regulated Quality Control Cycle for Surveillance of Secretory Protein Assembly. Molecular Cell vol. 50, (6) 783-792. 10.1016/j.molcel.2013.04.016

N Chakroun, A Fornili, S Prigent, J Kleinjung, CA Dreiss, H Rezaei, F Fraternali* (2013). Decrypting prion protein conversion into a β-rich conformer by molecular dynamics. Journal of Chemical Theory and Computation vol. 9, (5) 2455-2465. 10.1021/ct301118j

Lu H-C, Fornili A, Fraternali F* (2013). Protein-Protein interaction networks studies and importance of 3D structure knowledge. Expert Review of Proteomics vol. 10, (6) 511-520. 10.1586/14789450.2013.856764

A Pandini*, A Fornili, F Fraternali, J Kleinjung* (2012). Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics. FASEB Journal vol. 26, (2) 868-881. 10.1096/fj.11-190868

A Fornili, F Autore, N Chakroun, P Martinez, F Fraternali* (2012). Protein-water interactions in MD simulations: POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites. Methods in Molecular Biology vol. 819, 375-392. 10.1007/978-1-61779-465-0_23

A Fornili*, B Giabbai, G Garau, M Degano* (2010). Energy landscapes associated with macromolecular conformational changes from endpoint structures. Journal of the American Chemical Society vol. 132, (49) 17570-17577. 10.1021/ja107640u

F Autore, B Pagano, A Fornili, K Rittinger*, F Fraternali* (2010). In silico phosphorylation of the autoinhibited form of p47phox: Insights into the mechanism of activation. Biophysical Journal vol. 99, (11) 3716-3725. 10.1016/j.bpj.2010.09.008

A Pandini, A Fornili, J Kleinjung (2010)*. Structural alphabets derived from attractors in conformational space. BMC Bioinformatics vol. 11, 10.1186/1471-2105-11-97

 

Supervision

PhD supervision

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