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Mapping of Protein Binding Sites using clustering algorithms development of a pharmacophore based drug discovery tool. J Mol Graph Model 2022; 115:108228. [DOI: 10.1016/j.jmgm.2022.108228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 11/22/2022]
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Santoro AM, D’Urso A, Cunsolo A, Milardi D, Purrello R, Sbardella D, Tundo GR, Diana D, Fattorusso R, Dato AD, Paladino A, Persico M, Coletta M, Fattorusso C. Cooperative Binding of the Cationic Porphyrin Tris-T4 Enhances Catalytic Activity of 20S Proteasome Unveiling a Complex Distribution of Functional States. Int J Mol Sci 2020; 21:ijms21197190. [PMID: 33003385 PMCID: PMC7582714 DOI: 10.3390/ijms21197190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/13/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022] Open
Abstract
The present study provides new evidence that cationic porphyrins may be considered as tunable platforms to interfere with the structural “key code” present on the 20S proteasome α-rings and, by consequence, with its catalytic activity. Here, we describe the functional and conformational effects on the 20S proteasome induced by the cooperative binding of the tri-cationic 5-(phenyl)-10,15,20-(tri N-methyl-4-pyridyl) porphyrin (Tris-T4). Our integrated kinetic, NMR, and in silico analysis allowed us to disclose a complex effect on the 20S catalytic activity depending on substrate/porphyrin concentration. The analysis of the kinetic data shows that Tris-T4 shifts the relative populations of the multiple interconverting 20S proteasome conformations leading to an increase in substrate hydrolysis by an allosteric pathway. Based on our Tris-T4/h20S interaction model, Tris-T4 is able to affect gating dynamics and substrate hydrolysis by binding to an array of negatively charged and hydrophobic residues present on the protein surface involved in the 20S molecular activation by the regulatory proteins (RPs). Accordingly, despite the fact that Tris-T4 also binds to the α3ΔN mutant, allosteric modulation is not observed since the molecular mechanism connecting gate dynamics with substrate hydrolysis is impaired. We envisage that the dynamic view of the 20S conformational equilibria, activated through cooperative Tris-T4 binding, may work as a simplified model for a better understanding of the intricate network of 20S conformational/functional states that may be mobilized by exogenous ligands, paving the way for the development of a new generation of proteasome allosteric modulators.
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Affiliation(s)
- Anna Maria Santoro
- Istituto di Cristallografia—CNR Sede Secondaria di Catania, Via P. Gaifami 9/18, 95126 Catania, Italy; (A.M.S.); (D.M.)
| | - Alessandro D’Urso
- Dipartimento di Scienze Chimiche, Università Degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (A.D.); (A.C.); (R.P.)
| | - Alessandra Cunsolo
- Dipartimento di Scienze Chimiche, Università Degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (A.D.); (A.C.); (R.P.)
- Department of Molecular Medicine, The University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78245, USA
| | - Danilo Milardi
- Istituto di Cristallografia—CNR Sede Secondaria di Catania, Via P. Gaifami 9/18, 95126 Catania, Italy; (A.M.S.); (D.M.)
| | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università Degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (A.D.); (A.C.); (R.P.)
| | - Diego Sbardella
- IRCCS-Fondazione Bietti, 00198 Rome, Italy; (D.S.); (G.R.T.)
| | - Grazia R. Tundo
- IRCCS-Fondazione Bietti, 00198 Rome, Italy; (D.S.); (G.R.T.)
| | - Donatella Diana
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy;
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli” Via Vivaldi 43, 81100 Caserta, Italy;
| | - Antonio Di Dato
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (A.D.D.); (M.P.)
| | - Antonella Paladino
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via M. Bianco 9, 20131 Milano, Italy;
| | - Marco Persico
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (A.D.D.); (M.P.)
- Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, 80131 Napoli, Italy
| | - Massimo Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Via Montpellier 1, 00133 Roma, Italy
- Correspondence: (M.C.); (C.F.); Tel.: +39-06-72596365 (M.C.); +39-081-678544 (C.F.)
| | - Caterina Fattorusso
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (A.D.D.); (M.P.)
- Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, 80131 Napoli, Italy
- Correspondence: (M.C.); (C.F.); Tel.: +39-06-72596365 (M.C.); +39-081-678544 (C.F.)
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Sharma T, Harioudh MK, Kuldeep J, Kumar S, Banerjee D, Ghosh JK, Siddiqi MI. Identification of Potential Inhibitors of Cathepsin-B using Shape & Pharmacophore-based Virtual Screening, Molecular Docking and Explicit Water Thermodynamics. Mol Inform 2019; 39:e1900023. [PMID: 31648416 DOI: 10.1002/minf.201900023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022]
Abstract
Lysosome has been long understood as a vital digestive organelle. Increasing reports indicate that the lysosome also plays a crucial role in the pathogenesis of a variety of neurodegenerative diseases, including Huntington's disease, Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. Abnormal protein degradation and deposition stimulated by lysosomal dysfunction may cause age-related neurodegeneration. Enormous efforts have been devoted to the development of effective therapeutics against Alzheimer's disease, the most debilitating neurodegenerative disease. Endopeptidase activity of the Cathepsin-B is associated with the pathological processes. Work presented here focuses on identification of new inhibitors against Cathepsin-B protein using diverse computational approaches together. The inhibitors identified were further tested for in-vitro activity using enzyme based assay method. The identified inhibitors provided interesting understanding on how the water thermodynamic properties along with hydrophobic, steric, electronic, and structural requirements contribute to cathepsin-B inhibitory activity. These water thermodynamic studies, may further be used in computer aided drug discovery pipeline to design and predict more potent derivatives of various scaffolds as cathepsin-B inhibitors.
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Affiliation(s)
- Tanuj Sharma
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Munesh Kumar Harioudh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Jitendra Kuldeep
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Sushil Kumar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Dibyendu Banerjee
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Research Institute, Campus, Lucknow, 226031, India
| | - Jimut Kanti Ghosh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Research Institute, Campus, Lucknow, 226031, India
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Research Institute, Campus, Lucknow, 226031, India
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Dato AD, Cunsolo A, Persico M, Santoro AM, D'Urso A, Milardi D, Purrello R, Stefanelli M, Paolesse R, Tundo GR, Sbardella D, Fattorusso C, Coletta M. Electrostatic Map Of Proteasome α-Rings Encodes The Design of Allosteric Porphyrin-Based Inhibitors Able To Affect 20S Conformation By Cooperative Binding. Sci Rep 2017; 7:17098. [PMID: 29213119 PMCID: PMC5719074 DOI: 10.1038/s41598-017-17008-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/20/2017] [Indexed: 12/13/2022] Open
Abstract
The importance of allosteric proteasome inhibition in the treatment of cancer is becoming increasingly evident. Motivated by this urgent therapeutic need, we have recently identified cationic porphyrins as a highly versatile class of molecules able to regulate proteasome activity by interfering with gating mechanisms. In the present study, the mapping of electrostatic contacts bridging the regulatory particles with the α-rings of the human 20S proteasome led us to the identification of (meso-tetrakis(4-N-methylphenyl pyridyl)-porphyrin (pTMPyPP4) as a novel non-competitive inhibitor of human 20S proteasome. pTMPyPP4 inhibition mechanism implies a positive cooperative binding to proteasome, which disappears when a permanently open proteasome mutant (α-3ΔN) is used, supporting the hypothesis that the events associated with allosteric proteasome inhibition by pTMPyPP4 interfere with 20S gating and affect its "open-closed" equilibrium. Therefore, we propose that the spatial distribution of the negatively charged residues responsible for the interaction with regulatory particles at the α-ring surface of human 20S may be exploited as a blueprint for the design of allosteric proteasome regulators.
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Affiliation(s)
- Antonio Di Dato
- Dipartimento di Farmacia Università di Napoli "Federico II", Via D. Montesano, 49 I, 80131, Napoli, Italy
| | - Alessandra Cunsolo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Marco Persico
- Dipartimento di Farmacia Università di Napoli "Federico II", Via D. Montesano, 49 I, 80131, Napoli, Italy
| | - Anna Maria Santoro
- Istituto di Biostrutture e Bioimmagini-CNR sede secondaria di Catania, Via P. Gaifami, 9- 95126, Catania, Italy
| | - Alessandro D'Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Danilo Milardi
- Istituto di Biostrutture e Bioimmagini-CNR sede secondaria di Catania, Via P. Gaifami, 9- 95126, Catania, Italy
| | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Manuela Stefanelli
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata-Via della Ricerca Scientifica, 00133, Roma, Italy
| | - Roberto Paolesse
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata-Via della Ricerca Scientifica, 00133, Roma, Italy
| | - Grazia R Tundo
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Via Montpellier 1, 00133, Roma, Italy
| | - Diego Sbardella
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Via Montpellier 1, 00133, Roma, Italy
| | - Caterina Fattorusso
- Dipartimento di Farmacia Università di Napoli "Federico II", Via D. Montesano, 49 I, 80131, Napoli, Italy.
| | - Massimo Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Via Montpellier 1, 00133, Roma, Italy.
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