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Heider J, Kilian J, Garifulina A, Hering S, Langer T, Seidel T. Apo2ph4: A Versatile Workflow for the Generation of Receptor-based Pharmacophore Models for Virtual Screening. J Chem Inf Model 2023; 63:101-110. [PMID: 36526584 PMCID: PMC9832483 DOI: 10.1021/acs.jcim.2c00814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Indexed: 12/23/2022]
Abstract
Pharmacophore models are widely used as efficient virtual screening (VS) filters for the target-directed enrichment of large compound libraries. However, the generation of pharmacophore models that have the power to discriminate between active and inactive molecules traditionally requires structural information about ligand-target complexes or at the very least knowledge of one active ligand. The fact that the discovery of the first known active ligand of a newly investigated target represents a major hurdle at the beginning of every drug discovery project underscores the need for methods that are able to derive high-quality pharmacophore models even without the prior knowledge of any active ligand structures. In this work, we introduce a novel workflow, called apo2ph4, that enables the rapid derivation of pharmacophore models solely from the three-dimensional structure of the target receptor. The utility of this workflow is demonstrated retrospectively for the generation of a pharmacophore model for the M2 muscarinic acetylcholine receptor. Furthermore, in order to show the general applicability of apo2ph4, the workflow was employed for all 15 targets of the recently published LIT-PCBA dataset. Pharmacophore-based VS runs using the apo2ph4-derived models achieved a significant enrichment of actives for 13 targets. In the last presented example, a pharmacophore model derived from the etomidate site of the α1β2γ2 GABAA receptor was used in VS campaigns. Subsequent in vitro testing of selected hits revealed that 19 out of 20 (95%) tested compounds were able to significantly enhance GABA currents, which impressively demonstrates the applicability of apo2ph4 for real-world drug design projects.
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Affiliation(s)
- Jörg Heider
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz
2, 1090Vienna, Austria
- Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090Vienna, Austria
| | - Jonas Kilian
- Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090Vienna, Austria
- Department
of Biomedical Imaging and Image-Guided Therapy, Division of Nuclear
Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090Vienna, Austria
| | - Aleksandra Garifulina
- Division
of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090Vienna, Austria
| | - Steffen Hering
- Division
of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090Vienna, Austria
| | - Thierry Langer
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz
2, 1090Vienna, Austria
| | - Thomas Seidel
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz
2, 1090Vienna, Austria
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Simeone X, Ernst M, Seidel T, Heider J, Enz D, Monticelli S, Vogel FD, Koniuszewski F, Langer T, Scholze P, Pace V, Miele M. Novel alpha6 preferring GABA-A receptor ligands based on loreclezole. Eur J Med Chem 2022; 244:114780. [DOI: 10.1016/j.ejmech.2022.114780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/04/2022]
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Aquatic Freshwater Vertebrate Models of Epilepsy Pathology: Past Discoveries and Future Directions for Therapeutic Discovery. Int J Mol Sci 2022; 23:ijms23158608. [PMID: 35955745 PMCID: PMC9368815 DOI: 10.3390/ijms23158608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 12/04/2022] Open
Abstract
Epilepsy is an international public health concern that greatly affects patients’ health and lifestyle. About 30% of patients do not respond to available therapies, making new research models important for further drug discovery. Aquatic vertebrates present a promising avenue for improved seizure drug screening and discovery. Zebrafish (Danio rerio) and African clawed frogs (Xenopus laevis and tropicalis) are increasing in popularity for seizure research due to their cost-effective housing and rearing, similar genome to humans, ease of genetic manipulation, and simplicity of drug dosing. These organisms have demonstrated utility in a variety of seizure-induction models including chemical and genetic methods. Past studies with these methods have produced promising data and generated questions for further applications of these models to promote discovery of drug-resistant seizure pathology and lead to effective treatments for these patients.
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Chatzigoulas A, Cournia Z. Rational design of allosteric modulators: Challenges and successes. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1529] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alexios Chatzigoulas
- Biomedical Research Foundation Academy of Athens Athens Greece
- Department of Informatics and Telecommunications National and Kapodistrian University of Athens Athens Greece
| | - Zoe Cournia
- Biomedical Research Foundation Academy of Athens Athens Greece
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Zhang Y, Wang K, Yu Z. Drug Development in Channelopathies: Allosteric Modulation of Ligand-Gated and Voltage-Gated Ion Channels. J Med Chem 2020; 63:15258-15278. [PMID: 33253554 DOI: 10.1021/acs.jmedchem.0c01304] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ion channels have been characterized as promising drug targets for treatment of numerous human diseases. Functions of ion channels can be fine-tuned by allosteric modulators, which interact with channels and modulate their activities by binding to sites spatially discrete from those of orthosteric ligands. Positive and negative allosteric modulators have presented a plethora of potential therapeutic advantages over traditionally orthosteric agonists and antagonists in terms of selectivity and safety. This thematic review highlights the discovery of representative allosteric modulators for ligand-gated and voltage-gated ion channels, discussing in particular their identifications, locations, and therapeutic uses in the treatment of a range of channelopathies. Additionally, structures and functions of selected ion channels are briefly described to aid in the rational design of channel modulators. Overall, allosteric modulation represents an innovative targeting approach, and the corresponding modulators provide an abundant but challenging landscape for novel therapeutics targeting ligand-gated and voltage-gated ion channels.
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Affiliation(s)
- Yanyun Zhang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Ke Wang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Zhiyi Yu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
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Senatore R, Malik M, Spreitzer M, Holzer W, Pace V. Direct and Chemoselective Electrophilic Monofluoromethylation of Heteroatoms ( O-, S-, N-, P-, Se-) with Fluoroiodomethane. Org Lett 2020; 22:1345-1349. [PMID: 32004004 PMCID: PMC7205393 DOI: 10.1021/acs.orglett.9b04654] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The commercially available fluoroiodomethane represents a valuable and effective electrophilic source for transferring the CH2F unit to a series of heteroatom-centered nucleophiles under mild basic conditions. The excellent manipulability offered by its liquid physical state (bp 53.4 °C) enables practical and straightforward one-step nucleophilic substitutions to retain the chiral information embodied, thus allowing it to overcome de facto the requirement for fluoromethylating agents with no immediate access. The high-yielding methodology was successfully applied to a variety of nucleophiles including a series of drugs currently in the market.
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Affiliation(s)
- Raffaele Senatore
- University of Vienna , Department of Pharmaceutical Chemistry , Althanstrasse , 14-1090 Vienna , Austria
| | - Monika Malik
- University of Vienna , Department of Pharmaceutical Chemistry , Althanstrasse , 14-1090 Vienna , Austria
| | - Markus Spreitzer
- University of Vienna , Department of Pharmaceutical Chemistry , Althanstrasse , 14-1090 Vienna , Austria
| | - Wolfgang Holzer
- University of Vienna , Department of Pharmaceutical Chemistry , Althanstrasse , 14-1090 Vienna , Austria
| | - Vittorio Pace
- University of Vienna , Department of Pharmaceutical Chemistry , Althanstrasse , 14-1090 Vienna , Austria
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Monticelli S, Holzer W, Langer T, Roller A, Olofsson B, Pace V. Sustainable Asymmetric Organolithium Chemistry: Enantio- and Chemoselective Acylations through Recycling of Solvent, Sparteine, and Weinreb "Amine". CHEMSUSCHEM 2019; 12:1147-1154. [PMID: 30614208 PMCID: PMC6704367 DOI: 10.1002/cssc.201802815] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 12/20/2018] [Indexed: 05/10/2023]
Abstract
The well-established Hoppe-Beak chemistry, which involves enantioselective generation of organolithium compounds in the presence of (-)-sparteine, was revisited and applied to unprecedented acylations with Weinreb amides to access highly enantioenriched α-oxyketones and cyclic α-aminoketones. Recycling of the sustainable solvent cyclopentyl methyl ether, sparteine, and the released Weinreb "amine" [HNMe(OMe)] was possible through a simple work-up procedure that enabled full recovery of these precious materials. The methodology features a robust scope and flexibility, thus allowing the enantioselective preparation of scaffolds amenable of further derivatization.
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Affiliation(s)
- Serena Monticelli
- Department of Pharmaceutical ChemistryUniversity of ViennaAlthanstrasse,14Vienna1090Austria
| | - Wolfgang Holzer
- Department of Pharmaceutical ChemistryUniversity of ViennaAlthanstrasse,14Vienna1090Austria
| | - Thierry Langer
- Department of Pharmaceutical ChemistryUniversity of ViennaAlthanstrasse,14Vienna1090Austria
| | - Alexander Roller
- X-Ray Structure Analysis CenterUniversity of ViennaWaehringerstrasse 42Vienna1090Austria
| | - Berit Olofsson
- Department of Organic Chemistry, Arrhenius LaboratoryStockholm UniversitySe-106 91StockholmSweden
| | - Vittorio Pace
- Department of Pharmaceutical ChemistryUniversity of ViennaAlthanstrasse,14Vienna1090Austria
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de la Vega-Hernández K, Senatore R, Miele M, Urban E, Holzer W, Pace V. Chemoselective reduction of isothiocyanates to thioformamides mediated by the Schwartz reagent. Org Biomol Chem 2019; 17:1970-1978. [DOI: 10.1039/c8ob02312c] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Thioformamides are easily prepared – under full chemocontrol – through the partial reduction of isothiocyanates with the in situ generated Schwartz reagent.
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Affiliation(s)
| | - Raffaele Senatore
- University of Vienna
- Department of Pharmaceutical Chemistry
- 1090 Vienna
- Austria
| | - Margherita Miele
- University of Vienna
- Department of Pharmaceutical Chemistry
- 1090 Vienna
- Austria
| | - Ernst Urban
- University of Vienna
- Department of Pharmaceutical Chemistry
- 1090 Vienna
- Austria
| | - Wolfgang Holzer
- University of Vienna
- Department of Pharmaceutical Chemistry
- 1090 Vienna
- Austria
| | - Vittorio Pace
- University of Vienna
- Department of Pharmaceutical Chemistry
- 1090 Vienna
- Austria
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