The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations

The translocator protein (TSPO) is a 18kDa transmembrane protein, ubiquitously present in human mitochondria. It is overexpressed in tumor cells and at the sites of neuroinflammation, thus representing an important biomarker, as well as a promising drug target. In mammalian TSPO, there are cholesterol–binding motifs, as well as a binding cavity able to accommodate different chemical compounds. Given the lack of structural information for the human protein, we built a model of human (h) TSPO in the apo state and in complex with PK11195, a molecule routinely used in positron emission tomography (PET) for imaging of neuroinflammatory sites. To better understand the interactions of PK11195 and cholesterol with this pharmacologically relevant protein, we ran molecular dynamics simulations of the apo and holo proteins embedded in a model membrane. We found that: (i) PK11195 stabilizes hTSPO structural fold; (ii) PK11195 might enter in the binding site through transmembrane helices I and II of hTSPO; (iii) PK11195 reduces the frequency of cholesterol binding to the lower, N–terminal part of hTSPO in the inner membrane leaflet, while this impact is less pronounced for the upper, C–terminal part in the outer membrane leaflet, where the ligand binding site is located; (iv) very interestingly, cholesterol most frequently binds simultaneously to the so-called CRAC and CARC regions in TM V in the free form (residues L150–X–Y152–X(3)–R156 and R135–X(2)–Y138–X(2)–L141, respectively). However, when the protein is in complex with PK11195, cholesterol binds equally frequently to the CRAC–resembling motif that we observed in TM I (residues L17–X(2)–F20–X(3)–R24) and to CRAC in TM V. We expect that the CRAC–like motif in TM I will be of interest in future experimental investigations. Thus, our MD simulations provide insight into the structural features of hTSPO and the previously unknown interplay between PK11195 and cholesterol interactions with this pharmacologically relevant protein.

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Identification of a New Hormone-Binding Site on the Surface of Thyroid Hormone Receptor

Molecular Endocrinology ◽

10.1210/me.2013-1359 ◽

2014 ◽

Vol 28 (4) ◽

pp. 534-545 ◽

Cited By ~ 23

Author(s):

P.C.T. Souza ◽

A.C. Puhl ◽

L. Martínez ◽

R. Aparício ◽

A.S. Nascimento ◽

...

Keyword(s):

Molecular Dynamics ◽

Thyroid Hormone ◽

Ligand Binding ◽

Molecular Dynamics Simulations ◽

Binding Site ◽

Nuclear Receptor ◽

Surface Binding ◽

X Ray ◽

Protein Dissociation ◽

Dynamics Simulations

Abstract Thyroid hormone receptors (TRs) are members of the nuclear receptor superfamily of ligand-activated transcription factors involved in cell differentiation, growth, and homeostasis. Although X-ray structures of many nuclear receptor ligand-binding domains (LBDs) reveal that the ligand binds within the hydrophobic core of the ligand-binding pocket, a few studies suggest the possibility of ligands binding to other sites. Here, we report a new x-ray crystallographic structure of TR-LBD that shows a second binding site for T3 and T4 located between H9, H10, and H11 of the TRα LBD surface. Statistical multiple sequence analysis, site-directed mutagenesis, and cell transactivation assays indicate that residues of the second binding site could be important for the TR function. We also conducted molecular dynamics simulations to investigate ligand mobility and ligand-protein interaction for T3 and T4 bound to this new TR surface-binding site. Extensive molecular dynamics simulations designed to compute ligand-protein dissociation constant indicate that the binding affinities to this surface site are of the order of the plasma and intracellular concentrations of the thyroid hormones, suggesting that ligands may bind to this new binding site under physiological conditions. Therefore, the second binding site could be useful as a new target site for drug design and could modulate selectively TR functions.

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Binding site opening by loop C shift and chloride ion-pore interaction in the GABAAreceptor model

Physical Chemistry Chemical Physics ◽

10.1039/c7cp00582b ◽

2017 ◽

Vol 19 (21) ◽

pp. 13664-13678 ◽

Cited By ~ 6

Author(s):

M. A. Michałowski ◽

S. Kraszewski ◽

J. W. Mozrzymas

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Molecular Dynamics Simulations ◽

Binding Site ◽

Transmembrane Domain ◽

Chloride Ion ◽

Homology Model ◽

Interaction Sites ◽

Dynamics Simulations ◽

Ion Pore

Molecular dynamics simulations of the shut α1β2γ2GABAAheteropentamer receptor homology model reveal significant differences between intersubunit interfaces (ligand binding G1, G2 and non-binding) compared to homomeric receptor assemblies and possible ion interaction sites in the top part of the transmembrane domain (TMD).

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Design of Inhibitors for Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) Enzyme of Leishmania mexicana

Medicinal Chemistry ◽

10.2174/1573406415666190712111139 ◽

2020 ◽

Vol 16 (6) ◽

pp. 784-795

Author(s):

Krisnna M.A. Alves ◽

Fábio José Bonfim Cardoso ◽

Kathia M. Honorio ◽

Fábio A. de Molfetta

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Binding Site ◽

Point Of View ◽

New Drugs ◽

Leishmania Mexicana ◽

Receptor Complexes ◽

Starting Point ◽

Dynamics Simulations ◽

Selection Of

Background:: Leishmaniosis is a neglected tropical disease and glyceraldehyde 3- phosphate dehydrogenase (GAPDH) is a key enzyme in the design of new drugs to fight this disease. Objective:: The present study aimed to evaluate potential inhibitors of GAPDH enzyme found in Leishmania mexicana (L. mexicana). Methods: A search for novel antileishmanial molecules was carried out based on similarities from the pharmacophoric point of view related to the binding site of the crystallographic enzyme using the ZINCPharmer server. The molecules selected in this screening were subjected to molecular docking and molecular dynamics simulations. Results:: Consensual analysis of the docking energy values was performed, resulting in the selection of ten compounds. These ligand-receptor complexes were visually inspected in order to analyze the main interactions and subjected to toxicophoric evaluation, culminating in the selection of three compounds, which were subsequently submitted to molecular dynamics simulations. The docking results showed that the selected compounds interacted with GAPDH from L. mexicana, especially by hydrogen bonds with Cys166, Arg249, His194, Thr167, and Thr226. From the results obtained from molecular dynamics, it was observed that one of the loop regions, corresponding to the residues 195-222, can be related to the fitting of the substrate at the binding site, assisting in the positioning and the molecular recognition via residues responsible for the catalytic activity. Conclusion:: he use of molecular modeling techniques enabled the identification of promising compounds as inhibitors of the GAPDH enzyme from L. mexicana, and the results obtained here can serve as a starting point to design new and more effective compounds than those currently available.

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Cavity hydration dynamics in cytochrome c oxidase and functional implications

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1707922114 ◽

2017 ◽

Vol 114 (42) ◽

pp. E8830-E8836 ◽

Cited By ~ 13

Author(s):

Chang Yun Son ◽

Arun Yethiraj ◽

Qiang Cui

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Proton Transfer ◽

Molecular Dynamics Simulations ◽

Transmembrane Protein ◽

Wetting Transition ◽

Protonation State ◽

Hydration Level ◽

Level Change ◽

Dynamics Simulations

Cytochrome c oxidase (CcO) is a transmembrane protein that uses the free energy of O2 reduction to generate the proton concentration gradient across the membrane. The regulation of competitive proton transfer pathways has been established to be essential to the vectorial transport efficiency of CcO, yet the underlying mechanism at the molecular level remains lacking. Recent studies have highlighted the potential importance of hydration-level change in an internal cavity that connects the proton entrance channel, the site of O2 reduction, and the putative proton exit route. In this work, we use atomistic molecular dynamics simulations to investigate the energetics and timescales associated with the volume fluctuation and hydration-level change in this central cavity. Extensive unrestrained molecular dynamics simulations (accumulatively ∼4 μs) and free energy computations for different chemical states of CcO support a model in which the volume and hydration level of the cavity are regulated by the protonation state of a propionate group of heme a3 and, to a lesser degree, the redox state of heme a and protonation state of Glu286. Markov-state model analysis of ∼2-μs trajectories suggests that hydration-level change occurs on the timescale of 100–200 ns before the proton-loading site is protonated. The computed energetic and kinetic features for the cavity wetting transition suggest that reversible hydration-level change of the cavity can indeed be a key factor that regulates the branching of proton transfer events and therefore contributes to the vectorial efficiency of proton transport.

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