1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Leung MCK, Meyer JN. Mitochondria as a target of organophosphate and carbamate pesticides: Revisiting common mechanisms of action with new approach methodologies. Reprod Toxicol 2019; 89:83-92. [PMID: 31315019 PMCID: PMC6766410 DOI: 10.1016/j.reprotox.2019.07.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 06/19/2019] [Accepted: 07/09/2019] [Indexed: 01/01/2023]
Abstract
Mitochondrial toxicity has been proposed as a potential cause of developmental defects in humans. We evaluated 51 organophosphate and carbamate pesticides using the U.S. EPA ToxCast and Tox21 databases. Only a small number of them bind directly to cholinesterases in the parent form. The hydrophobicity of organophosphate pesticides is correlated significantly to TSPO binding affinity, mitochondrial membrane potential reduction in HepG2 cells, and developmental toxicity in Caenorhabditis elegans and Danio rerio (p < 0.05). Structural analysis suggests that in some cases the Krebs cycle is a potential target of organophosphate and carbamate exposure at early life stages. The results support the hypothesis that mitochondrial effects of some organophosphate pesticides-particularly those that require enzymatic activation to the oxon form-may augment the documented effects of disruption of acetylcholine signaling. This study provides a proof of concept for applying new approach methodologies to interrogate mechanisms of action for cumulative risk assessment.
Collapse
Affiliation(s)
- Maxwell C K Leung
- Department of Environmental Toxicology, University of California, Davis, CA, United States; Nicholas School of the Environment, Duke University, Durham, NC, United States.
| | - Joel N Meyer
- Nicholas School of the Environment, Duke University, Durham, NC, United States
| |
Collapse
|
3
|
Discovery of antiviral molecules for dengue: In silico search and biological evaluation. Eur J Med Chem 2016; 110:87-97. [PMID: 26807547 DOI: 10.1016/j.ejmech.2015.12.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 11/08/2015] [Accepted: 12/14/2015] [Indexed: 12/24/2022]
Abstract
BACKGROUND Dengue disease is a global disease that has no effective treatment. The dengue virus (DENV) NS2B/NS3 protease complex is a target for designing specific antivirals due to its importance in viral replication and its high degree of conservation. METHODS NS2B/NS3 protease complex structural information was employed to find small molecules that are capable of inhibiting the activity of the enzyme complex. This inhibitory activity was probed with in vitro assays using a fluorescent substrate and the complex NS2B/NS3 obtained by recombinant DNA techniques. HepG2 cells infected with dengue virus serotype 2 were used to test the activity against dengue virus replication. RESULTS A total of 210,903 small molecules from PubChem were docked in silico to the NS2B/NS3 structure (PDB: 2FOM) to find molecules that were capable of inhibiting this protein complex. Five of the best 500 leading compounds, according to their affinity values (-11.6 and -13.5 kcal/mol), were purchased. The inhibitory protease activity on the recombinant protein and antiviral assays was tested. CONCLUSIONS Chemicals CID 54681617, CID 54692801 and CID 54715399 were strong inhibitors of NS2B/NS3, with IC50 values (μM) and percentages of viral titer reductions of 19.9, 79.9%; 17.5, 69.8%; and 9.1, 73.9%, respectively. Multivariate methods applied to the molecular descriptors showed two compounds that were structurally different from other DENV inhibitors. GENERAL SIGNIFICANCE This discovery opens new possibilities for obtaining drug candidates against Dengue virus.
Collapse
|
4
|
Castellano S, Taliani S, Viviano M, Milite C, Da Pozzo E, Costa B, Barresi E, Bruno A, Cosconati S, Marinelli L, Greco G, Novellino E, Sbardella G, Da Settimo F, Martini C. Structure–Activity Relationship Refinement and Further Assessment of 4-Phenylquinazoline-2-carboxamide Translocator Protein Ligands as Antiproliferative Agents in Human Glioblastoma Tumors. J Med Chem 2014; 57:2413-28. [DOI: 10.1021/jm401721h] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sabrina Castellano
- Dipartimento
di Farmacia, Universitá di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Sabrina Taliani
- Dipartimento
di Farmacia, Universitá di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Monica Viviano
- Dipartimento
di Farmacia, Universitá di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Ciro Milite
- Dipartimento
di Farmacia, Universitá di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Eleonora Da Pozzo
- Dipartimento
di Farmacia, Universitá di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Barbara Costa
- Dipartimento
di Farmacia, Universitá di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Elisabetta Barresi
- Dipartimento
di Farmacia, Universitá di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Agostino Bruno
- Dipartimento
di Farmacia, Universitá di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Sandro Cosconati
- DiSTABiF, Seconda Universitá di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luciana Marinelli
- Dipartimento
di Farmacia, Universitá di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Giovanni Greco
- Dipartimento
di Farmacia, Universitá di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Ettore Novellino
- Dipartimento
di Farmacia, Universitá di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Gianluca Sbardella
- Dipartimento
di Farmacia, Universitá di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Federico Da Settimo
- Dipartimento
di Farmacia, Universitá di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Claudia Martini
- Dipartimento
di Farmacia, Universitá di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| |
Collapse
|
5
|
Li GB, Yang LL, Xu Y, Wang WJ, Li LL, Yang SY. A combined molecular docking-based and pharmacophore-based target prediction strategy with a probabilistic fusion method for target ranking. J Mol Graph Model 2013; 44:278-85. [DOI: 10.1016/j.jmgm.2013.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/11/2013] [Accepted: 07/12/2013] [Indexed: 12/11/2022]
|
6
|
Reynolds A, Hanani R, Hibbs D, Damont A, Da Pozzo E, Selleri S, Dollé F, Martini C, Kassiou M. Pyrazolo[1,5-a]pyrimidine acetamides: 4-Phenyl alkyl ether derivatives as potent ligands for the 18 kDa translocator protein (TSPO). Bioorg Med Chem Lett 2010; 20:5799-802. [PMID: 20727749 DOI: 10.1016/j.bmcl.2010.07.135] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 07/29/2010] [Accepted: 07/30/2010] [Indexed: 11/16/2022]
Abstract
Herein, we report the synthesis of four new phenyl alkyl ether derivatives (7, 9-11) of the pyrazolo[1,5-a]pyrimidine acetamide class, all of which showed high binding affinity and selectivity for the TSPO and, in the case of the propyl, propargyl, and butyl ether derivatives, the ability to increase pregnenolone biosynthesis by 80-175% over baseline in rat C6 glioma cells. While these compounds fit our in silico generated pharmacophore for TSPO binding the current model does not account for the observed functional activity.
Collapse
Affiliation(s)
- Aaron Reynolds
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | | | | | | | | | | | | | | | | |
Collapse
|