1
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Zhang Y, Shaabani S, Vowinkel K, Trombetta-Lima M, Sabogal-Guáqueta AM, Chen T, Hoekstra J, Lembeck J, Schmidt M, Decher N, Dömling A, Dolga AM. Novel SK channel positive modulators prevent ferroptosis and excitotoxicity in neuronal cells. Biomed Pharmacother 2024; 171:116163. [PMID: 38242037 DOI: 10.1016/j.biopha.2024.116163] [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: 10/23/2023] [Revised: 01/07/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024] Open
Abstract
Small conductance calcium-activated potassium (SK) channel activity has been proposed to play a role in the pathology of several neurological diseases. Besides regulating plasma membrane excitability, SK channel activation provides neuroprotection against ferroptotic cell death by reducing mitochondrial Ca2+ uptake and reactive oxygen species (ROS). In this study, we employed a multifaceted approach, integrating structure-based and computational techniques, to strategically design and synthesize an innovative class of potent small-molecule SK2 channel modifiers through highly efficient multicomponent reactions (MCRs). The compounds' neuroprotective activity was compared with the well-studied SK positive modulator, CyPPA. Pharmacological SK channel activation by selected compounds confers neuroprotection against ferroptosis at low nanomolar ranges compared to CyPPA, that mediates protection at micromolar concentrations, as shown by an MTT assay, real-time cell impedance measurements and propidium iodide staining (PI). These novel compounds suppress increased mitochondrial ROS and Ca2+ level induced by ferroptosis inducer RSL3. Moreover, axonal degeneration was rescued by these novel SK channel activators in primary mouse neurons and they attenuated glutamate-induced neuronal excitability, as shown via microelectrode array. Meanwhile, functional afterhyperpolarization of the novel SK2 channel modulators was validated by electrophysiological measurements showing more current change induced by the novel modulators than the reference compound, CyPPA. These data support the notion that SK2 channel activation can represent a therapeutic target for brain diseases in which ferroptosis and excitotoxicity contribute to the pathology.
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Affiliation(s)
- Yuequ Zhang
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Shabnam Shaabani
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Kirsty Vowinkel
- Institute of Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, 35037 Marburg, Germany
| | - Marina Trombetta-Lima
- Department of Pharmaceutical Technologies and Biopharmacy, Research Institute of Pharmacy, University of Groningen, the Netherlands
| | | | - Tingting Chen
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Jan Hoekstra
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Jan Lembeck
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Martina Schmidt
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Niels Decher
- Institute of Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, 35037 Marburg, Germany
| | - Alexander Dömling
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands.
| | - Amalia M Dolga
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands.
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2
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Patil P, Zheng Q, Kurpiewska K, Dömling A. The isocyanide S N2 reaction. Nat Commun 2023; 14:5807. [PMID: 37726293 PMCID: PMC10509164 DOI: 10.1038/s41467-023-41253-2] [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: 03/25/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023] Open
Abstract
The SN2 nucleophilic substitution reaction is a vital organic transformation used for drug and natural product synthesis. Nucleophiles like cyanide, oxygen, nitrogen, sulfur, or phosphorous replace halogens or sulfonyl esters, forming new bonds. Isocyanides exhibit unique C-centered lone pair σ and π* orbitals, enabling diverse radical and multicomponent reactions. Despite this, their nucleophilic potential in SN2 reactions remains unexplored. We have uncovered that isocyanides act as versatile nucleophiles in SN2 reactions with alkyl halides. This yields highly substituted secondary amides through in situ nitrilium ion hydrolysis introducing an alternative bond break compared to classical amide synthesis. This novel 3-component process accommodates various isocyanide and electrophile structures, functional groups, scalability, late-stage drug modifications, and complex compound synthesis. This reaction greatly expands chemical diversity, nearly doubling the classical amid coupling's chemical space. Notably, the isocyanide nucleophile presents an unconventional Umpolung amide carbanion synthon (R-NHC(-) = O), an alternative to classical amide couplings.
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Affiliation(s)
- Pravin Patil
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry and Czech Advanced Technology and Research Institute, Palackӯ University in Olomouc, Olomouc, Czech Republic
- Department of Drug Design, University of Groningen, Groningen, The Netherlands
| | - Qiang Zheng
- Department of Drug Design, University of Groningen, Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry, Jagiellonian University, 30-387, Kraków, Poland
| | - Alexander Dömling
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry and Czech Advanced Technology and Research Institute, Palackӯ University in Olomouc, Olomouc, Czech Republic.
- Department of Drug Design, University of Groningen, Groningen, The Netherlands.
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3
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Richard AM, Wong NR, Harris K, Sundar R, Scott EE, Pochapsky TC. Selective steroidogenic cytochrome P450 haem iron ligation by steroid-derived isonitriles. Commun Chem 2023; 6:183. [PMID: 37660137 PMCID: PMC10475101 DOI: 10.1038/s42004-023-00994-3] [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: 02/06/2023] [Accepted: 08/23/2023] [Indexed: 09/04/2023] Open
Abstract
Alkyl isonitriles, R-NC, have previously been shown to ligate the heme (haem) iron of cytochromes P450 in both accessible oxidation states (ferrous, Fe2+, and ferric, Fe3+). Herein, the preparation of four steroid-derived isonitriles and their interactions with several P450s, including the steroidogenic CYP17A1 and CYP106A2, as well as the more promiscuous drug metabolizers CYP3A4 and CYP2D6, is described. It was found that successful ligation of the heme iron by the isonitrile functionality for a given P450 depends on both the position and stereochemistry of the isonitrile on the steroid skeleton. Spectral studies indicate that isonitrile ligation of the ferric heme is stable upon reduction to the ferrous form, with reoxidation resulting in the original complex. A crystallographic structure of CYP17A1 with an isonitrile derived from pregnanalone further confirmed the interaction and identified the absolute stereochemistry of the bound species.
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Affiliation(s)
- Alaina M Richard
- Chemical Biology Program, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Nathan R Wong
- Dept. of Biochemistry, Brandeis University, 415 South St., Waltham, 02454-9110, MA, USA
| | - Kurt Harris
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, 48109-1065, MI, USA
| | - Reethy Sundar
- Dept. of Biochemistry, Brandeis University, 415 South St., Waltham, 02454-9110, MA, USA
| | - Emily E Scott
- Chemical Biology Program, University of Michigan, Ann Arbor, 48109, MI, USA
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, 48109-1065, MI, USA
- Departments of Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Thomas C Pochapsky
- Dept. of Biochemistry, Brandeis University, 415 South St., Waltham, 02454-9110, MA, USA.
- Dept. of Chemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South St, Waltham, 02454-9110, MA, USA.
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4
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Hooshmand SE, Zhang W. Ugi Four-Component Reactions Using Alternative Reactants. Molecules 2023; 28:molecules28041642. [PMID: 36838630 PMCID: PMC9961709 DOI: 10.3390/molecules28041642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
The Ugi four-component reaction (Ugi-4CR) undoubtedly is the most prominent multicomponent reaction (MCRs) that has sparked organic chemists' interest in the field. It has been widely used in the synthesis of diverse heterocycle molecules such as potential drugs, natural product analogs, pseudo peptides, macrocycles, and functional materials. The Ugi-4CRs involve the use of an amine, an aldehyde or ketone, an isocyanide, and a carboxylic acid to produce an α-acetamido carboxamide derivative, which has significantly advanced the field of isocyanide-based MCRs. The so-called intermediate nitrilium ion could be trapped by a nucleophile such as azide, N-hydroxyphthalimide, thiol, saccharin, phenol, water, and hydrogen sulfide instead of the original carboxylic acid to allow for a wide variety of Ugi-type reactions to occur.β In addition to isocyanide, there are alternative reagents for the other three components: amine, isocyanide, and aldehyde or ketone. All these alternative components render the Ugi reaction an aptly diversity-oriented synthesis of a myriad of biologically active molecules and complex scaffolds. Consequently, this review will delve deeper into alternative components used in the Ugi MCRs, particularly over the past ten years.
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Affiliation(s)
- Seyyed Emad Hooshmand
- Department of Chemistry, Faculty of Physics and Chemistry, Alzahra University, Tehran 1993893973, Iran
| | - Wei Zhang
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125, USA
- Correspondence: ; Tel.: +1-617-287-6147
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5
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A Brief Review: Advancement in the Synthesis of Amine through the Leuckart Reaction. REACTIONS 2023. [DOI: 10.3390/reactions4010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
This review presents a summary of reactions that take place during the “Leuckart-type reaction”. The significance of, as well as recent advancements in, the synthesis of amines through simple and inexpensive methods using readily available raw materials is discussed. This review includes all catalytic and noncatalytic reactions that involve the Leuckart method. Recent studies have shown that at least a quarter of C–N bond-forming reactions in the pharmaceutical industry are occur with the support of reductive amination. Recently, experimental conditions have achieved excellent yields. The “Leuckart-type reaction” is technically associated with Eschweiler–Clarke methylation. Compounds are grouped in accordance with the precept of action. This includes drugs affecting the central nervous system, cardiovascular system and gastrointestinal tract; anticancer drugs, antibiotics, antiviral and antifungal drugs; drugs affecting anxiety; convulsant, biotic, and HIV drugs; and antidiabetic drugs. Therefore, this review supports the development of the Leuckart-type preparation of nitrogenous compounds, as well as their advancement in other areas of human development.
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6
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Singh M, Vaishali, Jamra R, Deepika, Kumar S, Singh V. Iodine‐Catalysed Synthesis of β‐Carboline Tethered α‐Amino Amidines Through Ugi‐Type Multicomponent Reaction. ChemistrySelect 2022. [DOI: 10.1002/slct.202202392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Manpreet Singh
- Department of Chemistry Baba Farid Group of Institutions Bathinda Punjab 151001 India
| | - Vaishali
- Department of Chemistry Dr B. R. Ambedkar National Institute of Technology (NIT) Jalandhar Punjab India 144011
| | - Rahul Jamra
- Department of Chemistry Dr B. R. Ambedkar National Institute of Technology (NIT) Jalandhar Punjab India 144011
- Department of Chemistry Central University of Punjab Bathinda Punjab India 151401
| | - Deepika
- Department of Chemistry Dr B. R. Ambedkar National Institute of Technology (NIT) Jalandhar Punjab India 144011
| | - Sunit Kumar
- Department of Chemistry Dr B. R. Ambedkar National Institute of Technology (NIT) Jalandhar Punjab India 144011
| | - Virender Singh
- Department of Chemistry Dr B. R. Ambedkar National Institute of Technology (NIT) Jalandhar Punjab India 144011
- Department of Chemistry Central University of Punjab Bathinda Punjab India 151401
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7
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Grychowska K, Olejarz-Maciej A, Blicharz K, Pietruś W, Karcz T, Kurczab R, Koczurkiewicz P, Doroz-Płonka A, Latacz G, Keeri AR, Piska K, Satała G, Pęgiel J, Trybała W, Jastrzębska-Więsek M, Bojarski AJ, Lamaty F, Partyka A, Walczak M, Krawczyk M, Malikowska-Racia N, Popik P, Zajdel P. Overcoming undesirable hERG affinity by incorporating fluorine atoms: A case of MAO-B inhibitors derived from 1 H-pyrrolo-[3,2-c]quinolines. Eur J Med Chem 2022; 236:114329. [DOI: 10.1016/j.ejmech.2022.114329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/24/2022] [Accepted: 03/26/2022] [Indexed: 11/16/2022]
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8
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Affiliation(s)
- Qiang Zheng
- Department of Drug Design University of Groningen Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry Jagiellonian University 30-387 Kraków Poland
| | - Alexander Dömling
- Department of Drug Design University of Groningen Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
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9
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Bhat SI, Kigga M, Heravi MM. Multicomponent Reactions Based on In Situ Generated Isocyanides for the Construction of Heterocycles. Chem Heterocycl Compd (N Y) 2021. [DOI: 10.1007/s10593-021-02972-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Wang Q, Mgimpatsang KC, Li X, Dömling A. Isoquinolone-4-Carboxylic Acids by Ammonia-Ugi-4CR and Copper-Catalyzed Domino Reaction. J Org Chem 2021; 86:9771-9780. [PMID: 34184894 PMCID: PMC8291606 DOI: 10.1021/acs.joc.1c01170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Highly substituted isoquinolone-4-carboxylic
acid is an important
bioactive scaffold; however, it is challenging to access it in a general
and short way. A Cu-catalyzed cascade reaction was successfully designed
involving the Ugi postcyclization strategy by using ammonia and 2-halobenzoic
acids as crucial building blocks. Privileged polysubstituted isoquinolin-1(2H)-ones were constructed in a combinatorial format with
generally moderate to good yields. The protocol, with a ligand-free
catalytic system, shows a broad substrate scope and good functional
group tolerance toward excellent molecular diversity. Free 4-carboxy-isoquinolone
is now for the first time generally accessible by a convergent multicomponent
reaction protocol.
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Affiliation(s)
- Qian Wang
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Kumchok C Mgimpatsang
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Xin Li
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, Groningen 9713 AV, The Netherlands
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11
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Dömling A, Neochoritis CG, Lei X, Thomaidi M, Angeli GK. Fluorene-Based Multicomponent Reactions. Synlett 2021. [DOI: 10.1055/a-1471-9080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractFluorene and fluorenone are privileged structures with extensive utility in both materials science and drug discovery. Here, we describe syntheses of those moieties through isocyanide-based multicomponent reactions (IMCRs) and the incorporation of the products in diverse and complex derivatives that can be further utilized. We performed six different IMCRs, based on the dual functionality of 9-isocyano-9H-fluorene, and we describe 23 unprecedented adducts.
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Affiliation(s)
| | | | - Xiaofang Lei
- Department of Chemistry, University of Crete
- Department of Pharmacy, Drug Design Group, University of Groningen
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12
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Srinivasulu C, Sagar NR, Vishwanatha TM, Durgamma S, Sureshbabu VV. Synthesis of N β-Protected Amino Sulfenyl Methyl Formamides and Sulfonyl Methyl Formamides: A Simple Protocol. ACS OMEGA 2021; 6:4680-4686. [PMID: 33644575 PMCID: PMC7905828 DOI: 10.1021/acsomega.0c05419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
Chiral amino acid-derived formamides represent one of the most versatile components in multicomponent reactions. Herein, we describe a facile synthesis of Nβ-protected amino sulfenyl methyl formamides and sulfonyl methyl formamides via the Mannich reaction of Nα-protected amino alkyl thiols followed by oxidation using 3-chloroperbenzoic acid (m-CPBA). This protocol is applicable to a wide range of Fmoc- and Cbz-protected amino acids. Notably, the reaction provides high yield and retains the stereochemistry of the chiral center of the starting component.
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13
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Sutanto F, Shaabani S, Neochoritis CG, Zarganes-Tzitzikas T, Patil P, Ghonchepour E, Dömling A. Multicomponent reaction-derived covalent inhibitor space. SCIENCE ADVANCES 2021; 7:eabd9307. [PMID: 33536213 PMCID: PMC7857676 DOI: 10.1126/sciadv.abd9307] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/15/2020] [Indexed: 05/16/2023]
Abstract
The area of covalent inhibitors is gaining momentum due to recently introduced clinical drugs, but libraries of these compounds are scarce. Multicomponent reaction (MCR) chemistry is well known for its easy access to a very large and diverse chemical space. Here, we show that MCRs are highly suitable to generate libraries of electrophiles based on different scaffolds and three-dimensional shapes and highly compatible with multiple functional groups. According to the building block principle of MCR, acrylamide, acrylic acid ester, sulfurylfluoride, chloroacetic acid amide, nitrile, and α,β-unsaturated sulfonamide warheads can be easily incorporated into many different scaffolds. We show examples of each electrophile on 10 different scaffolds on a preparative scale as well as in a high-throughput synthesis mode on a nanoscale to produce libraries of potential covalent binders in a resource- and time-saving manner. Our operational procedure is simple, mild, and step economical to facilitate future covalent library synthesis.
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Affiliation(s)
- Fandi Sutanto
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Shabnam Shaabani
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | | | - Tryfon Zarganes-Tzitzikas
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Pravin Patil
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Ehsan Ghonchepour
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9700 AD Groningen, The Netherlands.
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14
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Konstantinidou M, Magari F, Sutanto F, Haupenthal J, Jumde VR, Ünver MY, Heine A, Camacho CJ, Hirsch AKH, Klebe G, Dömling A. Rapid Discovery of Aspartyl Protease Inhibitors Using an Anchoring Approach. ChemMedChem 2020; 15:680-684. [PMID: 32187447 PMCID: PMC7317454 DOI: 10.1002/cmdc.202000024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/20/2020] [Indexed: 11/11/2022]
Abstract
Pharmacophore searches that include anchors, fragments contributing above average to receptor binding, combined with one‐step syntheses are a powerful approach for the fast discovery of novel bioactive molecules. Here, we are presenting a pipeline for the rapid and efficient discovery of aspartyl protease inhibitors. First, we hypothesized that hydrazine could be a multi‐valent warhead to interact with the active site Asp carboxylic acids. We incorporated the hydrazine anchor in a multicomponent reaction and created a large virtual library of hydrazine derivatives synthetically accessible in one‐step. Next, we performed anchor‐based pharmacophore screening of the libraries and resynthesized top‐ranked compounds. The inhibitory potency of the molecules was finally assessed by an enzyme activity assay and the binding mode confirmed by several soaked crystal structures supporting the validity of the hypothesis and approach. The herein reported pipeline of tools will be of general value for the rapid generation of receptor binders beyond Asp proteases.
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Affiliation(s)
- Markella Konstantinidou
- Department of Pharmacy Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Francesca Magari
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Fandi Sutanto
- Department of Pharmacy Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Jörg Haupenthal
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Varsha R Jumde
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - M Yagiz Ünver
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Carlos Jamie Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Anna K H Hirsch
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Alexander Dömling
- Department of Pharmacy Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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15
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Konstandaras N, Dunn MH, Guerry MS, Barnett CD, Cole ML, Harper JB. The impact of cation structure upon the acidity of triazolium salts in dimethyl sulfoxide. Org Biomol Chem 2019; 18:66-75. [PMID: 31746919 DOI: 10.1039/c9ob02258a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A series of triazolium salts, selected for their varying electronic and steric properties, were prepared and their pKa values were determined in DMSO at 25 °C using the bracketing indicator method. The effect of each systematic structural variation upon the acidity of the triazolium cation has been considered, in particular examining the effects of systematically altering electronic properties, quantified through the use of Hammett σ parameters. The first pKa value for an azolium salt that generates a mesionic carbene is also reported. These new data allow for the selection of appropriate bases for the deprotonation of such triazolium salts and the potential to correlate the pKa values determined herein with the nucleophilicity of the corresponding carbenes.
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16
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Boltjes A, Dömling A. The Groebke-Blackburn-Bienaymé Reaction. EUROPEAN JOURNAL OF CHEMISTRY (PRINT) 2019; 2019:7007-7049. [PMID: 34012704 PMCID: PMC8130801 DOI: 10.1002/ejoc.201901124] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Indexed: 12/23/2022]
Abstract
Imidazo[1,2-a]pyridine is a well-known scaffold in many marketed drugs, such as Zolpidem, Minodronic acid, Miroprofen and DS-1 and it also serves as a broadly applied pharmacophore in drug discovery. The scaffold revoked a wave of interest when Groebke, Blackburn and Bienaymé reported independently a new three component reaction resulting in compounds with the imidazo[1,2-a]-heterocycles as a core structure. During the course of two decades the Groebke Blackburn Bienaymé (GBB-3CR) reaction has emerged as a very important multicomponent reaction (MCR), resulting in over a hundred patents and a great number of publications in various fields of interest. Now two compounds derived from GBB-3CR chemistry received FDA approval. To celebrate the first 20 years of GBB-chemistry, we present an overview of the chemistry of the GBB-3CR, including an analysis of each of the three starting material classes, solvents and catalysts. Additionally, a list of patents and their applications and a more in-depth summary of the biological targets that were addressed, including structural biology analysis, is given.
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Affiliation(s)
- André Boltjes
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, The Netherlands
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17
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Hitting on the move: Targeting intrinsically disordered protein states of the MDM2-p53 interaction. Eur J Med Chem 2019; 182:111588. [PMID: 31421630 DOI: 10.1016/j.ejmech.2019.111588] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/22/2019] [Accepted: 08/04/2019] [Indexed: 01/17/2023]
Abstract
Intrinsically disordered proteins are an emerging class of proteins without a folded structure and currently disorder-based drug targeting remains a challenge. p53 is the principal regulator of cell division and growth whereas MDM2 consists its main negative regulator. The MDM2-p53 recognition is a dynamic and multistage process that amongst other, employs the dissociation of a transient α-helical N-terminal ''lid'' segment of MDM2 from the proximity of the p53-complementary interface. Several small molecule inhibitors have been reported to inhibit the formation of the p53-MDM2 complex with the vast majority mimicking the p53 residues Phe19, Trp23 and Leu26. Recently, we have described the transit from the 3-point to 4-point pharmacophore model stabilizing this intrinsically disordered N-terminus by increasing the binding affinity by a factor of 3. Therefore, we performed a thorough SAR analysis, including chiral separation of key compound which was evaluated by FP and 2D NMR. Finally, p53-specific anti-cancer activity towards p53-wild-type cancer cells was observed for several representative compounds.
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18
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Neochoritis CG, Shaabani S, Ahmadianmoghaddam M, Zarganes-Tzitzikas T, Gao L, Novotná M, Mitríková T, Romero AR, Irianti MI, Xu R, Olechno J, Ellson R, Helan V, Kossenjans M, Groves MR, Dömling A. Rapid approach to complex boronic acids. SCIENCE ADVANCES 2019; 5:eaaw4607. [PMID: 31281893 PMCID: PMC6611686 DOI: 10.1126/sciadv.aaw4607] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/30/2019] [Indexed: 05/28/2023]
Abstract
The compatibility of free boronic acid building blocks in multicomponent reactions to readily create large libraries of diverse and complex small molecules was investigated. Traditionally, boronic acid synthesis is sequential, synthetically demanding, and time-consuming, which leads to high target synthesis times and low coverage of the boronic acid chemical space. We have performed the synthesis of large libraries of boronic acid derivatives based on multiple chemistries and building blocks using acoustic dispensing technology. The synthesis was performed on a nanomole scale with high synthesis success rates. The discovery of a protease inhibitor underscores the usefulness of the approach. Our acoustic dispensing-enabled chemistry paves the way to highly accelerated synthesis and miniaturized reaction scouting, allowing access to unprecedented boronic acid libraries.
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Affiliation(s)
- Constantinos G. Neochoritis
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Shabnam Shaabani
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Maryam Ahmadianmoghaddam
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Tryfon Zarganes-Tzitzikas
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Li Gao
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Michaela Novotná
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Tatiana Mitríková
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Atilio Reyes Romero
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Marina Ika Irianti
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Ruixue Xu
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Joe Olechno
- Labcyte Inc., 170 Rose Orchard Way, San Jose, CA 95134, USA
| | - Richard Ellson
- Labcyte Inc., 170 Rose Orchard Way, San Jose, CA 95134, USA
| | - Victoria Helan
- Hit Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Gothenburg SE-43183, Sweden
| | - Michael Kossenjans
- Hit Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Gothenburg SE-43183, Sweden
| | - Matthew R. Groves
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Alexander Dömling
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
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19
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Abstract
Tetrazole derivatives are a prime class of heterocycles, very important to medicinal chemistry and drug design due to not only their bioisosterism to carboxylic acid and amide moieties but also to their metabolic stability and other beneficial physicochemical properties. Although more than 20 FDA-approved drugs contain 1 H- or 2 H-tetrazole substituents, their exact binding mode, structural biology, 3D conformations, and in general their chemical behavior is not fully understood. Importantly, multicomponent reaction (MCR) chemistry offers convergent access to multiple tetrazole scaffolds providing the three important elements of novelty, diversity, and complexity, yet MCR pathways to tetrazoles are far from completely explored. Here, we review the use of multicomponent reactions for the preparation of substituted tetrazole derivatives. We highlight specific applications and general trends holding therein and discuss synthetic approaches and their value by analyzing scope and limitations, and also enlighten their receptor binding mode. Finally, we estimated the prospects of further research in this field.
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Affiliation(s)
- Constantinos G. Neochoritis
- Drug Design Group, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Ting Zhao
- Drug Design Group, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Alexander Dömling
- Drug Design Group, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
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20
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Neochoritis CG, Ghonchepour E, Miraki MK, Zarganes-Tzitzikas T, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Structure and Reactivity of Glycosyl Isocyanides. European J Org Chem 2019; 2019:50-55. [PMID: 33981183 DOI: 10.1002/ejoc.201801588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
3D structural information was obtained from mono-, di- and trisaccharide formamide and isocyanide derivatives by analysis of their X-ray crystal structure and NMR spectroscopy. The isocyanide anomeric effect was observed. Data mining of the Cambridge Structural Database (CSD) was performed and statistically confirmed our findings. Application of the glycoside isocyanides in the synthesis of novel glycoconjugates as drug-like scaffolds by MCR chemistry underscores the usefulness of the novel building blocks.
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Affiliation(s)
- Constantinos G Neochoritis
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ehsan Ghonchepour
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Maryam Kazemi Miraki
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Tryfon Zarganes-Tzitzikas
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University, Ingardena Street 3, 30-060 Kraków, Poland
| | | | - Alexander Dömling
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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21
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Skachilova SY, Zheltukhin NK, Sergeev VN, Davydova NK. Reductive Amination of Sterically Hindered Arylaminoketones Using a Modified Leuckart Reaction. Pharm Chem J 2018. [DOI: 10.1007/s11094-018-1857-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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22
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Estrada-Ortiz N, Neochoritis CG, Twarda-Clapa A, Musielak B, Holak TA, Dömling A. Artificial Macrocycles as Potent p53-MDM2 Inhibitors. ACS Med Chem Lett 2017; 8:1025-1030. [PMID: 29057045 PMCID: PMC5641952 DOI: 10.1021/acsmedchemlett.7b00219] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/20/2017] [Indexed: 11/28/2022] Open
Abstract
Based on a combination of an Ugi four component reaction and a ring closing metathesis, a library of novel artificial macrocyclic inhibitors of the p53-MDM2 interaction was designed and synthesized. These macrocycles, alternatively to stapled peptides, target for the first time the large hydrophobic surface area formed by Tyr67, Gln72, His73, Val93, and Lys94 yielding derivatives with affinity to MDM2 in the nanomolar range. Their binding affinity with MDM2 was evaluated using fluorescence polarization (FP) assay and 1H-15N two-dimensional HSQC nuclear magnetic resonance experiments.
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Affiliation(s)
- Natalia Estrada-Ortiz
- Department of Drug
Design, University of Groningen, A. Deusinglaan 1, Groningen 9700AV, The Netherlands
| | | | - Aleksandra Twarda-Clapa
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska Centre
of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Bogdan Musielak
- Department of Chemistry, Jagiellonian University, Ingardena
3, 30-060 Krakow, Poland
| | - Tad A. Holak
- Malopolska Centre
of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
- Department of Chemistry, Jagiellonian University, Ingardena
3, 30-060 Krakow, Poland
| | - Alexander Dömling
- Department of Drug
Design, University of Groningen, A. Deusinglaan 1, Groningen 9700AV, The Netherlands
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23
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Karawajczyk A, Orrling KM, de Vlieger JSB, Rijnders T, Tzalis D. The European Lead Factory: A Blueprint for Public-Private Partnerships in Early Drug Discovery. Front Med (Lausanne) 2017; 3:75. [PMID: 28154815 PMCID: PMC5243859 DOI: 10.3389/fmed.2016.00075] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 12/23/2016] [Indexed: 11/17/2022] Open
Abstract
The European Lead Factory (ELF) is a public–private partnership (PPP) that provides researchers in Europe with a unique platform for translation of innovative biology and chemistry into high-quality starting points for drug discovery. It combines an exceptional collection of small molecules, high-throughput screening (HTS) infrastructure, and hit follow-up capabilities to advance research projects from both private companies and publicly funded researchers. By active interactions with the wider European life science community, ELF connects and unites bright ideas, talent, and experience from several disciplines. As a result, ELF is a unique, collaborative lead generation engine that has so far resulted in >4,500 hit compounds with a defined biological activity from 83 successfully completed HTS and hit evaluation campaigns. The PPP has also produced more than 120,000 novel innovative library compounds that complement the 327,000 compounds contributed by the participating pharmaceutical companies. Intrinsic to its setup, ELF enables breakthroughs in areas with unmet medical and societal needs, where no individual entity would be able to create a comparable impact in such a short time.
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24
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Neochoritis CG, Livadiotou D, Tsiaras V, Zarganes-Tzitzikas T, Samatidou E. The indoleacetic acids in IMCRs: a three-component Ugi reaction involving TosMIC. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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25
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Karawajczyk A, Giordanetto F, Benningshof J, Hamza D, Kalliokoski T, Pouwer K, Morgentin R, Nelson A, Müller G, Piechot A, Tzalis D. Expansion of chemical space for collaborative lead generation and drug discovery: the European Lead Factory Perspective. Drug Discov Today 2015; 20:1310-6. [PMID: 26429298 DOI: 10.1016/j.drudis.2015.09.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/02/2015] [Accepted: 09/11/2015] [Indexed: 01/06/2023]
Abstract
High-throughput screening (HTS) represents a major cornerstone of drug discovery. The availability of an innovative, relevant and high-quality compound collection to be screened often dictates the final fate of a drug discovery campaign. Given that the chemical space to be sampled in research programs is practically infinite and sparsely populated, significant efforts and resources need to be invested in the generation and maintenance of a competitive compound collection. The European Lead Factory (ELF) project is addressing this challenge by leveraging the diverse experience and know-how of academic groups and small and medium enterprises (SMEs) engaged in synthetic and/or medicinal chemistry. Here, we describe the novelty, diversity, structural complexity, physicochemical characteristics and overall attractiveness of this first batch of ELF compounds for HTS purposes.
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Affiliation(s)
- Anna Karawajczyk
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Str. 76a, 44227 Dortmund, Germany
| | | | | | - Daniel Hamza
- Sygnature Discovery, BioCity, Nottingham NG1 1GF, UK
| | - Tuomo Kalliokoski
- Lead Discovery Center GmbH, Otto-Hahn-Strabe 15, 44227 Dortmund, Germany
| | - Kees Pouwer
- Syncom BV, Kadijk 3, 9747 AT Groningen, The Netherlands
| | | | - Adam Nelson
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Gerhard Müller
- Mercachem, Kerkenbos 1013, 6546 BB Nijmegen, The Netherlands
| | - Alexander Piechot
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Str. 76a, 44227 Dortmund, Germany
| | - Dimitrios Tzalis
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Str. 76a, 44227 Dortmund, Germany.
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