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Zuo K, Kranjc A, Capelli R, Rossetti G, Nechushtai R, Carloni P. Metadynamics simulations of ligands binding to protein surfaces: a novel tool for rational drug design. Phys Chem Chem Phys 2023; 25:13819-13824. [PMID: 37184538 DOI: 10.1039/d3cp01388j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Structure-based drug design protocols may encounter difficulties to investigate poses when the biomolecular targets do not exhibit typical binding pockets. In this study, by providing two concrete examples from our labs, we suggest that the combination of metadynamics free energy methods (validated against affinity measurements), along with experimental structural information (by X-ray crystallography and NMR), can help to identify the poses of ligands on protein surfaces. The simulation workflow proposed here was implemented in a widely used code, namely GROMACS, and it could straightforwardly be applied to various drug-design campaigns targeting ligands' binding to protein surfaces.
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Affiliation(s)
- Ke Zuo
- Computational Biomedicine, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
- Department of Physics, RWTH Aachen University, Aachen 52074, Germany
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
- Department of Physics, Università degli Studi di Ferrara, Ferrara 44121, Italy
| | - Agata Kranjc
- Computational Biomedicine, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
| | - Riccardo Capelli
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, Milan 20133, Italy
| | - Giulia Rossetti
- Computational Biomedicine, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
- Jülich Supercomputing Center (JSC), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
- Department of Neurology, Faculty of Medicine, RWTH Aachen University, Aachen 52074, Germany
| | - Rachel Nechushtai
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Paolo Carloni
- Computational Biomedicine, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
- Department of Physics, RWTH Aachen University, Aachen 52074, Germany
- JARA Institute: Molecular Neuroscience and Imaging, Institute of Neuroscience and Medicine INM-11, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
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Kumar A, Vigato C, Boschi D, Lolli ML, Kumar D. Phenothiazines as anti-cancer agents: SAR overview and synthetic strategies. Eur J Med Chem 2023; 254:115337. [PMID: 37060756 DOI: 10.1016/j.ejmech.2023.115337] [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: 01/09/2023] [Revised: 03/31/2023] [Accepted: 04/02/2023] [Indexed: 04/17/2023]
Abstract
Cancer is a leading cause of death worldwide and there are still limited options for cure. Chemotherapy is the most significant treatment for cancer which increased survival rates, despite this, it is associated with numerous side effects, as well as cancer relapsing due to drug resistance insurgence; consequently, it is still a challenging task to develop new potent and less toxic anti-cancer agents for patients' care. Phenothiazine moiety, which leads a class of well-known antipsychotic drugs, possesses a wide range of biological activities and has been also introduced in cancer chemotherapy. This review aims in disclosing the use of phenothiazines during the last five years for the development of different anti-cancer drug candidates. The design and the synthetic strategies adopted, the SAR investigations and the role of reviewed phenothiazine derivatives as anti-cancer agents and multi-drug resistance (MDR) reversals are here fully described and discussed.
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Affiliation(s)
- Arun Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173 229, India
| | - Chiara Vigato
- Department of Science and Drug Technology, University of Torino, via Pietro Giuria 9, 10125, Torino, Italy
| | - Donatella Boschi
- Department of Science and Drug Technology, University of Torino, via Pietro Giuria 9, 10125, Torino, Italy
| | - Marco Lucio Lolli
- Department of Science and Drug Technology, University of Torino, via Pietro Giuria 9, 10125, Torino, Italy.
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173 229, India.
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