1
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Giladi M, Montgomery AP, Kassiou M, Danon JJ. Structure-based drug design for TSPO: Challenges and opportunities. Biochimie 2024:S0300-9084(24)00120-2. [PMID: 38782353 DOI: 10.1016/j.biochi.2024.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/27/2024] [Accepted: 05/21/2024] [Indexed: 05/25/2024]
Abstract
The translocator protein 18 kDa (TSPO) is an evolutionarily conserved mitochondrial transmembrane protein implicated in various neuropathologies and inflammatory conditions, making it a longstanding diagnostic and therapeutic target of interest. Despite the development of various classes of TSPO ligand chemotypes, and the elucidation of bacterial and non-human mammalian experimental structures, many unknowns exist surrounding its differential structural and functional features in health and disease. There are several limitations associated with currently used computational methodologies for modelling the native structure and ligand-binding behaviour of this enigmatic protein. In this perspective, we provide a critical analysis of the developments in the uses of these methods, outlining their uses, inherent limitations, and continuing challenges. We offer suggestions of unexplored opportunities that exist in the use of computational methodologies which offer promise for enhancing our understanding of the TSPO.
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Affiliation(s)
- Mia Giladi
- School of Chemistry, The University of Sydney, 2050, Sydney, NSW, Australia
| | | | - Michael Kassiou
- School of Chemistry, The University of Sydney, 2050, Sydney, NSW, Australia.
| | - Jonathan J Danon
- School of Chemistry, The University of Sydney, 2050, Sydney, NSW, Australia.
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2
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Floch A, Galochkina T, Pirenne F, Tournamille C, de Brevern AG. Molecular dynamics of the human RhD and RhAG blood group proteins. Front Chem 2024; 12:1360392. [PMID: 38566898 PMCID: PMC10985258 DOI: 10.3389/fchem.2024.1360392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction: Blood group antigens of the RH system (formerly known as "Rhesus") play an important role in transfusion medicine because of the severe haemolytic consequences of antibodies to these antigens. No crystal structure is available for RhD proteins with its partner RhAG, and the precise stoichiometry of the trimer complex remains unknown. Methods: To analyse their structural properties, the trimers formed by RhD and/or RhAG subunits were generated by protein modelling and molecular dynamics simulations were performed. Results: No major differences in structural behaviour were found between trimers of different compositions. The conformation of the subunits is relatively constant during molecular dynamics simulations, except for three large disordered loops. Discussion: This work makes it possible to propose a reasonable stoichiometry and demonstrates the potential of studying the structural behaviour of these proteins to investigate the hundreds of genetic variants relevant to transfusion medicine.
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Affiliation(s)
- Aline Floch
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, DSIMB Bioinformatics team, Paris, France
| | - France Pirenne
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Christophe Tournamille
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Alexandre G. de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, DSIMB Bioinformatics team, Paris, France
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3
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Rao RM, El Dhaybi I, Cadet F, Etchebest C, Diharce J. The mutual and dynamic role of TSPO and ligands in their binding process: An example with PK-11195. Biochimie 2024:S0300-9084(24)00067-1. [PMID: 38494108 DOI: 10.1016/j.biochi.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/12/2024] [Accepted: 03/15/2024] [Indexed: 03/19/2024]
Abstract
Translocator protein (TSPO) is an 18 kDa transmembrane protein, localized primarily on the outer mitochondrial membrane. It has been found to be involved in various physiological processes and pathophysiological conditions. Though studies on its structure have been performed only recently, there is little information on the nature of dynamics and doubts about some structures referenced in the literature, especially the NMR structure of mouse TSPO. In the present work, we thoroughly study the dynamics of mouse TSPO protein by means of atomistic molecular dynamics simulations, in presence as well as in absence of the diagnostic ligand PKA. We considered two starting structures: the NMR structure and a homology model (HM) generated on the basis of X-ray structures from bacterial TSPO. We examine the conformational landscape in both the modes for both starting points, in presence and absence of the ligand, in order to measure its impact for both structures. The analysis highlights high flexibility of the protein globally, but NMR simulations show a surprisingly flexibility even in the presence of the ligand. Interestingly, this is not the case for HM calculations, to the point that the ligand seems not so stable as in the NMR system and an unbinding event process is partially sampled. All those results tend to show that the NMR structure of mTSPO seems not deficient but is just in another portion of the global conformation space of TSPO.
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Affiliation(s)
- Rajas M Rao
- Data Analytics, Bioinformatics and Structural Biology Division, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India; Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France
| | - Ibaa El Dhaybi
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France
| | - Frédéric Cadet
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France; Laboratory of Excellence GR-Ex, Paris, France; Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715, Saint Denis Messag, France; PEACCEL, Artificial Intelligence Department, Paris, 75013 France
| | - Catherine Etchebest
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France; Laboratory of Excellence GR-Ex, Paris, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France; Laboratory of Excellence GR-Ex, Paris, France.
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4
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Duma L, Senicourt L, Rigaud B, Papadopoulos V, Lacapère JJ. Solid-state NMR study of structural heterogeneity of the apo WT mouse TSPO reconstituted in liposomes. Biochimie 2023; 205:73-85. [PMID: 36029902 DOI: 10.1016/j.biochi.2022.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/08/2022] [Accepted: 08/18/2022] [Indexed: 11/02/2022]
Abstract
In the last decades, ligand binding to human TSPO has been largely used in clinical neuroimaging, but little is known about the interaction mechanism. Protein conformational mobility plays a key role in the ligand recognition and both, ligand-free and ligand-bound structures, are mandatory for characterizing the molecular binding mechanism. In the absence of crystals for mammalian TSPO, we have exploited solid-state nuclear magnetic resonance (ssNMR) spectroscopy under magic-angle spinning (MAS) to study the apo form of recombinant mouse TSPO (mTSPO) reconstituted in lipids. This environment has been previously described to permit binding of its high-affinity drug ligand PK11195 and appears therefore favourable for the study of molecular dynamics. We have optimized the physical conditions to get the best resolution for MAS ssNMR spectra of the ligand-free mTSPO. We have compared and combined various ssNMR spectra to get dynamical information either for the lipids or for the mTSPO. Partial assignment of residue types suggests few agreements with the published solution NMR assignment of the PK11195-bound mTSPO in DPC detergent. Moreover, we were able to observe some lateral chains of aromatic residues that were not assigned in solution. 13C double-quantum NMR spectroscopy shows remarkable dynamics for ligand-free mTSPO in lipids which may have significant implications on the recognition of the ligand and/or other protein partners.
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Affiliation(s)
- Luminita Duma
- Champagne-Ardenne University, CNRS, ICMR UMR, 7312, Reims, France.
| | - Lucile Senicourt
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 4 Place Jussieu, F-75005, Paris, France
| | - Baptiste Rigaud
- CNRS Institut des Matériaux de Paris Centre (FR2482), 4 Place Jussieu, 75005, Paris, France
| | - Vassilios Papadopoulos
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jean-Jacques Lacapère
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 4 Place Jussieu, F-75005, Paris, France
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Adhikari A, Pandey A, Kumar D, Tiwari AK. Determination of Hybrid TSPO Ligands with Minimal Impact of SNP
(rs6971) through Molecular Docking and MD Simulation Study. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210413130326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
In an endeavor to ascertain high-affinity TSPO ligands with minimal single
nucleotide polymorphism (SNP), six hybrid molecules have been identified as new leads for future
inflammation PET imaging.
Objective:
Genesis for chemical design was encouraged from structural families of well-known ligands
FEBMP and PBR28/ DAA1106 that have demonstrated remarkable TSPO binding characteristics.
Methods:
All proposed hybrid ligands 1-6 are subjected to molecular docking and simulation studies
with wild and mutant protein to study their interactions, binding, consistency of active conformations
and are correlated with well-established TSPO ligands.
Results:
Each hybrid ligand demonstrate better docking score > -11.00 kcal/mol with TSPO with
respect to gold standard PK11195, i.e., -11.00 kcal/mol for 4UC3 and -12.94 kcal/mol for 4UC1. On
comparison with FEBMP and GE-180 (-12.57, -7.24 kcal/mol for 4UC3 and -14.10, -11.32
kcal/mol for 4UC1), ligand 3 demonstrates maximum docking energy (> -15.50 kcal/mol) with
minimum SNP (0.26 kcal/mol).
Discussion:
Presence of strong hydrogen bond Arg148-3.27Å (4UC1) and Trp50-2.43Å, Asp28-
2.57Å (4UC3) apart from short-range interactions, including π–π interactions with the aromatic residues,
such as (Trp39, Phe46, Trp135) and (Trp39, Trp108), attributes towards its strong binding.
Conclusion:
Utilizing the results of binding energy, we concluded stable complex formation of these
hybrid ligands that could bind to TSPO with the least effect of SNP with similar interactions to
known ligands. Overall, ligand 3 stands out as the best ligand having insignificant deviations per
residue of protein that can be further explored and assessed in detail for future inflammation PET
application after subsequent detailed biological evaluation.
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Affiliation(s)
- Anupriya Adhikari
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
| | - Anwesh Pandey
- Department of
Physics, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
| | - Devesh Kumar
- Department of
Physics, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
| | - Anjani K. Tiwari
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
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6
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Adhikari A, Singh P, Mahar KS, Adhikari M, Adhikari B, Zhang MR, Tiwari AK. Mapping of Translocator Protein (18 kDa) in Peripheral Sterile Inflammatory Disease and Cancer through PET Imaging. Mol Pharm 2021; 18:1507-1529. [PMID: 33645995 DOI: 10.1021/acs.molpharmaceut.1c00002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Positron emission tomography (PET) imaging of the translocator 18 kDa protein (TSPO) with radioligands has become an effective means of research in peripheral inflammatory conditions that occur in many diseases and cancers. The peripheral sterile inflammatory diseases (PSIDs) are associated with a diverse group of disorders that comprises numerous enduring insults including the cardiovascular, respiratory, gastrointestinal, or musculoskeletal system. TSPO has recently been introduced as a potential biomarker for peripheral sterile inflammatory diseases (PSIDs). The major critical issue related to PSIDs is its timely characterization and localization of inflammatory foci for proper therapy of patients. As an alternative to metabolic imaging, protein imaging expressed on immune cells after activation is of great importance. The five transmembrane domain translocator protein-18 kDa (TSPO) is upregulated on the mitochondrial cell surface of macrophages during inflammation, serving as a potential ligand for PET tracers. Additionally, the overexpressed TSPO protein has been positively correlated with various tumor malignancies. In view of the association of escalated TSPO expression in both disease conditions, it is an immensely important biomarker for PET imaging in oncology and PSIDs. In this review, we summarize the most outstanding advances on TSPO-targeted PSIDs and cancer in the development of TSPO ligands as a potential diagnostic tool, specifically discussing the last five years.
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Affiliation(s)
- Anupriya Adhikari
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, (A Central University), Lucknow, Uttar Pradesh 226025, India
| | - Priya Singh
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, A Central University, Lucknow, Uttar Pradesh 226025, India
| | - Kamalesh S Mahar
- Birbal Sahni Institute of Palaeosciences, Lucknow, Uttar Pradesh 226007, India
| | - Manish Adhikari
- The George Washington University, Washington, D.C. 20052, United States
| | - Bhawana Adhikari
- Plasma Bio-science Research Center, Kwangwoon University, Seoul 01897, South Korea
| | - Ming-Rong Zhang
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Anjani Kumar Tiwari
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, (A Central University), Lucknow, Uttar Pradesh 226025, India
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7
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The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations. Molecules 2021; 26:molecules26051250. [PMID: 33652554 PMCID: PMC7956637 DOI: 10.3390/molecules26051250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/28/2021] [Accepted: 02/03/2021] [Indexed: 12/23/2022] Open
Abstract
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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Si Chaib Z, Marchetto A, Dishnica K, Carloni P, Giorgetti A, Rossetti G. Impact of Cholesterol on the Stability of Monomeric and Dimeric Forms of the Translocator Protein TSPO: A Molecular Simulation Study. Molecules 2020; 25:molecules25184299. [PMID: 32961709 PMCID: PMC7570527 DOI: 10.3390/molecules25184299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/25/2022] Open
Abstract
The translocator protein (TSPO) is a transmembrane protein present across the three domains of life. Its functional quaternary structure consists of one or more subunits. In mice, the dimer-to-monomer equilibrium is shifted in vitro towards the monomer by adding cholesterol, a natural component of mammalian membranes. Here, we present a coarse-grained molecular dynamics study on the mouse protein in the presence of a physiological content and of an excess of cholesterol. The latter turns out to weaken the interfaces of the dimer by clusterizing mostly at the inter-monomeric space and pushing the contact residues apart. It also increases the compactness and the rigidity of the monomer. These two factors might play a role for the experimentally observed incremented stability of the monomeric form with increased content of cholesterol. Comparison with simulations on bacterial proteins suggests that the effect of cholesterol is much less pronounced for the latter than for the mouse protein.
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Affiliation(s)
- Zeineb Si Chaib
- Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, 52425 Jülich, Germany; (Z.S.C.); (A.M.); (P.C.)
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52062 Aachen, Germany
| | - Alessandro Marchetto
- Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, 52425 Jülich, Germany; (Z.S.C.); (A.M.); (P.C.)
- Department of Biotechnology, University of Verona, 37134 Verona, Italy;
| | - Klevia Dishnica
- Department of Biotechnology, University of Verona, 37134 Verona, Italy;
| | - Paolo Carloni
- Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, 52425 Jülich, Germany; (Z.S.C.); (A.M.); (P.C.)
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52062 Aachen, Germany
- Institute for Neuroscience and Medicine (INM-11) “Molecular Neuroscience and Neuroimaging”, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Alejandro Giorgetti
- Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, 52425 Jülich, Germany; (Z.S.C.); (A.M.); (P.C.)
- Department of Biotechnology, University of Verona, 37134 Verona, Italy;
- Correspondence: (A.G.); (G.R.)
| | - Giulia Rossetti
- Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, 52425 Jülich, Germany; (Z.S.C.); (A.M.); (P.C.)
- Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52425 Jülich, Germany
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation University Hospital Aachen, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
- Correspondence: (A.G.); (G.R.)
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