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Georgiou K, Konstantinidi A, Hutterer J, Freudenberger K, Kolarov F, Lambrinidis G, Stylianakis I, Stampelou M, Gauglitz G, Kolocouris A. Accurate calculation of affinity changes to the close state of influenza A M2 transmembrane domain in response to subtle structural changes of adamantyl amines using free energy perturbation methods in different lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184258. [PMID: 37995846 DOI: 10.1016/j.bbamem.2023.184258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/18/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
Experimental binding free energies of 27 adamantyl amines against the influenza M2(22-46) WT tetramer, in its closed form at pH 8, were measured by ITC in DPC micelles. The measured Kd's range is ~44 while the antiviral potencies (IC50) range is ~750 with a good correlation between binding free energies computed with Kd and IC50 values (r = 0.76). We explored with MD simulations (ff19sb, CHARMM36m) the binding profile of complexes with strong, moderate and weak binders embedded in DMPC, DPPC, POPC or a viral mimetic membrane and using different experimental starting structures of M2. To predict accurately differences in binding free energy in response to subtle changes in the structure of the ligands, we performed 18 alchemical perturbative single topology FEP/MD NPT simulations (OPLS2005) using the BAR estimator (Desmond software) and 20 dual topology calculations TI/MD NVT simulations (ff19sb) using the MBAR estimator (Amber software) for adamantyl amines in complex with M2(22-46) WT in DMPC, DPPC, POPC. We observed that both methods with all lipids show a very good correlation between the experimental and calculated relative binding free energies (r = 0.77-0.87, mue = 0.36-0.92 kcal mol-1) with the highest performance achieved with TI/MBAR and lowest performance with FEP/BAR in DMPC bilayers. When antiviral potencies are used instead of the Kd values for computing the experimental binding free energies we obtained also good performance with both FEP/BAR (r = 0.83, mue = 0.75 kcal mol-1) and TI/MBAR (r = 0.69, mue = 0.77 kcal mol-1).
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Affiliation(s)
- Kyriakos Georgiou
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Athina Konstantinidi
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Johanna Hutterer
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Kathrin Freudenberger
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Felix Kolarov
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany; Roche, Penzberg, Bavaria, Germany
| | - George Lambrinidis
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Ioannis Stylianakis
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Margarita Stampelou
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Günter Gauglitz
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece.
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Mazzanti A, Drakopoulos A, Christina T, Kolocouris A. Rotation Barriers of 1‐Adamantyl‐Csp
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Bonds Measured with Dynamic NMR. ChemistrySelect 2019. [DOI: 10.1002/slct.201901042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andrea Mazzanti
- Department of Industrial Chemistry “Toso Montanari”Alma Mater Studiorum-University of Bologna Viale del Risorgimento 4 40136 Bologna Italy
| | - Antonios Drakopoulos
- Faculty of PharmacyDepartment of Pharmaceutical ChemistryUniversity of Athens, Panepistimioupolis-Zografou 15771 Athens Greece
- current address: Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food ChemistryJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Tzitzoglaki Christina
- Faculty of PharmacyDepartment of Pharmaceutical ChemistryUniversity of Athens, Panepistimioupolis-Zografou 15771 Athens Greece
| | - Antonios Kolocouris
- Faculty of PharmacyDepartment of Pharmaceutical ChemistryUniversity of Athens, Panepistimioupolis-Zografou 15771 Athens Greece
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Ioannidis H, Drakopoulos A, Tzitzoglaki C, Homeyer N, Kolarov F, Gkeka P, Freudenberger K, Liolios C, Gauglitz G, Cournia Z, Gohlke H, Kolocouris A. Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM. J Chem Inf Model 2016; 56:862-76. [DOI: 10.1021/acs.jcim.6b00079] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Harris Ioannidis
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Drakopoulos
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Christina Tzitzoglaki
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Nadine Homeyer
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Felix Kolarov
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Paraskevi Gkeka
- Biomedical
Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Kathrin Freudenberger
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Christos Liolios
- Demokritos, National Center for Scientific Research, 15310 Athens, Greece
| | - Günter Gauglitz
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Antonios Kolocouris
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
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