Multiple Poses and Thermodynamics of Ligands Targeting Protein Surfaces: The Case of Furosemide Binding to mitoNEET in Aqueous Solution

Linh Gia Hoang; Jonas Goßen; Riccardo Capelli; Toan T Nguyen; Zhaoxi Sun; Ke Zuo; Jörg B Schulz; Giulia Rossetti; Paolo Carloni

doi:10.3389/fcell.2022.886568

Multiple Poses and Thermodynamics of Ligands Targeting Protein Surfaces: The Case of Furosemide Binding to mitoNEET in Aqueous Solution

Front Cell Dev Biol. 2022 Apr 26:10:886568. doi: 10.3389/fcell.2022.886568. eCollection 2022.

Authors

Linh Gia Hoang^{1

2}, Jonas Goßen^{3

4}, Riccardo Capelli⁵, Toan T Nguyen², Zhaoxi Sun⁶, Ke Zuo^{3

7

8}, Jörg B Schulz^{1

9}, Giulia Rossetti^{3

9

10}, Paolo Carloni^{1

2

3}

Affiliations

¹ INM-11, Forschungszentrum, Jülich, Germany.
² Key Laboratory for Multiscale Simulations of Complex Systems, VNU University of Science, Vietnam National University, Hanoi, Vietnam.
³ IAS-5/INM-9, Forschungszentrum, Jülich, Germany.
⁴ Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, Aachen, Germany.
⁵ Department of Applied Science and Technology (DISAT), Politecnico di Torino, Torino, Italy.
⁶ College of Chemistry and Molecular Engineering, Institute of Theoretical and Computational Chemistry, Peking University, Beijing, China.
⁷ The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem, Israel.
⁸ Department of Physics, RWTH Aachen University, Aachen, Germany.
⁹ Department of Neurology, University Hospital Aachen (UKA), RWTH Aachen University, Aachen, Germany.
¹⁰ Jülich Supercomputing Centre (JSC), Forschungszentrum, Jülich, Germany.

Abstract

Human NEET proteins, such as NAF-1 and mitoNEET, are homodimeric, redox iron-sulfur proteins characterized by triple cysteine and one histidine-coordinated [2Fe-2S] cluster. They exist in an oxidized and reduced state. Abnormal release of the cluster is implicated in a variety of diseases, including cancer and neurodegeneration. The computer-aided and structure-based design of ligands affecting cluster release is of paramount importance from a pharmaceutical perspective. Unfortunately, experimental structural information so far is limited to only one ligand/protein complex. This is the X-ray structure of furosemide bound to oxidized mitoNEET. Here we employ an enhanced sampling approach, Localized Volume-based Metadynamics, developed by some of us, to identify binding poses of furosemide to human mitoNEET protein in solution. The binding modes show a high variability within the same shallow binding pocket on the protein surface identified in the X-ray structure. Among the different binding conformations, one of them is in agreement with the crystal structure's one. This conformation might have been overstabilized in the latter because of the presence of crystal packing interactions, absent in solution. The calculated binding affinity is compatible with experimental data. Our protocol can be used in a straightforward manner in drug design campaigns targeting this pharmaceutically important family of proteins.

Keywords: NEET proteins; [2Fe-2S] cluster; furosemide; furosemide binding pose and affinity; localized volume-based metadynamics; molecular dynamics; rational drug design.