Publications

Preprints

1

Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations

Mey, A. S. J. S.. ; Juárez-Jiménez, J.. ;  Michel, J.  
 doi:10.1101/150474 [bioRxivbioRxiv]

Journal Publications

39

Pushing The Limits Of Detection Of Weak Binding Using Fragment Based Drug Discovery: Identification Of New Cyclophilin Binders

Georgiou, C. ; McNae, I. W. ; Wear, M. A. ; Ioannidis, H. ; Michel, J. ; Walkinshaw, M. D.  

J Mol. Biol., 429(16), 2556-2570, 2017  doi:10.1016/j.jmb.2017.06.016doi:10.1016/j.jmb.2017.06.016 [bioRxivbioRxiv]

38

Assessment of Hydration Thermodynamics at Protein Interfaces with Grid Cell Theory

Gerogiokas, G. ; Southey, M. W. Y. ; Mazanetz, M. P. ; Heifetz, A. ; Bodkin, M. ; Law, R. J. ; Henchman, R. H. H. ; Michel, J.

J. Phys. Chem. B, 120(40), 10442-10452, 2016 doi:10.1021/acs.jpcb.6b07993doi:10.1021/acs.jpcb.6b07993

37

Blinded predictions of distribution coefficients in the SAMPL5 challenge

Bosiso, S ; Mey, A. S. J. S. ; Michel, J. 
J. Comput. Aided Mol. Des., 30:1101-1114, 2016 doi:10.1007/s10822-016-9969-1doi:10.1007/s10822-016-9969-1

36

Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge

Bosiso, S ; Mey, A. S. J. S. ; Michel, J. 
J. Comput. Aided Mol. Des., 31:61-70, 2017 doi:10.1007/s10822-016-9933-0doi:10.1007/s10822-016-9933-0 [ PDF ] 

35

Blinded predictions of binding modes and energies of HSP90-alpha ligands for the 2015 D3R Grand Challenge

Mey, A. S. J. S. ; Juárez-Jiménez J. ; Hennessy, A. ; Michel, J. 
Bioorg. Med. Chem., 24(20), 4890-4899, 2016 doi:10.1016/j.bmc.2016.07.044doi:10.1016/j.bmc.2016.07.044 [ PDF ] 

34

Elucidation of Non-Additive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study

Calabro, G. ; Woods, C. J. ; Powlesland, F. ; Mey, A. S. J. S.; Mulholland, A. J. ; Michel, J. 
J. Phys. Chem. B, 120 (24), 5340-5350, 2016 doi:10.1021/acs.jpcb.6b03296doi:10.1021/acs.jpcb.6b03296 [ PDF ] 

33

Impact of Ser17 phosphorylation on the conformational dynamics of the oncoprotein MDM2

Bueren-Calabuig, J. A. ; Michel, J. 
Biochemistry, 55 (17), 2500-2509, 2016 doi:10.1021/acs.biochem.6b00127doi:10.1021/acs.biochem.6b00127 [ PDF ]

32

FESetup: Automating Setup for Alchemical Free Energy Simulations

Loeffler, H. H. ; Michel, J. ; Woods, C. J. 
J. Chem. Inf Model., 55 (12), 2485-2490, 2015 doi:10.1021/acs.jcim.5b00368doi:10.1021/acs.jcim.5b00368

31

Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate complexes

Sushil K. Mishra, S. K. ; Calabró, G. ; Loeffler, H. H. ; Michel, J.. ; Koca J.
J. Chem. Theory Comput., 11 (7), 3333-3345, 2015 doi:10.1021/acs.jctc.5b00159doi:10.1021/acs.jctc.5b00159 [ PDF ] 

30

Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2

Bueren-Calabuig, J. A. ; Michel, J. 
PLoS Comput. Biol. , 11(6): e1004282, 2015 doi:10.1371/journal.pcbi.1004282doi:10.1371/journal.pcbi.1004282

29

A Collective Variable for the Rapid Exploration of Protein Druggability

Cuchillo, R. ; Pinto-Gil, K. ; Michel, J. 
J. Chem. Theory Comput., 11 (3), 1292-1307, 2015 doi:10.1021/ct501072tdoi:10.1021/ct501072t [ PDF ] 

28

Evaluation of Water Displacement Energetics in Protein Binding Sites with Grid Cell Theory

Gerogiokas, G. ; Southey, M. W. Y. ; Mazanetz, M. P. ; Heifetz, A. ; Bodkin, M. ; Law, R. J. ; Michel, J.
Phys. Chem. Chem. Phys., 17, 8416-8426, 2015 doi:10.1039/C4CP05572Adoi:10.1039/C4CP05572A [ PDF ] 

27

Evaluation of Host/Guest Binding Thermodynamics of Model Cavities with Grid Cell Theory

Michel, J. ; Henchman, R.H. ; Gerogiokas, G. ; Southey, M. W. Y. ; Mazanetz, M. P. ; Law, R. J. ; 
J. Chem. Theory Comput., 10 (9), 4055-4068, 2014 doi:10.1021/ct500368pdoi:10.1021/ct500368p [ PDF ] 

26

Strategies to calculate water binding free energies in protein-ligand complexes

Bodnarchuk, M. S. ; Viner, R. ; Michel, J. ; Essex, J. W. 
J. Chem. Inf. Model., 54 (6), 1623-1633, 2014 doi:10.1021/ci400674kdoi:10.1021/ci400674k

25

Rapid Decomposition and Visualisation of Protein-Ligand Binding Free Energies by Residue and by Water

Woods, C. J. ; Malaisree, M. ; Michel, J. ; Long, B. ; McIntosh-Smith, S. ; Mulholland, A. J.
Faraday Discuss., 169, 477-499 2014 doi:10.1039/C3FD00125Cdoi:10.1039/C3FD00125C

24

Current and Emerging Opportunities for Molecular Simulations in Structure-Based Drug Design

Michel, J. 
Phys. Chem. Chem. Phys., 16, 4465-4477, 2014 doi:10.1039/C3CP54164Adoi:10.1039/C3CP54164A

23

Prediction of Small Molecule Hydration Thermodynamics with Grid Cell Theory

Gerogiokas, G. ; Calabro, G. ; Henchman, R.H. ; Southey, M. W. Y. ; Law, R. J. ; Michel, J. 
J. Chem. Theory Comput., 10 (1), 35 - 48, 2014 doi:10.1021/ct400783hdoi:10.1021/ct400783h

22

Luminescent, Enantiopure, Phenylatopyridine Iridium-Based Coordination Capsules

Chepelin, O.; Ujma, J.; Wu, X.; Slawin, A.; Pitak, M. B.; Coles, S., J.; Michel, J.; Jones, A. C.; Barran, P. E.; Lusby, P. J.
J. Am. Chem. Soc., 134 (47), 19334-19337, 2012 doi:10.1021/ja309031hdoi:10.1021/ja309031h

21

Mechanisms of small-molecule binding to intrinsically disordered proteins

Cuchillo, R.; Michel, J.
Biochem. Soc. Trans., 40 (5), 1004 -1008, 2012 doi:10.1042/BST20120086doi:10.1042/BST20120086

20

The Impact of Small Molecule Binding on the Energy Landscape of the Intrinsically Disordered Protein c-Myc

Michel, J. ; Cuchillo, R.
PLoS ONE, 7 (7): e41070, 2012 doi:10.1371/journal.pone.0041070doi:10.1371/journal.pone.0041070

19

Targeting the von Hippel–Lindau E3 Ubiquitin Ligase Using Small Molecules To Disrupt the VHL/HIF-1a Interaction

Buckley, D. L. ; Van Molle, I. ; Gareiss P. C. ; Seop Tae H. ; Michel, J. ; Noblin, D. J. ; Jorgensen, W. L. ; Ciulli, A. ; Crews, C. M.
J. Am. Chem. Soc., 134 (10), 4465 -4468, 2012 doi:10.1021/ja209924vdoi:10.1021/ja209924v

18

A Simple QM/MM Approach for Capturing Polarization Effects in Protein-Ligand Binding Free Energy Calculations

Beierlein, F. B. ; Michel, J. ; Essex, J. W.
J. Phys. Chem. B, 115 (17), 4911 -4926, 2011 doi:10.1021/jp109054jdoi:10.1021/jp109054j

17

Effects of Water Placement on Predictions of Binding Affinities for p38 MAPalpha Kinase Inhibitors

Lucarelli, J. ; Michel, J. ; Tirado-Rives, J. ; Jorgensen W. L.
J. Chem. Theory Comput., 6 (12), 3850 -3856, 2010 doi:10.1021/ct100504hdoi:10.1021/ct100504h

16

A Remote Arene Binding Site on Prostate Specific Membrane Antigen Revealed by Antibody-Recruiting Small Molecules

Zhang, A. X. ; Murelli, R. P. ; Barinka, C. ; Michel, J. ; Cocleaza, A. ; Jorgensen, W. L. ; Lubkowski, J. ; Spiegel, D. A.
J. Am. Chem. Soc., 132 (36), 12711 -12716, 2010 doi:10.1021/ja104591mdoi:10.1021/ja104591m

15

Rigorous free energy calculations in structure-based drug design

Michel, J. ; Foloppe, N. ; Essex, J. W.
Mol. Inf., 29, 570 - 578, 2010 doi:10.1002/minf.201000051doi:10.1002/minf.201000051

14

Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

Michel, J. ; Essex, J. W.
J. Comput. Aided Mol. Des., 24 (8), 639 -658 2010 doi:10.1007/s10822-010-9363-3doi:10.1007/s10822-010-9363-3

13

Bridged beta3-Peptide Inhibitors of p53-hDM2 Complexation - Correlation Between Affinity and Cell Permeability

Bautista, A. D. ; Appelbaum, J. S. ; Craig, C. J. ; Michel, J. ; Schepartz, A.
J. Am. Chem. Soc., 132 (9), 2904 -2906, 2010 doi:10.1021/ja910715udoi:10.1021/ja910715u

12

Coarse-grain modelling of DMPC and DOPC lipid bilayers

Orsi, M. ; Michel, J. ; Essex, J. W.
J. Phys.: Condens. Matter, 22 (15), 155106, 2010 doi:10.1088/0953-8984/22/15/155106doi:10.1088/0953-8984/22/15/155106

11

Chemical Control Over Immune Recognition: A Class of Antibody-Recruiting Small Molecules (ARMs) that Target Prostate Cancer

Murelli, R. P. ; Zhang, A. X. ; Michel, J. ; Jorgensen W. L. ; Spiegel, D. A.
J. Am. Chem. Soc., 131 (47), 17090 -17092, 2009 doi:10.1021/ja906844edoi:10.1021/ja906844e

10

Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization

Michel, J. ; Tirado-Rives, J. ; Jorgensen W. L. 
J. Am. Chem. Soc., 131 (42), 15403 -15411, 2009 doi:10.1021/ja906058wdoi:10.1021/ja906058w

09

Prediction of the water content in protein binding sites

Michel, J. ; Tirado-Rives, J. ; Jorgensen W. L. 
J. Phys. Chem. B,113 (40), 13337 -13346, 2009 doi:10.1021/jp9047456doi:10.1021/jp9047456

08

In silico improvement of b3-peptide inhibitors of p53•hDM2 and p53•hDMX

Michel, J. ; Harker, E. A. ; Tirado-Rives, J. ; Jorgensen W. L. ; Schepartz, A.
J. Am. Chem. Soc., 131 (18), 6356 -6357, 2009 doi:10.1021/ja901478edoi:10.1021/ja901478e

07

Hit identification and binding mode predictions by rigorous free energy simulations

Michel, J. ; Essex, J. W. 
J. Med. Chem., 51 (21), 6654 -6664, 2008 doi:10.1021/jm800524sdoi:10.1021/jm800524s

06

Prediction of partition coefficients by multiscale hybrid atomic level/coarse-grain simulations

Michel, J. ; Orsi, M. ; Essex, J. W. 
J. Phys. Chem. B, 112 (3), 657 -660, 2008 doi:10.1021/jp076142ydoi:10.1021/jp076142y

05

Protein-ligand complexes: computation of the relative free energy of different scaffolds and binding modes

Michel, J. ; Verdonk, M.L ; Essex, J. W. 
J. Chem. Theory Comput., 3 (5), 1645 -1655, 2007 doi:10.1021/ct700081tdoi:10.1021/ct700081t

04

Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization?

Michel, J. ; Verdonk, M. L. ; Essex, J. W. 
J. Med. Chem. , 49 (25), 7427 -7439, 2006 doi:10.1021/jm061021sdoi:10.1021/jm061021s

03

The use of free energy simulations as scoring functions

Michel, J. 
PhD thesis, University of Southampton, 2006 pdf

02

Efficient generalized Born models for Monte Carlo simulations

Michel, J. ; Taylor, R. D. ; Essex, J. W. 
J. Chem. Theory Comput., 2 (3), 732 -739, 2006 doi:10.1021/ct600069rdoi:10.1021/ct600069r

01

The parameterization and validation of generalized Born models using the pairwise descreening approximation

Michel, J. ; Taylor, R. D. ; Essex, J. W.
J. Comput. Chem., 25, 1760-1770, 2004 doi:10.1002/jcc.20105doi:10.1002/jcc.20105

Patents

02

Compounds & methods for the inhibition of VCB E3 ubiquitin ligase

Crews, Craig, M.; Buckley, Dennis; Ciulli, Alessio; Jorgensen, William; Gareiss, Peter, C.; Molle, Inge, Van; Gustafson, Jeffrey; Tae, Hyun-Seop ; Michel, Julien ; Hoyer, Dentin, Wade; Roth, Anke, G.; Harling, John, David; Smith, Ian Edward, David; Miah, Afjal, Hussain; Campos, Sebastien, Andre; Le, Joelle

PCT Int. Appl. (2013), WO 2013/106646WO 2013/106646

01

Compounds & methods for the enhanced degradation of targeted proteins & other polypeptides by an E3 ubiquitin ligase

Crews, Craig, M.; Buckley, Dennis; Ciulli, Alessio; Jorgensen, William; Gareiss, Peter, C.; Molle, Inge, Van; Gustafson, Jeffrey; Tae, Hyun-Seop ; Michel, Julien ; Hoyer, Dentin, Wade; Roth, Anke, G.; Harling, John, David; Smith, Ian Edward, David; Miah, Afjal, Hussain; Campos, Sebastien, Andre; Le, Joelle

PCT Int. Appl. (2013), WO 2013/106643WO 2013/106643

East Chem