Publications

Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning
Chatzigoulas A, Cournia Z
Brief Bioinform 2022 Feb 12;bbab518. Online ahead of print.
doi: 10.1093/bib/bbab518

Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability
Andreadelis I, Kiriakidi S, Lamprakis C, Theodoropoulou A, Doerr S, Chatzigoulas A, Manchester J, Velez-Vega C, Duca J. S., Cournia Z
J Phys Chem B, 2022, Online ahead of print
DOI: 10.1021/ACS.JPCB.1C01184

Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations
Makurat S, Cournia Z, Rak J
J Chem Inf Model 2021, 62, 1, 142–149
https://doi.org/10.1021/acs.jcim.1c01157

Free Energy Methods in Drug Discovery—Introduction
Cournia Z, Chipot C, Roux B, York DM, Sherman W. Free Energy Methods in Drug Discovery: Current State and Future Directions, In: "Free Energy Methods in Drug Discovery", ACS Symposium Series #1397, Eds. Armacost KA and Thompson DC, 2021
https://10.1021/bk-2021-1397.ch001

Advancing Women in Chemistry
Cournia Z, Soares TA, Wahab HA, Amaro RE.
J Chem Inf Model. 2021, 61(11):5305-5306.
https://10.1021/acs.jcim.1c01185

The effect of S427F mutation on RXRα activity depends on its dimeric partner
Galdadas I, Bonis V, Vgenopoulou P, Papadourakis M, Kakoulidis P, Stergiou G, Cournia Z, Klinakis A
Chemical Science 2021, 12(44):14700-14710.
https://doi.org/10.1039/D1SC04465F

N-terminal domain mutations of the spike protein are structurally implicated in epitope recognition in emerging SARS-CoV-2 strains
​Klinakis A, Cournia Z, Rampias T
Comput Struct Biotechnol J 2021, 19:5556-5567.
https://doi.org/10.1016/j.csbj.2021.10.004

Radical collaboration during a global health emergency: development of the RDA COVID-19 data sharing recommendations and guidelines
Pickering B et al
Open Research Europe, 1:1-69
DOI: 10.12688/OPENRESEUROPE.13369.1
​
FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations
Zavitsanou S, Tsengenes A, Papadourakis M, Amendola G, Chatzigoulas A, Dellis D, Cosconati S, Cournia Z.
J Chem Inf Model. 2021, 61(9):4131-4138
https://doi.org/10.1021/acs.jcim.1c00215

Rational Design of Allosteric Modulators: Challenges and Successes
Chatzigoulas A, Cournia Z.
WIREs Computational Molecular Science, 2021, 11(6):e1529
https://doi.org/10.1002/wcms.1529
free preprint in Zenodo

Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments
Lamprakis C, Andreadelis I, Manchester J, Velez-Vega C, Duca JS, Cournia Z.
J Chem Theory Comput. 2021 May 11;17(5):3088-3102
https://doi.org/10.1021/acs.jctc.0c00507
free preprint here: https://pubs.acs.org/articlesonrequest/AOR-EMXPIH7FPZHYTG9DUUSC

​Interplay of cholesterol, membrane bilayers and the AT1R: A cholesterol consensus motif on AT1R is revealed
Kiriakidi S, Chatzigiannis C, Papaemmanouil C, Tzakos AG, Cournia Z, Mavromoustakos T
Comput Struct Biotechnol J 2021, 19:110-120
https://doi.org/10.1016/j.csbj.2020.11.042

Editorial: Advances in computational molecular biophysics
Jerome B, Bondar A-N, Cournia  Z, Parks JM, Petridis L, Roux B
Biochimica et Biophysica Acta (BBA) - General Subjects 2021, 1865(6):129888
DOI: 10.1016/J.BBAGEN.2021.129888

Editorial: Method and Data Sharing and Reproducibility of Scientific Results
Merz KM, Jr, Rommie A, Cournia Z, Rarey M, Soares T, Tropsha A, Wahab HA, Wang R
J Chem Inf Model 2021, 60, 12, 5868–5869
DOI: 10.1021/ACS.JCIM.0C01389

Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 Working Group
Austin C et al, Wellcome Open Res. 2020, 5:267
https://doi.org/10.12688/wellcomeopenres.16378.1

Coating of magnetic nanoparticles affects their interactions with model cell membranes.
Lazaratos M, Karathanou K, Mainas L, Chatzigoulas A, Pippa N, Demetzos C, Cournia Z.
Biochim Biophys Acta Gen Subj. 2020, 1864(11):129671
https://doi.org/10.1016/j.bbagen.2020.129671

Rigorous free energy simulations in virtual screening
Cournia Z, Allen BK, Beuming T, Pearlman DA, Radak BK, Sherman W
J Chem Inf Model, 2020, Epub ahead of print
https://doi.org/10.1021/acs.jcim.0c00116

Allostery in Membrane Proteins
Cournia Z and Chatzigoulas A
Curr Op Struct Biol, 2020, 62, 197-204
https://doi.org/10.1016/j.sbi.2020.03.006

Unravelling the effect of the E545K mutation on PI3Kα kinase
Galdadas I, Gervasio, FL, Cournia Z
Chem Sci, 2020, 11, 3511-3515
https://doi.org/10.1039/C9SC05903B

The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations
Rizzi A, Jensen T, Slochower DR, Aldeghi M, Gapsys V, Ntekoumes D, Bosisio S, Papadourakis M, Henriksen NM,  de Groot BL, Cournia Z, Dickson A, Michel J,  Gilson MK, Shirts MR,  Mobley DL, Chodera JD.
J Comput Aided Mol Des, 2020, 34, 601–633
http://dx.doi.org/10.1007/s10822-020-00290-5
For the free BioRxiv version click here.

Novel Directions in Free Energy Methods and Applications
Armacost K, Riniker S, Cournia Z
J Chem Inf Model, 2020 60(1):1-5
http://dx.doi.org/10.1021/acs.jcim.9b01174

ChemBioServer2.0: An Advanced Web Server for Filtering, Clustering and Networking of Chemical Compounds Facilitating Both Drug Discovery and Repurposing
Karatzas E, Zamora JE, Athanasiadis E, Dellis D, Cournia Z, Spyrou G
Bioinformatics 2020, pii: btz976
http://dx.doi.org/10.1093/bioinformatics/btz976
for a free version read the article in ChemRXiv

Compounds for use in treating or preventing cancerous diseases
Stellas D, Tamvakopoulos C, Klinakis A, Efstratiadis A, Cournia Z
US Patent 2019 10,287,294B2

Phase Diagram of a Stratum Corneum Lipid Mixture.
Podewitz M, Wang Y, Gkeka P, von Grafenstein S, Liedl KR, Cournia Z.
J Phys Chem B. 2018, 122(46):10505-10521
http://dx.doi.org/10.1021/acs.jpcb.8b07200

Nano-Crystal: A web-based crystallographic tool for the construction of nanoparticles based on their crystal habit.
​Chatzigoulas A, Karathanou K, Dellis D, Cournia Z*
J Chem Inf Model, 2018, 58(12):2380-2386
http://dx.doi.org/10.1021/acs.jcim.8b00269
Read the Free preprint on ChemRxiv

Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations.
Leontiadou H, Galdadas I, Athanasiou C, Cournia Z*
Sci Rep, 2018, 8(1):15544.
http://dx.doi.org/10.1038/s41598-018-27044-6

Women in Computational Chemistry
Wahab HA, Amaro RE, Cournia Z
J Chem Inf Model 2018, 58(11):2175-2177.
https://pubs.acs.org/doi/10.1021/acs.jcim.8b00642

Effect of 5-trans Isomer of Arachidonic Acid on Model Liposomal Membranes Studied by a Combined Simulation and Experimental Approach
Tremi I, Anagnostopoulos D, Spyratou E, Gkeka P, Georgakilas AG*, Chatgilialoglu C*, Cournia Z*
J Memb Biol 2018, 251(3), 475-489
https://doi.org/10.1007/s00232-018-0029-8
Read the Free preprint on BioRxiv

Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2
Athanasiou C, Vasilakaki S, Dellis D, Cournia Z*
​J Comput Aid Mol Des, 2018, 32(1):21-44.
DOWNLOAD the article here!
DOWNLOAD the SI here!
http://dx.doi.org/10.1007/s10822-017-0075-9

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations
Cournia Z*, Allen B, Sherman W*
J Chem Inf Model 2017, 57(12):2911-2937.
http://10.1021/acs.jcim.7b00564 (Open Access)

Multiscale simulations reveal IRMOF-74-III as a potent drug carrier for gemcitabine delivery
Kotzabasaki M, Galdadas I, Tylianakis E, Klontza E, Cournia Z*, Froudakis G*.
J Mater Chem B, 2017, 5, 3277-3282
http://dx.doi.org/10.1039/C7TB00220C

Magnetic nanoparticles coated with polyarabic acid demonstrate enhanced drug delivery and imaging properties for cancer theranostic applications.
Patitsa M, Karathanou K, Kanaki Z, Tzioga L, Pippa N, Demetzos C, Verganelakis DA, Cournia Z*, Klinakis A*.
Sci Rep. 2017, 7, 1, pp. 775-777
http://dx.doi.org/10.1038/s41598-017-00836-y

Nurr1:RXRα heterodimer activation as monotherapy for Parkinson’s disease
Spathis AD, Asvos X, Ziavra D, Karampelas T, Topouzis S, Cournia Z, Qing X, Alexakos P, Smits LM, Dalla C, Rideout HJ, Schwamborn JC, Tamvakopoulos C, Fokas D, Vassilatis DK.
Proc Natl Acad Sci U S A 2017, 114, 15, pp. 3999-4004
http://dx.doi.org/10.1073/pnas.1616874114

Self-assembly of anionic, ligand-coated nanoparticles in lipid membranes
Angelikopoulos P, Sarkisov L, Cournia Z, Gkeka P.
Nanoscale. 2017, 9, pp. 1040-1048
http://dx.doi.org/10.1039/C6NR05853A

Pyrazole-based potent inhibitors of GGT1: Synthesis, biological evaluation, and molecular docking studies
Mansha M, Kumari UU, Cournia Z, Ullah N.
Eur J Med Chem. 2016, 124, pp. 666-676
http://dx.doi.org/10.1016/j.ejmech.2016.09.002

DPPC-cholesterol phase diagram using coarse-grained MD simulations
Wang Y, Gkeka P, Fuchs JE, Liedl, KR, Cournia Z*.
BBA Biomembranes. 2016, 1858(11), pp. 2846-2857
http://dx.doi.org/10.1016/j.bbamem.2016.08.005

Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM
Ioannidis H, Drakopoulos A, Tzitzoglaki C, Homeyer N, Kolarov F, Gkeka P, Freudenberger K, Liolios C, Gauglitz G, Cournia Z*, Gohlke H*, Kolocouris A*.
J Chem Inf Model. 2016, 56(5), pp. 862-876
http://dx.doi.org/10.1021/acs.jcim.6b00079

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.
Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, Del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, Bondar AN.
J Membr Biol. 2015 Aug;248(4):611-40.
http://dx.doi.org/10.1007/s00232-015-9802-0

Exploring a Non-ATP Pocket for Potential Allosteric Modulation of PI3Kα.
Gkeka P, Papafotika A, Christoforidis S, Cournia Z.
J Phys Chem B. 2015, 119 (3), pp. 1002-1016.
http://dx.doi.org/10.1021/jp506423e

Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion
Gkeka, P, Angelikopoulos P, Sarkisov L, Cournia Z.
PLoS Comput Biol. 2014, 10 (10):e1003917
http://dx.doi.org/10.1371/journal.pcbi.1003917

Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant.
Gkeka P, Evangelidis T, Pavlaki M, Lazani V, Christoforidis S, Agianian B, Cournia Z.
PLoS Comput Biol. 2014, 10 (10):e1003895.
http://dx.doi.org/10.1371/journal.pcbi.1003895

Therapeutic effects of an anti-myc drug on mouse pancreatic cancer.
Stellas D, Szabolcs M, Koul S, Li Z, Polyzos A, Anagnostopoulos C, Cournia Z, Tamvakopoulos C, Klinakis A, Efstratiadis A.
J Natl Cancer Inst. 2014, 106 (12), pii: dju320.
http://dx.doi.org/10.1093/jnci/dju320

Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances
Lionta E, Spyrou G, Vassilatis D, Cournia Z
Curr Top Med Chem, 2014, 14 (16), pp. 1923-1938.
Download Free PDF
http://dx.doi.org/10.2174/1568026614666140929124445

Insights into the Molecular Basis of Action of the AT1 Antagonist Losartan Using a Combined NMR Spectroscopy and Computational Approach
Zervou M, Cournia Z, Potamitis C, Patargias G, Durdagi S, Golic Grdadolnik S, Mavromoustakos T
Biochim Biophys Acta. 2014, 1838 (3), pp. 1031–1046.
http://www.sciencedirect.com/science/article/pii/S0005273613004513

Free Energy Calculations Reveal the Origin of Binding Preference for Aminoadamantane Blockers of Influenza A/M2TM Pore.
Gkeka P, Eleftheratos S, Kolocouris A, Cournia Z.
J Chem Theor Comp. 2013 Epub ahead of print
http://dx.doi.org/10.1021/ct300899n

ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery. 
Athanasiadis E, Cournia Z, Spyrou G.
Bioinformatics. 2012 Nov 15;28(22):3002-3. Epub 2012 Sep 8.
http://dx.doi.org/10.1093/bioinformatics/bts551

Structural characterization and computer-aided optimization of a small-molecule inhibitor of the Arp2/3 complex, a key regulator of the actin cytoskeleton.
Baggett AW, Cournia Z, Han MS, Patargias G, Glass AC, Liu SY, Nolen BJ.
ChemMedChem. 2012 Jul;7(7):1286-94. Epub 2012 May 23.
http://dx.doi.org/10.1002/cmdc.201200104

Optimization of N-benzyl-benzoxazol-2-ones as receptor antagonists of macrophage migration inhibitory factor (MIF).
Hare AA, Leng L, Gandavadi S, Du X, Cournia Z, Bucala R, Jorgensen WL.
Bioorg Med Chem Lett. 2010 Oct 1;20(19):5811-4. Epub 2010 Aug 3.
http://dx.doi.org/10.1016/j.bmcl.2010.07.129

Discovery of human macrophage migration inhibitory factor (MIF)-CD74 antagonists via virtual screening.
Cournia Z, Leng L, Gandavadi S, Du X, Bucala R, Jorgensen WL.
J Med Chem. 2009 Jan 22;52(2):416-24.
http://dx.doi.org/10.1021/jm801100v

Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics.
de Hatten X, Cournia Z, Huc I, Smith JC, Metzler-Nolte
N. Chemistry. 2007;13(29):8139-52.
http://dx.doi.org/10.1002/chem.200700358

Differential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: a molecular dynamics simulation study.
Cournia Z, Ullmann GM, Smith JC.
J Phys Chem B. 2007 Feb 22;111(7):1786-801. Epub 2007 Jan 30.
http://dx.doi.org/10.1021/jp065172i

A molecular mechanics force field for biologically important sterols.
Cournia Z, Smith JC, Ullmann GM
J Comput Chem. 2005 Oct;26(13):1383-99.
http://dx.doi.org/10.1002/jcc.20277

AFMM: A molecular mechanics force-field vibrational parametrization program.
Vaiana AC, Cournia Z, Costescu IB, Smith JC
Comput. Phys. Commun 2005, 167:34-42.
http://dx.doi.org/10.1016/j.cpc.2004.12.005

Derivation of a Molecular Mechanics Force-Field for Cholesterol.
Cournia Z, Vaiana AC, Smith JC, Ullmann GM
Pure Appl. Chem. 2004, 76:189-196.
http://dx.doi.org/10.1351/pac200476010189