Dr Arianna Fornili

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

School of Physical and Chemical Sciences
Queen Mary University of London

a.fornili@qmul.ac.uk

www.qmul.ac.uk/spcs/staff/academics/profiles/ariannafornili.html

Centre for Chemical Research

Research
Publications
Grants

Research

Molecular dynamics, Protein dynamics, Myosin, Molecular Modelling, Machine Learning, Protein-ligand interactions

Interests

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

One of the main interests of the group is the study of structural, dynamical and mechanical properties of proteins from skeletal and cardiac muscle. The group is also involved in the development of computational methods for the study of conformational transitions in proteins and for advanced analysis of simulation data.

Publications

Publications of specific relevance to the Centre for Chemical Research

2024

Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor
Matsingos C, Howell LA, McCormick PJ and Fornili A
Journal of Molecular Biology, Elsevier vol. 436 (16)

DOI 10.1016/j.jmb.2024.168688

QMRO

25-06-2024

The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans
Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Baczynska M, Adams CO, Portlock T, Richardson K, Shaw R, Oregioni A, Mastroianni G, Whittaker SB-M, Kelly G, Lorenz CD, Fornili A, Cianciotto NP and Garnett JA
Nature Communications, Springer Nature vol. 15 (1)

DOI 10.1038/s41467-024-49255-4

QMRO

08-06-2024

N4BP1 functions as a dimerization-dependent linear ubiquitin reader which regulates TNF signalling
Kliza KW, Song W, Pinzuti I, Schaubeck S, Kunzelmann S, Kuntin D, Fornili A, Pandini A, Hofmann K, Garnett JA, Stieglitz B and Husnjak K
Cell Death Discovery, Springer Nature vol. 10 (1)

DOI 10.1038/s41420-024-01913-8

QMRO

20-04-2024

2023

The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans
Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Adams CO, Portlock T, Richardson K, Shaw R, Oregioni A, Mastroianni G, Whittaker SB-M, Kelly G, Fornili A, Cianciotto NP and Garnett JA
, Cold Spring Harbor Laboratory vol. 4 (12-15)

DOI 10.1101/2023.12.10.570962

10-12-2023

Abnormal myosin post‐translational modifications and ATP turnover time associated with human congenital myopathy‐related RYR1 mutations
Sonne A, Antonovic AK, Melhedegaard E, Akter F, Andersen JL, Jungbluth H, Witting N, Vissing J, Zanoteli E, Fornili A and Ochala J
Acta Physiologica, Wiley vol. 239 (2)

DOI 10.1111/apha.14035

QMRO

21-08-2023

Binding pocket dynamics along the recovery stroke of human β-cardiac myosin
Akter F, Ochala J and Fornili A
Plos Computational Biology, Public Library of Science (Plos) vol. 19 (5)

DOI 10.1371/journal.pcbi.1011099

QMRO

18-05-2023

A rational approach to selective targeting of skeletal myosin
Antonovic AK, Ochala J and Fornili A
Biophysical Journal, Elsevier vol. 122 (3)

DOI 10.1016/j.bpj.2022.11.806

QMRO

01-02-2023

2022

Comparative study of binding pocket structure and dynamics in cardiac and skeletal myosin
Antonovic AK, Ochala J and Fornili A
Biophysical Journal, Biophysical Society vol. 122 (1), 54-62.

DOI 10.1016/j.bpj.2022.11.2942

QMRO

29-11-2022

Targeting the HER3 pseudokinase domain with small molecule inhibitors
Colomba A, Claus J, Gao F, George R, Fornili A and Cameron AJM
Methods in Enzymology, Elsevier vol. 667, 455-505.

DOI 10.1016/bs.mie.2022.03.044

01-01-2022

2021

Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks
Motta S, Pandini A, Fornili A and Bonati L
Journal of Chemical Theory and Computation, American Chemical Society

DOI 10.1021/acs.jctc.0c01308

QMRO

29-03-2021

2020

Heart Failure Drug Modifies the Intrinsic Dynamics of the Pre-Power Stroke State of Cardiac Myosin
Fornili A, Hashem S and Davies WG
Journal of Chemical Information and Modeling, American Chemical Society

DOI 10.1021/acs.jcim.0c00953

QMRO

07-12-2020

Structure and functional analysis of the Legionella pneumophila chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradation
Rehman S, Grigoryeva LS, Richardson KH, Corsini P, White RC, Shaw R, Portlock TJ, Dorgan B, Zanjani ZS, Fornili A, Cianciotto NP and Garnett JA
Plos Pathogens, Public Library of Science (Plos) vol. 16 (5)

DOI 10.1371/journal.ppat.1008342

QMRO

04-05-2020

Reconstruction of ARNT PAS-B Unfolding Paths by Steered MD and Artificial Neural Network Reveals New Putative Binding Conformations
Motta S, Pandini A, Fornili A and Bonati L
Biophysical Journal, Biophysical Society vol. 118 (3), 297A-297A.

DOI 10.1016/j.bpj.2019.11.1681

QMRO

07-02-2020

2018

Binding Pockets in Proteins Induced by Mechanical Stress.
Tiberti M, Lechner B-D and Fornili A
Journal of Chemical Theory and Computation, American Chemical Society (Acs) vol. 15 (1), 1-6.

DOI 10.1021/acs.jctc.8b00755

QMRO

10-12-2018

Allosteric Modulation of Cardiac Myosin Dynamics by Omecamtiv Mecarbil
Hashem S, Tiberti M and Fornili A
Biophysical Journal. vol. 114 (3), 36a-37a.

DOI 10.1016/j.bpj.2017.11.251

01-02-2018

In Silico Identification of Rescue Sites by Double Force Scanning
Tiberti M, Pandini A, Fraternali F and Fornili A
Biophysical Journal. vol. 114 (3)

DOI 10.1016/j.bpj.2017.11.285

01-02-2018

Binding Pockets Under Mechanical Stress
Tiberti M, Lechner B-D and Fornili A
Biophysical Journal. vol. 114 (3)

DOI 10.1016/j.bpj.2017.11.218

01-02-2018

2017

Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil
Hashem S, Tiberti M and Fornili A
Plos Computational Biology vol. 13 (11), e1005826-e1005826. Editors: Wei G.

DOI 10.1371/journal.pcbi.1005826

QMRO

06-11-2017

In silico identification of rescue sites by double force scanning
Tiberti M, Pandini A, Fraternali F and FORNILI A
Bioinformatics, Oxford University Press (Oup)

DOI 10.1093/bioinformatics/btx515

QMRO

14-08-2017

2016

Using Local States To Drive the Sampling of Global Conformations in Proteins
Pandini A and Fornili A
Journal of Chemical Theory and Computation, American Chemical Society (Acs) vol. 12 (3), 1368-1379.

DOI 10.1021/acs.jctc.5b00992

QMRO

12-02-2016

Effect of RlC N-Terminal Tails on the Structure and Dynamics of Cardiac Myosin
Fornili A, Rostkova E, Fraternali F and Pfuhl M
Biophysical Journal. vol. 110 (3)

DOI 10.1016/j.bpj.2015.11.1600

01-02-2016

Biasing the Sampling of Local States to Drive the Exploration of Global Conformations in Proteins
Pandini A and Fornili A
Biophysical Journal. vol. 110 (3), 187a-188a.

DOI 10.1016/j.bpj.2015.11.1045

01-02-2016

2015

Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase
Carluccio C, Fraternali F, Salvatore F, Fornili A and Zagari A
Journal of Biomolecular Structure and Dynamics, Taylor & Francis vol. 34 (3), 497-507.

DOI 10.1080/07391102.2015.1052016

19-10-2015

Anatomy of protein disorder, flexibility and disease-related mutations
Lu H-C, Chung SS, Fornili A and Fraternali F
Frontiers in Molecular Biosciences, Frontiers vol. 2

DOI 10.3389/fmolb.2015.00047

QMRO

12-08-2015

2014

Phosphorylation Modulates the Dynamics of the N-Terminal Tail in Cardiac RLC
FORNILI A, Rostkova E, Fraternali F and Pfuhl M
Biophysical Journal, Biophysical Society vol. 106 (2), 33A-33A. Editors: NA .

DOI 10.1016/j.bpj.2013.11.253

01-01-2014

Gsatools: Analysis of Allosteric Communication and Functional Local Motions using a Structural Alphabet
Pandini A, Fornili A, Fraternali F and Kleinjung J
Biophysical Journal. vol. 106 (2)

DOI 10.1016/j.bpj.2013.11.3586

01-01-2014

2013

Structural features of the regulatory ACT domain of phenylalanine hydroxylase
Carluccio C, Fraternali F, Salvatore F, Fornili A and Zagari A
Plos One, Public Library of Science vol. 8 (11)

DOI 10.1371/journal.pone.0079482

14-11-2013

Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles
Fornili A, Pandini A, Lu H-C and Fraternali F
Journal of Chemical Theory and Computation, American Chemical Society vol. 9 (11), 5127-5147.

DOI 10.1021/ct400486p

12-11-2013

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

DOI 10.1093/bioinformatics/btt326

15-08-2013

A pH-Regulated Quality Control Cycle for Surveillance of Secretory Protein Assembly
Vavassori S, Cortini M, Masui S, Sannino S, Anelli T, Caserta IR, Fagioli C, Mossuto MF, Fornili A, vanAnken E, Degano M, Inaba K and Sitia R
Molecular Cell, Elsevier/Science Direct vol. 50 (6), 783-792.

DOI 10.1016/j.molcel.2013.04.016

27-06-2013

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

DOI 10.1021/ct301118j

14-05-2013

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

DOI 10.1586/14789450.2013.856764

01-01-2013

2012

Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics
Pandini A, Fornili A, Fraternali F and Kleinjung J
Faseb Journal, American Societies For Experimental Biology vol. 26 (2), 868-881.

DOI 10.1096/fj.11-190868

01-02-2012

Protein-water interactions in MD simulations: POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites
Fornili A, Autore F, Chakroun N, Martinez P and Fraternali F
Methods in Molecular Biology, Springer Verlag vol. 819, 375-392.

DOI 10.1007/978-1-61779-465-0_23

01-01-2012

Intrinsic Dynamics of the Regulatory Light Chain: Implications on Muscle Contraction
Fornili A, Pfuhl M and Fraternali F
Biophysical Journal. vol. 102 (3)

DOI 10.1016/j.bpj.2011.11.2472

01-01-2012

Detection of Allosteric Signal Transmission by Information-Theoretic Analysis of Protein Dynamics
Pandini A, Fornili A, Fraternali F and Kleinjung J
Biophysical Journal. vol. 102 (3)

DOI 10.1016/j.bpj.2011.11.1237

01-01-2012

2010

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

DOI 10.1021/ja107640u

15-12-2010

In silico phosphorylation of the autoinhibited form of p47phox: Insights into the mechanism of activation
Autore F, Pagano B, Fornili A, Rittinger K and Fraternali F
Biophysical Journal, Elsevier/Science Direct vol. 99 (11), 3716-3725.

DOI 10.1016/j.bpj.2010.09.008

01-12-2010

Structural alphabets derived from attractors in conformational space
Pandini A, Fornili A and Kleinjung J
Bmc Bioinformatics, Biomed Central vol. 11

DOI 10.1186/1471-2105-11-97

20-02-2010

Interface Dynamics In Hub Proteins
Fornili A, Pandini A and Fraternali F
Biophysical Journal. vol. 98 (3)

DOI 10.1016/j.bpj.2009.12.1294

01-01-2010

2008

Structural Basis for Substrate Specificity in Group I Nucleoside Hydrolases ,
Iovane E, Giabbai B, Muzzolini L, Matafora V, Fornili A, Minici C, Giannese F and Degano M
Biochemistry, American Chemical Society (Acs) vol. 47 (15), 4418-4426.

DOI 10.1021/bi702448s

25-03-2008

2007

Accurate Description of Nitrogenous Base Flexibility in Classical Molecular Dynamics Simulations of Nucleotides Bound to Proteins
Fornili A, Sironi M and Degano M
The Journal of Physical Chemistry B, American Chemical Society (Acs) vol. 111 (23), 6297-6302.

DOI 10.1021/jp0713357

18-05-2007

Removing extra frontier parameters in QM/MM methods : a tentative with the Local Self-Consistent Field approach
Loos P-F, FORNILI A, Sironi M and Assfeld X
Computing Letters, Brill vol. 3 (2), 473-486. Editors: NA .

DOI 10.1163/157404007782913309

01-01-2007

2006

Frozen core orbitals as an alternative to specific frontier bond potential in hybrid Quantum Mechanics/Molecular Mechanics methods
Fornili A, Loos P-F, Sironi M and Assfeld X
Chemical Physics Letters, Elsevier vol. 427 (1-3), 236-240.

DOI 10.1016/j.cplett.2006.06.095

01-08-2006

On the suitability of strictly localized orbitals for hybrid QM/MM calculations
Fornili A, Moreau Y, Sironi M and Assfeld X
Journal of Computational Chemistry, Wiley vol. 27 (4), 515-523.

DOI 10.1002/jcc.20366

27-01-2006

2005

Evidence for a Nucleophilic anti‐Attack on the Cleaved C(2)‐Oxygen Bond in Cl2‐AlH‐Catalyzed Ring‐Opening of 2‐Substituted 1,3‐Dioxolanes.
Morelli CF, Fornili A, Sironi M, Duri L, Speranza G and Manitto P
Cheminform, Wiley vol. 36 (27), no-no.

DOI 10.1002/chin.200527030

16-06-2005

Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals
Genoni A, Fornili A and Sironi M
Journal of Computational Chemistry, Wiley vol. 26 (8), 827-835.

DOI 10.1002/jcc.20213

06-04-2005

Evidence for a nucleophilic anti-attack on the cleaved C(2)–oxygen bond in Cl2AlH-catalyzed ring-opening of 2-substituted 1,3-dioxolanes
Morelli CF, Fornili A, Sironi M, Durì L, Speranza G and Manitto P
Tetrahedron Letters, Elsevier vol. 46 (11), 1837-1840.

DOI 10.1016/j.tetlet.2005.01.108

01-03-2005

2003

Determination of extremely localized molecular orbitals and their application to quantum mechanics/molecular mechanics methods and to the study of intramolecular hydrogen bonding
Fornili A, Sironi M and Raimondi M
Computational and Theoretical Chemistry, Elsevier vol. 632 (1-3), 157-172.

DOI 10.1016/s0166-1280(03)00296-3

01-08-2003

Regio‐ and Diastereoselectivity in TiCl4‐Promoted Reduction of 2‐Aryl‐Substituted cis‐4‐Methyl‐5‐trifluoromethyl‐1,3‐dioxolanes.
Morelli CF, Fornili A, Sironi M, Duri L, Speranza G and Manittoa P
Cheminform, Wiley vol. 34 (15), no-no.

DOI 10.1002/chin.200315042

21-03-2003

Molecular dynamics simulation of aqueous solutions of trimethylamine-N-oxide and tert-butyl alcohol
Fornili A, Civera M, Sironi M and Fornili SL
Physical Chemistry Chemical Physics, Royal Society of Chemistry (Rsc) vol. 5 (21), 4905-4910.

DOI 10.1039/b308248b

01-01-2003

Molecular dynamics simulation of aqueous solutions of glycine betaine
Civera M, Fornili A, Sironi M and Fornili SL
Chemical Physics Letters, Elsevier vol. 367 (1-2), 238-244.

DOI 10.1016/s0009-2614(02)01707-4

01-01-2003

2002

Regio- and diastereoselectivity in TiCl4-promoted reduction of 2-aryl-substituted cis-4-methyl-5-trifluoromethyl-1,3-dioxolanes
Morelli CF, Fornili A, Sironi M, Durı̀ L, Speranza G and Manitto P
Tetrahedron Asymmetry, Elsevier vol. 13 (23), 2609-2618.

DOI 10.1016/s0957-4166(02)00687-0

01-11-2002

2001

Water interaction with glycine betaine: A hybrid QM/MM molecular dynamics simulation.
FORNILI A
Physical Chemistry Chemical Physics, Royal Society of Chemistry vol. 3, 1081-1085.

DOI 10.1039/B009779I

01-01-2001

Grants

Grants of specific relevance to the Centre for Chemical Research

Developing novel antibody tools to modulate GPR20
Andrew Tinker, Arianna Fornili, Ahuva Nissim and Peter McCormick
£74,767 Barts and the London Charity
01-02-2024 - 31-03-2025

BBSRC AIDD CTP CASE Award: Yu-Yuan Yang
Richard Pickersgill and Arianna Fornili
£8,600 Evotec EVOTEC (UK) LIMITED
01-10-2023 - 30-09-2027

TG: Cheminformatics and machine learning approaches for GPCR computer aided drug design
Arianna Fornili
£125,091 BBSRC Biotechnology and Biological Sciences Research Council
01-10-2023 - 30-09-2027

Wei Dai Studentship - Sosei Heptares
Arianna Fornili and Emma Tjong
£21,600 Nxera Pharma UK Ltd
01-10-2023 - 30-09-2027

Discovering missing links in neuropeptide evolution and function
Maurice Elphick and Arianna Fornili
£576,040 BBSRC Biotechnology and Biological Sciences Research Council
01-06-2023 - 31-05-2026

The cardiovascular function of the orphan G-protein coupled receptor GPR20
Andrew Tinker, Peter McCormick, Arianna Fornili and Patricia Munroe
£307,773 BHF British Heart Foundation
01-05-2023 - 30-04-2026

Structure of the assembly platform of the type II secretion system
Richard Pickersgill, Vidya Chandran Darbari and Arianna Fornili
£579,168 BBSRC Biotechnology and Biological Sciences Research Council
28-10-2022 - 27-10-2025

CTP Training Grant:
Arianna Fornili
£124,909 BBSRC Biotechnology and Biological Sciences Research Council
01-10-2022 - 30-09-2026

Structural bioinformatics and chemogenomics approaches to navigate GPCR ligand interaction space - CTP
Arianna Fornili
£123,829 BBSRC Biotechnology and Biological Sciences Research Council
01-10-2022 - 30-09-2026

Structural Bioinformatics and chemogenomics approaches
Arianna Fornili
£21,600 Nxera Pharma UK Ltd
26-09-2022 - 25-09-2026

Rational design of selective modulators of skeletal myosin
Arianna Fornili
£109,387 MDA Muscular Dystrophy Association
01-01-2020 - 31-12-2023

RSC UG Bursary: William George Davis
Arianna Fornili
£2,200 RSC The Royal Society of Chemistry
01-06-2019 - 31-08-2019