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Paulraj MS, Eringathodi S, Mollah AKMM, Alexis Thayaparan CT, Kuldeep SA, Subramanian PS, M I, Dhanaraj P. 2-[( E)-(2-carboxybenzylidene) amino] ethan ammonium-like amino acid zwitterions: crystal structure, functional studies and its molecular dynamic simulation study with drug target receptors. J Biomol Struct Dyn 2024; 42:6081-6090. [PMID: 37403277 DOI: 10.1080/07391102.2023.2230296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/22/2023] [Indexed: 07/06/2023]
Abstract
The novel synthetic amino acid-like zwitterion containing imine bond ionic compound 2-[(E)-(2-carboxy benzylidene) amino] ethan ammonium salt, C10H12N2O2, was synthesized. Computational functional characterization is now being used to predict novel compounds. Here, we report on a titled combination that has been crystallizing in orthorhombic space group Pcc2 with Z = 4. The zwitterions form centrosymmetric dimers to polymeric supramolecular network via intermolecular N-H… O hydrogen bonds between the carboxylate groups and ammonium ion. The components are linked by ionic (N+-H-O-) and hydrogen bonds (N+-H-O), forming a complex three-dimensional supramolecular network. Further, molecular computational docking characterization study was performed with compound against multi-disease drug target biomolecule of anticancer target molecule of HDAC8 (PDB ID 1T69) receptor and antiviral molecular target protease (PDB ID 6LU7) to evaluate the interaction stability, conformational changes and to get insights into the natural dynamics on different timescales in solution. HighlightsThe novel zwitter ionic amino acid compound 2-[(E)-(2-carboxybenzylidene) amino] ethan ammonium salt, C10H12N2O2.The crystal structure determined for this compound illustrates the presence of intermolecular ionic N+-H-O- and N+-H-O hydrogen bonds between the carboxylate groups and ammonium ion, which influence the formation of a complex three-dimensional supramolecular polymeric network.Molecular docking studies helps to understand the conformational stability and interaction stabilityThe novel molecule can be considered for anticancer treatment.
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Affiliation(s)
| | - Suresh Eringathodi
- Analytical and Environmental Science Division and Centralized Instrument Facility, CSIR - Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
| | | | | | | | - Palani Sivagnana Subramanian
- Inorganic Materials and Catalysis Division, CSIR - Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
| | - Indiraleka M
- Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India
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Ogawa K, Nishizawa K, Washiyama K, Munekane M, Fuchigami T, Echigo H, Mishiro K, Hirata S, Wakabayashi H, Takahashi K, Kinuya S. Astatine-211-labeled aza-vesamicol derivatives as sigma receptor ligands for targeted alpha therapy. Nucl Med Biol 2023; 122-123:108369. [PMID: 37516066 DOI: 10.1016/j.nucmedbio.2023.108369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 07/31/2023]
Abstract
INTRODUCTION As sigma receptors are abundantly expressed on different types of cancer cells, several radiolabeled sigma receptor ligands have been developed for cancer imaging and therapy. Previously, we synthesized and evaluated radioiodinated aza-vesamicol derivatives, [125I]pIC3NV, [125I]mIC2N5V, and [125I]mIC3N5V. They accumulated in tumors, and [125I]mIC2N5V and [125I]mIC3N5V showed higher tumor to non-target tissue ratios than [125I]pIC3NV. Therefore, we synthesized and evaluated the corresponding 211At-labeled compounds, [211At]mAtC2N5V and [211At]mAtC3N5V, for targeted alpha therapy (TAT). METHODS [211At]mAtC2N5V and [211At]mAtC3N5V were prepared by the standard method of electrophilic astatodestannylation of the corresponding trimethylstannyl precursors. Cellular uptake experiments, and biodistribution experiments and therapeutic experiments in tumor-bearing mice were performed. RESULTS The radiochemical yields of [211At]mAtC2N5V and [211At]mAtC3N5V were 45.5 ± 14.4% and 56.9 ± 13.8%, respectively. After HPLC purification, their radiochemical purities were over 95%. [211At]mAtC2N5V and [211At]mAtC3N5V showed high uptake in DU-145 cells. They demonstrated high accumulation in tumors (6.9 ± 1.4%injected dose/g and 5.1 ± 1.4%injected dose/g at 1 h, respectively) and similar biodistribution tendencies compared with the corresponding 125I-labeled compounds. A single injection of [211At]mAtC2N5V (0.48 MBq) or [211At]mAtC3N5V (0.48 MBq) significantly inhibited tumor growth. CONCLUSION These results indicated that [211At]mAtC2N5V and [211At]mAtC3N5V could be potential candidates for TAT.
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Affiliation(s)
- Kazuma Ogawa
- Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
| | - Kota Nishizawa
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Kohshin Washiyama
- Advanced Clinical Research Center, Fukushima Global Medical Science Center, Fukushima Medical University, 1 Hikarigaoka, Fukushima 960-1295, Japan
| | - Masayuki Munekane
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Takeshi Fuchigami
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hiroaki Echigo
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Kenji Mishiro
- Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Saki Hirata
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hiroshi Wakabayashi
- Department of Nuclear Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Takara-machi, Kanazawa, Ishikawa 920-8641, Japan
| | - Kazuhiro Takahashi
- Advanced Clinical Research Center, Fukushima Global Medical Science Center, Fukushima Medical University, 1 Hikarigaoka, Fukushima 960-1295, Japan
| | - Seigo Kinuya
- Department of Nuclear Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Takara-machi, Kanazawa, Ishikawa 920-8641, Japan
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Fu K, Xu W, Yang R, Zhao H, Xu H, Wei Y, Liu H, Qiu Y, Chen D, Guo D, Xiong B. 2,6-diazaspiro[3.4]octan-7-one derivatives as potent sigma-1 receptor antagonists that enhanced the antinociceptive effect of morphine and rescued morphine tolerance. Eur J Med Chem 2023; 249:115178. [PMID: 36753922 DOI: 10.1016/j.ejmech.2023.115178] [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: 12/13/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023]
Abstract
Opioids are efficacious analgesics for pain treatments. However, their repeated use in large doses often leads to analgesic tolerance, which limits the clinical application. Sigma-1 receptor (σ1R) antagonists were reported to synergistically enhance the analgesic effect of mu opioid receptor (MOR) agonists without amplifying the adverse effects. Therefore, the σ1R is considered a promising drug target for pain management. Based on the recently elucidated co-crystal structure of σ1R with 4-IBP, we designed and developed a series of σ1R antagonists harboring the 2,6-diazaspiro[3.4]octan-7-one scaffold. Through a detailed structure-activity relationship study, we identified compound 32 as a potent σ1R antagonist, which significantly enhanced the antinociceptive effect of morphine and rescued morphine-induced analgesic tolerance. Our results support σ1R antagonism as a promising strategy to develop novel analgesics and highlight the therapeutic potential of compound 32 to prevent morphine tolerance.
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Affiliation(s)
- Kequan Fu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Wen Xu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China; School of Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Ruicong Yang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China; School of Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Huimin Zhao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Huanyu Xu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaqin Wei
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Hongli Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Yinli Qiu
- Institute of Pharmaceutical Research, Jiangsu Nhwa Pharmaceutical Co., Ltd., 1 Yunhe Road, Xuzhou, 221135, Jiangsu, China
| | - Danqi Chen
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
| | - Bing Xiong
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China; Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Li J, Satyshur KA, Guo LW, Ruoho AE. Sphingoid Bases Regulate the Sigma-1 Receptor-Sphingosine and N, N'-Dimethylsphingosine Are Endogenous Agonists. Int J Mol Sci 2023; 24:3103. [PMID: 36834510 PMCID: PMC9962145 DOI: 10.3390/ijms24043103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Both bioactive sphingolipids and Sigma-1 receptor (S1R) chaperones occur ubiquitously in mammalian cell membranes. Endogenous compounds that regulate the S1R are important for controlling S1R responses to cellular stress. Herein, we interrogated the S1R in intact Retinal Pigment Epithelial cells (ARPE-19) with the bioactive sphingoid base, sphingosine (SPH), or the pain-provoking dimethylated SPH derivative, N,N'-dimethylsphingosine (DMS). As informed by a modified native gel approach, the basal and antagonist (BD-1047)-stabilized S1R oligomers dissociated to protomeric forms in the presence of SPH or DMS (PRE-084 as control). We, thus, posited that SPH and DMS are endogenous S1R agonists. Consistently, in silico docking of SPH and DMS to the S1R protomer showed strong associations with Asp126 and Glu172 in the cupin beta barrel and extensive van der Waals interactions of the C18 alkyl chains with the binding site including residues in helices 4 and 5. Mean docking free energies were 8.73-8.93 kcal/mol for SPH and 8.56-8.15 kcal/mol for DMS, and calculated binding constants were ~40 nM for SPH and ~120 nM for DMS. We hypothesize that SPH, DMS, and similar sphingoid bases access the S1R beta barrel via a membrane bilayer pathway. We further propose that the enzymatic control of ceramide concentrations in intracellular membranes as the primary sources of SPH dictates availability of endogenous SPH and DMS to the S1R and the subsequent control of S1R activity within the same cell and/or in cellular environments.
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Affiliation(s)
- Jing Li
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Kenneth A. Satyshur
- Small Molecule Screening Facility, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
| | - Lian-Wang Guo
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Arnold E. Ruoho
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
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Thirunavukkarasu MK, Karuppasamy R. Drug repurposing combined with MM/PBSA based validation strategies towards MEK inhibitors screening. J Biomol Struct Dyn 2022; 40:12392-12403. [PMID: 34459701 DOI: 10.1080/07391102.2021.1970629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Emergence of oncogenic mutations in the MAPK pathway gaining more impact in the recent years. Importantly, MEK is a core element of this pathway as it is easy to inhibit and is a gatekeeper of multiple malignancies. Therefore, we performed in-silico strategy to screen repurposed candidate for MEK protein using a library of 11,808 compounds from different clusters in the DrugBank database. Glide docking, Prime-MM/GBSA and QikProp analysis were implemented to retrieve the hits with high precision. The stability of the binding mode and binding affinity of the resultant hit were explored using molecular dynamic simulations and MM/PBSA approach. The results highlight that Nebivolol (DB04861) not only achieved a stable conformation in the MEK binding pocket but also displayed highest binding affinity than the other molecules investigated in our study. Taken together, we hypothesized that Nebivolol is an excellent candidate for the inhibition of MEK in NSCLC patients in future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muthu Kumar Thirunavukkarasu
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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The Impact of Software Used and the Type of Target Protein on Molecular Docking Accuracy. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27249041. [PMID: 36558174 PMCID: PMC9788237 DOI: 10.3390/molecules27249041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
The modern development of computer technology and different in silico methods have had an increasing impact on the discovery and development of new drugs. Different molecular docking techniques most widely used in silico methods in drug discovery. Currently, the time and financial costs for the initial hit identification can be significantly reduced due to the ability to perform high-throughput virtual screening of large compound libraries in a short time. However, the selection of potential hit compounds still remains more of a random process, because there is still no consensus on what the binding energy and ligand efficiency (LE) of a potentially active compound should be. In the best cases, only 20-30% of compounds identified by molecular docking are active in biological tests. In this work, we evaluated the impact of the docking software used as well as the type of the target protein on the molecular docking results and their accuracy using an example of the three most popular programs and five target proteins related to neurodegenerative diseases. In addition, we attempted to determine the "reliable range" of the binding energy and LE that would allow selecting compounds with biological activity in the desired concentration range.
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7
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Zhu H, Zhang Y, Li W, Huang N. A Comprehensive Survey of Prospective Structure-Based Virtual Screening for Early Drug Discovery in the Past Fifteen Years. Int J Mol Sci 2022; 23:15961. [PMID: 36555602 PMCID: PMC9781938 DOI: 10.3390/ijms232415961] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Structure-based virtual screening (SBVS), also known as molecular docking, has been increasingly applied to discover small-molecule ligands based on the protein structures in the early stage of drug discovery. In this review, we comprehensively surveyed the prospective applications of molecular docking judged by solid experimental validations in the literature over the past fifteen years. Herein, we systematically analyzed the novelty of the targets and the docking hits, practical protocols of docking screening, and the following experimental validations. Among the 419 case studies we reviewed, most virtual screenings were carried out on widely studied targets, and only 22% were on less-explored new targets. Regarding docking software, GLIDE is the most popular one used in molecular docking, while the DOCK 3 series showed a strong capacity for large-scale virtual screening. Besides, the majority of identified hits are promising in structural novelty and one-quarter of the hits showed better potency than 1 μM, indicating that the primary advantage of SBVS is to discover new chemotypes rather than highly potent compounds. Furthermore, in most studies, only in vitro bioassays were carried out to validate the docking hits, which might limit the further characterization and development of the identified active compounds. Finally, several successful stories of SBVS with extensive experimental validations have been highlighted, which provide unique insights into future SBVS drug discovery campaigns.
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Affiliation(s)
- Hui Zhu
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
- National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Yulin Zhang
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
- National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Wei Li
- RPXDs (Suzhou) Co., Ltd., Suzhou 215028, China
| | - Niu Huang
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
- National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
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Keuler T, Lemke C, Elsinghorst PW, Iriepa I, Chioua M, Martínez-Grau MA, Beadle CD, Vetman T, López-Muñoz F, Wille T, Bartz U, Deuther-Conrad W, Marco-Contelles J, Gütschow M. The Chemotype of Chromanones as a Privileged Scaffold for Multineurotarget Anti-Alzheimer Agents. ACS Pharmacol Transl Sci 2022; 5:1097-1108. [PMID: 36407962 PMCID: PMC9667544 DOI: 10.1021/acsptsci.2c00097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 11/28/2022]
Abstract
The multifactorial nature of Alzheimer's disease necessitates the development of agents able to interfere with different relevant targets. A series of 22 tailored chromanones was conceptualized, synthesized, and subjected to biological evaluation. We identified one representative bearing a linker-connected azepane moiety (compound 19) with balanced pharmacological properties. Compound 19 exhibited inhibitory activities against human acetyl-, butyrylcholinesterase and monoamine oxidase-B, as well as high affinity to both the σ1 and σ2 receptors. Our study provides a framework for the development of further chromanone-based multineurotarget agents.
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Affiliation(s)
- Tim Keuler
- Pharmaceutical
Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Carina Lemke
- Pharmaceutical
Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Paul W. Elsinghorst
- Pharmaceutical
Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
- Central
Institute of the Bundeswehr Medical Service Munich, Ingolstädter Landstraße 102, 85748 Garching Germany
| | - Isabel Iriepa
- Universidad
de Alcalá, Departamento de Química
Orgánica y Química Inorgánica, Ctra. Madrid-Barcelona, 28871 Alcalá de Henares, Madrid España
| | - Mourad Chioua
- Laboratory
of Medicinal Chemistry, IQOG, CSIC, C/Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Christopher D. Beadle
- Lilly Research
Centre, Eli Lilly & Company, Erl Wood Manor, Windlesham, Surrey GU20
6PH, United Kingdom
| | - Tatiana Vetman
- Lilly
Research Laboratories, Eli Lilly & Company, Indianapolis, Indiana 46285, United States
| | - Francisco López-Muñoz
- Faculty
of Health, Camilo José Cela University of Madrid (UCJC), Neuropsychopharmacology Unit, “Hospital 12 de Octubre” Research
Institute, 28692 Madrid, Spain
| | - Timo Wille
- Bundeswehr
Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937 München, Germany
| | - Ulrike Bartz
- Department
of Natural Sciences, University of Applied
Sciences Bonn-Rhein-Sieg, von-Liebig-Straße 20, 53359 Rheinbach, Germany
| | - Winnie Deuther-Conrad
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, 04318 Leipzig, Germany
| | - José Marco-Contelles
- Laboratory
of Medicinal Chemistry, IQOG, CSIC, C/Juan de la Cierva 3, 28006 Madrid, Spain
| | - Michael Gütschow
- Pharmaceutical
Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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Fallica AN, Ciaffaglione V, Modica MN, Pittalà V, Salerno L, Amata E, Marrazzo A, Romeo G, Intagliata S. Structure-activity relationships of mixed σ1R/σ2R ligands with antiproliferative and anticancer effects. Bioorg Med Chem 2022; 73:117032. [DOI: 10.1016/j.bmc.2022.117032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/27/2022]
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10
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Mishiro K, Wang M, Hirata S, Fuchigami T, Shiba K, Kinuya S, Ogawa K. Development of tumor-targeting aza-vesamicol derivatives with high affinity for sigma receptors for cancer theranostics. RSC Med Chem 2022; 13:986-997. [PMID: 36092143 PMCID: PMC9384704 DOI: 10.1039/d2md00099g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/28/2022] [Indexed: 07/31/2023] Open
Abstract
As sigma receptors are highly expressed on various cancer cells, radiolabeled sigma receptor ligands have been developed as imaging and therapeutic probes for cancer. Previously, we synthesized and evaluated a radioiodinated vesamicol derivative, 2-(4-[125I](4-iodophenyl)piperidine)cyclohexanol ((+)-[125I]pIV), and a radioiodinated aza-vesamicol derivative, trans-2-(4-(3-[125I](4-iodophenyl)propyl)piperazin-1-yl)cyclohexan-1-ol ([125I]2), as sigma-1 receptor-targeting probes. In order to obtain sigma receptor-targeting probes with superior biodistribution characteristics, we firstly synthesized twelve bromine-containing aza-vesamicol derivatives and evaluated their affinity for sigma receptors. One such derivative exhibited high selectivity for the sigma-1 receptor and another exhibited high affinity for both the sigma-1 and sigma-2 receptors. Thus, their halogen-substituted iodine- and radioiodine-containing compounds were prepared. The 125I-labeled compounds exhibited high uptake in tumor and lower uptake in non-target tissues than the two previously developed and evaluated 125I-labeled sigma receptor-targeting probes, [125I]pIV and [125I]2. Therefore, these novel radioiodine-labeled compounds should be promising as sigma receptor-targeting probes.
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Affiliation(s)
- Kenji Mishiro
- Institute for Frontier Science Initiative, Kanazawa University Kakuma-machi Kanazawa Ishikawa 920-1192 Japan
| | - Mengfei Wang
- Graduate School of Pharmaceutical Sciences, Kanazawa University Kakuma-machi Kanazawa Ishikawa 920-1192 Japan
| | - Saki Hirata
- Graduate School of Pharmaceutical Sciences, Kanazawa University Kakuma-machi Kanazawa Ishikawa 920-1192 Japan
| | - Takeshi Fuchigami
- Graduate School of Pharmaceutical Sciences, Kanazawa University Kakuma-machi Kanazawa Ishikawa 920-1192 Japan
| | - Kazuhiro Shiba
- Research Center for Experimental Modeling of Human Disease, Kanazawa University Takara-machi Kanazawa Ishikawa 920-8640 Japan
| | - Seigo Kinuya
- Department of Nuclear Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University Takara-machi Kanazawa Ishikawa 920-8641 Japan
| | - Kazuma Ogawa
- Institute for Frontier Science Initiative, Kanazawa University Kakuma-machi Kanazawa Ishikawa 920-1192 Japan
- Graduate School of Pharmaceutical Sciences, Kanazawa University Kakuma-machi Kanazawa Ishikawa 920-1192 Japan
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Shimu MSS, Mahmud S, Tallei TE, Sami SA, Adam AA, Acharjee UK, Paul GK, Emran TB, Zaman S, Uddin MS, Saleh MA, Alshehri S, Ghoneim MM, Alruwali M, Obaidullah AJ, Jui NR, Kim J, Kim B. Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study. Molecules 2022; 27:molecules27030653. [PMID: 35163918 PMCID: PMC8840231 DOI: 10.3390/molecules27030653] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 02/04/2023] Open
Abstract
The spread of the Dengue virus over the world, as well as multiple outbreaks of different serotypes, has resulted in a large number of deaths and a medical emergency, as no viable medications to treat Dengue virus patients have yet been found. In this paper, we provide an in silico virtual screening and molecular dynamics-based analysis to uncover efficient Dengue infection inhibitors. Based on a Google search and literature mining, a large phytochemical library was generated and employed as ligand molecules. In this investigation, the protein target NS2B/NS3 from Dengue was employed, and around 27 compounds were evaluated in a docking study. Phellodendroside (−63 kcal/mole), quercimeritrin (−59.5 kcal/mole), and quercetin-7-O-rutinoside (−54.1 kcal/mole) were chosen based on their binding free energy in MM-GBSA. The tested compounds generated numerous interactions at Lys74, Asn152, and Gln167 residues in the active regions of NS2B/NS3, which is needed for the protein’s inhibition. As a result, the stable mode of docked complexes is defined by various descriptors from molecular dynamics simulations, such as RMSD, SASA, Rg, RMSF, and hydrogen bond. The pharmacological properties of the compounds were also investigated, and no toxicity was found in computational ADMET properties calculations. As a result, this computational analysis may aid fellow researchers in developing innovative Dengue virus inhibitors.
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Affiliation(s)
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Trina Ekwati Tallei
- Department of Biology, Faculty of Mathematics and Natural Science, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Saad Ahmed Sami
- Department of Pharmacy, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Ahmad Akroman Adam
- Dentistry Study Program, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Uzzal Kumar Acharjee
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh;
- Correspondence: (U.K.A.); (M.A.S.); (B.K.)
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh;
| | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Md. Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
- Correspondence: (U.K.A.); (M.A.S.); (B.K.)
| | - Sultan Alshehri
- Department of Pharamaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Mohammed M Ghoneim
- Department of Pharmacy Practice, College of Pharamcy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia; (M.M.G.); (M.A.)
| | - Maha Alruwali
- Department of Pharmacy Practice, College of Pharamcy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia; (M.M.G.); (M.A.)
| | - Ahmad J. Obaidullah
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nabilah Rahman Jui
- Department of Biochemistry and Biotechnology, University of Science and Technology, Chittagong 4202, Bangladesh;
| | - Junghwan Kim
- Department of Internal Medicine, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea;
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Korea
- Correspondence: (U.K.A.); (M.A.S.); (B.K.)
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12
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Dvorácskó S, Lázár L, Fülöp F, Palkó M, Zalán Z, Penke B, Fülöp L, Tömböly C, Bogár F. Novel High Affinity Sigma-1 Receptor Ligands from Minimal Ensemble Docking-Based Virtual Screening. Int J Mol Sci 2021; 22:8112. [PMID: 34360878 PMCID: PMC8347176 DOI: 10.3390/ijms22158112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Sigma-1 receptor (S1R) is an intracellular, multi-functional, ligand operated protein that also acts as a chaperone. It is considered as a pluripotent drug target in several pathologies. The publication of agonist and antagonist bound receptor structures has paved the way for receptor-based in silico drug design. However, recent studies on this subject payed no attention to the structural differences of agonist and antagonist binding. In this work, we have developed a new ensemble docking-based virtual screening protocol utilizing both agonist and antagonist bound S1R structures. This protocol was used to screen our in-house compound library. The S1R binding affinities of the 40 highest ranked compounds were measured in competitive radioligand binding assays and the sigma-2 receptor (S2R) affinities of the best S1R binders were also determined. This way three novel high affinity S1R ligands were identified and one of them exhibited a notable S1R/S2R selectivity.
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Affiliation(s)
- Szabolcs Dvorácskó
- Biological Research Centre, Institute of Biochemistry, Eötvös Loránd Research Network (ELKH), H-6726 Szeged, Hungary; (S.D.); (C.T.)
| | - László Lázár
- Institute of Pharmaceutical Chemistry, University of Szeged, H-6720 Szeged, Hungary; (L.L.); (F.F.); (M.P.); (Z.Z.)
| | - Ferenc Fülöp
- Institute of Pharmaceutical Chemistry, University of Szeged, H-6720 Szeged, Hungary; (L.L.); (F.F.); (M.P.); (Z.Z.)
| | - Márta Palkó
- Institute of Pharmaceutical Chemistry, University of Szeged, H-6720 Szeged, Hungary; (L.L.); (F.F.); (M.P.); (Z.Z.)
| | - Zita Zalán
- Institute of Pharmaceutical Chemistry, University of Szeged, H-6720 Szeged, Hungary; (L.L.); (F.F.); (M.P.); (Z.Z.)
| | - Botond Penke
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary;
| | - Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary;
| | - Csaba Tömböly
- Biological Research Centre, Institute of Biochemistry, Eötvös Loránd Research Network (ELKH), H-6726 Szeged, Hungary; (S.D.); (C.T.)
| | - Ferenc Bogár
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary;
- MTA-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H-6720 Szeged, Hungary
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13
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Fallica AN, Pittalà V, Modica MN, Salerno L, Romeo G, Marrazzo A, Helal MA, Intagliata S. Recent Advances in the Development of Sigma Receptor Ligands as Cytotoxic Agents: A Medicinal Chemistry Perspective. J Med Chem 2021; 64:7926-7962. [PMID: 34076441 PMCID: PMC8279423 DOI: 10.1021/acs.jmedchem.0c02265] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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Since their discovery
as distinct receptor proteins, the specific
physiopathological role of sigma receptors (σRs) has been deeply
investigated. It has been reported that these proteins, classified
into two subtypes indicated as σ1 and σ2, might play a pivotal role in cancer growth, cell proliferation,
and tumor aggressiveness. As a result, the development of selective
σR ligands with potential antitumor properties attracted significant
attention as an emerging theme in cancer research. This perspective
deals with the recent advances of σR ligands as novel cytotoxic
agents, covering articles published between 2010 and 2020. An up-to-date
description of the medicinal chemistry of selective σ1R and σ2R ligands with antiproliferative and cytotoxic
activities has been provided, including major pharmacophore models
and comprehensive structure–activity relationships for each
main class of σR ligands.
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Affiliation(s)
- Antonino N Fallica
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Valeria Pittalà
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Maria N Modica
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Loredana Salerno
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Giuseppe Romeo
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Agostino Marrazzo
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Mohamed A Helal
- University of Science and Technology, Biomedical Sciences Program, Zewail City of Science and Technology, October Gardens, sixth of October, Giza 12578, Egypt.,Medicinal Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Sebastiano Intagliata
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
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14
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Peng Y, Zhang Q, Welsh WJ. Novel Sigma 1 Receptor Antagonists as Potential Therapeutics for Pain Management. J Med Chem 2021; 64:890-904. [PMID: 33372782 DOI: 10.1021/acs.jmedchem.0c01964] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sigma 1 receptor (S1R) is a molecular chaperone protein located in the endoplasmic reticulum and plasma membranes and has been shown to play important roles in various pathological disorders including pain and, as recently discovered, COVID-19. Employing structure- and QSAR-based drug design strategies, we rationally designed, synthesized, and biologically evaluated a series of novel triazole-based S1R antagonists. Compound 10 exhibited potent binding affinity for S1R, high selectivity over S2R and 87 other human targets, acceptable in vitro metabolic stability, slow clearance in liver microsomes, and excellent blood-brain barrier permeability in rats. Further in vivo studies in rats showed that 10 exhibited negligible acute toxicity in the rotarod test and statistically significant analgesic effects in the formalin test for acute inflammatory pain and paclitaxel-induced neuropathic pain models during cancer chemotherapy. These encouraging results promote further development of our triazole-based S1R antagonists as novel treatments for pain of different etiologies.
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Affiliation(s)
- Youyi Peng
- Biomedical Informatics Shared Resource, Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, 195 Little Albany Street, New Brunswick, New Jersey 08903, United States
| | - Qiang Zhang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, 661 Hoes Lane West, Piscataway, New Jersey 08854, United States
| | - William J Welsh
- Biomedical Informatics Shared Resource, Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, 195 Little Albany Street, New Brunswick, New Jersey 08903, United States
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, 661 Hoes Lane West, Piscataway, New Jersey 08854, United States
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