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King E, Aitchison E, Li H, Luo R. Recent Developments in Free Energy Calculations for Drug Discovery. Front Mol Biosci 2021; 8:712085. [PMID: 34458321 PMCID: PMC8387144 DOI: 10.3389/fmolb.2021.712085] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/27/2021] [Indexed: 01/11/2023] Open
Abstract
The grand challenge in structure-based drug design is achieving accurate prediction of binding free energies. Molecular dynamics (MD) simulations enable modeling of conformational changes critical to the binding process, leading to calculation of thermodynamic quantities involved in estimation of binding affinities. With recent advancements in computing capability and predictive accuracy, MD based virtual screening has progressed from the domain of theoretical attempts to real application in drug development. Approaches including the Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA), Linear Interaction Energy (LIE), and alchemical methods have been broadly applied to model molecular recognition for drug discovery and lead optimization. Here we review the varied methodology of these approaches, developments enhancing simulation efficiency and reliability, remaining challenges hindering predictive performance, and applications to problems in the fields of medicine and biochemistry.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Erick Aitchison
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
- Department of Materials Science and Engineering, University of California, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, CA, United States
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Liu CZ, Mottinelli M, Nicholson HE, McVeigh BM, Wong NK, McCurdy CR, Bowen WD. Identification and characterization of MAM03055A: A novel bivalent sigma-2 receptor/TMEM97 ligand with cytotoxic activity. Eur J Pharmacol 2021; 906:174263. [PMID: 34144027 DOI: 10.1016/j.ejphar.2021.174263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 11/20/2022]
Abstract
Sigma-2 receptor/transmembrane protein 97 (TMEM97) is upregulated in cancer cells compared to normal cells. Traditional sigma-2 receptor agonists induce apoptosis and autophagy, making them of interest in cancer therapy. Recently, we reported a novel metabolically stimulative function of the sigma-2 receptor, showing increased 3-(4,5 dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction and stimulation of glycolytic hallmarks. 6-Substituted analogs of the canonical sigma-2 receptor antagonist, 6-acetyl-3-(4-(4-(4-fluorophenyl)piperazin-1-yl)butyl)benzo[d]oxazol-2(3H)-one (SN79), produce both metabolically stimulative and cytotoxic effects. Here, we compare the activities of two related compounds: 6-amino-3-(4-(4-(4-fluorophenyl)piperazin-1-yl)butyl)benzo[d]oxazol-2(3H)-one (CM571), the 6-amino derivative of SN79, which binds with high affinity to both sigma-1 and sigma-2 receptors, and 1,3-bis(3-(4-(4-(4-fluorophenyl)piperazin-1-yl)butyl)-2-oxo-2,3-dihydrobenzo[d]oxazol-6-yl)thiourea (MAM03055A), a homo-bivalent dimer of CM571. MAM03055A resulted from the degradation of 3-(4-(4-(4-fluorophenyl)piperazin-1-yl)butyl)-6-isothiocyanatobenzo[d]oxazol-2(3H)-one (CM572), the cytotoxic 6-isothiocyanato SN79 derivative. MAM03055A exhibited high affinity and strong preference for sigma-2 receptors (sigma-1 Ki = 3371 nM; sigma-2 receptor Ki = 55.9 nM). Functionally, MAM03055A treatment potently induced cell death in SK-N-SH neuroblastoma, MDA-MB-231 breast, and both SW48 and SW480 colorectal cancer cell lines, causing proapoptotic BH3 interacting-domain death agonist (BID) cleavage in SK-N-SH cells. Conversely, CM571 induced metabolic stimulation. CM571 bound reversibly to both receptors, while MAM03055A bound pseudo-irreversibly to sigma-2 receptors and caused residual cytotoxic activity after acute exposure and removal of the compound from the media. Interestingly, MAM03055A induced a time-dependent loss of sigma-2 receptor/TMEM97 protein from cells, whereas monomer CM571 had no effect on receptor levels. These results suggest that monovalent and bivalent sigma-2 receptor ligands in this series interact differently with the receptor, thus resulting in divergent effects.
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Affiliation(s)
- Cheri Z Liu
- Department of Molecular Pharmacology, Physiology, & Biotechnology, Brown University, Providence, RI, USA
| | - Marco Mottinelli
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Hilary E Nicholson
- Department of Molecular Pharmacology, Physiology, & Biotechnology, Brown University, Providence, RI, USA
| | - Bridget M McVeigh
- Department of Molecular Pharmacology, Physiology, & Biotechnology, Brown University, Providence, RI, USA
| | - Neelum K Wong
- Department of Molecular Pharmacology, Physiology, & Biotechnology, Brown University, Providence, RI, USA
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Wayne D Bowen
- Department of Molecular Pharmacology, Physiology, & Biotechnology, Brown University, Providence, RI, USA.
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Zhang Y, Li S, Zhang H, Xu H. Design and Application of Receptor-Targeted Fluorescent Probes Based on Small Molecular Fluorescent Dyes. Bioconjug Chem 2021; 32:4-24. [PMID: 33412857 DOI: 10.1021/acs.bioconjchem.0c00606] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In recent years, a variety of receptor-targeted fluorescent probes have been developed and widely used to realize the visualization of certain receptors, which facilitates the early diagnosis and treatment of diseases. In this Review, we focus on the recent achievements in design, chemical structure, imaging characterization, and potential applications of receptor-targeted fluorescent probes from the past 10 years. The development and application of receptor-targeted fluorescent probes will expand our knowledge of the distribution and function of disease-related receptors, shed light on the drug discovery for clinical diseases where receptors are implicated, and feed into the diagnosis and treatment of a plethora of diseases, including tumors.
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Affiliation(s)
- Yujie Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Shufeng Li
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Hang Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Haiwei Xu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
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Ye N, Qin W, Tian S, Xu Q, Wold EA, Zhou J, Zhen XC. Small Molecules Selectively Targeting Sigma-1 Receptor for the Treatment of Neurological Diseases. J Med Chem 2020; 63:15187-15217. [PMID: 33111525 DOI: 10.1021/acs.jmedchem.0c01192] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The sigma-1 (σ1) receptor, an enigmatic protein originally classified as an opioid receptor subtype, is now understood to possess unique structural and functional features of its own and play critical roles to widely impact signaling transduction by interacting with receptors, ion channels, lipids, and kinases. The σ1 receptor is implicated in modulating learning, memory, emotion, sensory systems, neuronal development, and cognition and accordingly is now an actively pursued drug target for various neurological and neuropsychiatric disorders. Evaluation of the five selective σ1 receptor drug candidates (pridopidine, ANAVEX2-73, SA4503, S1RA, and T-817MA) that have entered clinical trials has shown that reaching clinical approval remains an evasive and important goal. This review provides up-to-date information on the selective targeting of σ1 receptors, including their history, function, reported crystal structures, and roles in neurological diseases, as well as a useful collation of new chemical entities as σ1 selective orthosteric ligands or allosteric modulators.
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Affiliation(s)
- Na Ye
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Wangzhi Qin
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Sheng Tian
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Qingfeng Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Eric A Wold
- Chemical Biology Program, Department of Pharmacology and Toxicology, and Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, and Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Xue-Chu Zhen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
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