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Bouguenina H, Nicolaou S, Bihan YVL, Bowling EA, Calderon C, Caldwell JJ, Harrington B, Hayes A, McAndrew PC, Mitsopoulos C, Sialana FJ, Scarpino A, Stubbs M, Thapaliya A, Tyagi S, Wang HZ, Wood F, Burke R, Raynaud F, Choudhary J, van Montfort RL, Sadok A, Westbrook TF, Collins I, Chopra R. Erratum: iTAG an optimized IMiD-induced degron for targeted protein degradation in human and murine cells. iScience 2024; 27:109727. [PMID: 38646177 PMCID: PMC11031816 DOI: 10.1016/j.isci.2024.109727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024] Open
Abstract
[This corrects the article DOI: 10.1016/j.isci.2023.107059.].
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2
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Bouguenina H, Scarpino A, O'Hanlon JA, Warne J, Wang HZ, Wah Hak LC, Sadok A, McAndrew PC, Stubbs M, Pierrat OA, Hahner T, Cabry MP, Le Bihan YV, Mitsopoulos C, Sialana FJ, Roumeliotis TI, Burke R, van Montfort RLM, Choudhari J, Chopra R, Caldwell JJ, Collins I. A Degron Blocking Strategy Towards Improved CRL4 CRBN Recruiting PROTAC Selectivity. Chembiochem 2023; 24:e202300351. [PMID: 37418539 DOI: 10.1002/cbic.202300351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/16/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
Small molecules inducing protein degradation are important pharmacological tools to interrogate complex biology and are rapidly translating into clinical agents. However, to fully realise the potential of these molecules, selectivity remains a limiting challenge. Herein, we addressed the issue of selectivity in the design of CRL4CRBN recruiting PROteolysis TArgeting Chimeras (PROTACs). Thalidomide derivatives used to generate CRL4CRBN recruiting PROTACs have well described intrinsic monovalent degradation profiles by inducing the recruitment of neo-substrates, such as GSPT1, Ikaros and Aiolos. We leveraged structural insights from known CRL4CRBN neo-substrates to attenuate and indeed remove this monovalent degradation function in well-known CRL4CRBN molecular glues degraders, namely CC-885 and Pomalidomide. We then applied these design principles on a previously published BRD9 PROTAC (dBRD9-A) and generated an analogue with improved selectivity profile. Finally, we implemented a computational modelling pipeline to show that our degron blocking design does not impact PROTAC-induced ternary complex formation. We believe that the tools and principles presented in this work will be valuable to support the development of targeted protein degradation.
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Affiliation(s)
- Habib Bouguenina
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Andrea Scarpino
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Jack A O'Hanlon
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Justin Warne
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Hannah Z Wang
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Laura Chan Wah Hak
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Amine Sadok
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
- Monte Rosa Therapeutics AG, Aeschenvorstadt 36, 4051, Basel, Switzerland
| | - P Craig McAndrew
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Mark Stubbs
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Olivier A Pierrat
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Tamas Hahner
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Marc P Cabry
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Yann-Vaï Le Bihan
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Costas Mitsopoulos
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Fernando J Sialana
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London, SW3 6JB, UK
| | - Theodoros I Roumeliotis
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London, SW3 6JB, UK
| | - Rosemary Burke
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Rob L M van Montfort
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Jyoti Choudhari
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London, SW3 6JB, UK
| | - Rajesh Chopra
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
- Apple Tree Partners, The Gridiron Building, Suite 6.05, 1 St Pancras Square, London, N1 C 4AG, UK
| | - John J Caldwell
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Ian Collins
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
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Bouguenina H, Nicolaou S, Le Bihan YV, Bowling EA, Calderon C, Caldwell JJ, Harrington B, Hayes A, McAndrew PC, Mitsopoulos C, Sialana FJ, Scarpino A, Stubbs M, Thapaliya A, Tyagi S, Wang HZ, Wood F, Burke R, Raynaud F, Choudhary J, van Montfort RL, Sadok A, Westbrook TF, Collins I, Chopra R. iTAG an optimized IMiD-induced degron for targeted protein degradation in human and murine cells. iScience 2023; 26:107059. [PMID: 37360684 PMCID: PMC10285648 DOI: 10.1016/j.isci.2023.107059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/18/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
To address the limitation associated with degron based systems, we have developed iTAG, a synthetic tag based on IMiDs/CELMoDs mechanism of action that improves and addresses the limitations of both PROTAC and previous IMiDs/CeLMoDs based tags. Using structural and sequence analysis, we systematically explored native and chimeric degron containing domains (DCDs) and evaluated their ability to induce degradation. We identified the optimal chimeric iTAG(DCD23 60aa) that elicits robust degradation of targets across cell types and subcellular localizations without exhibiting the well documented "hook effect" of PROTAC-based systems. We showed that iTAG can also induce target degradation by murine CRBN and enabled the exploration of natural neo-substrates that can be degraded by murine CRBN. Hence, the iTAG system constitutes a versatile tool to degrade targets across the human and murine proteome.
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Affiliation(s)
- Habib Bouguenina
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Stephanos Nicolaou
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Yann-Vaï Le Bihan
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Elizabeth A. Bowling
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cheyenne Calderon
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - John J. Caldwell
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Brinley Harrington
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angela Hayes
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - P. Craig McAndrew
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Costas Mitsopoulos
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Fernando Jr. Sialana
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, UK
| | - Andrea Scarpino
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Mark Stubbs
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Arjun Thapaliya
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Siddhartha Tyagi
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hannah Z. Wang
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Francesca Wood
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Rosemary Burke
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Florence Raynaud
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Jyoti Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, UK
| | - Rob L.M. van Montfort
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Amine Sadok
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Thomas F. Westbrook
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ian Collins
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Rajesh Chopra
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
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Abstract
Drug discovery efforts for new covalent inhibitors have drastically increased in the last few years. The binding mechanism of covalent compounds entails the formation of a chemical bond between their electrophilic warhead group and the protein of interest. The use of moderately reactive warheads targeting nonconserved nucleophilic residues can improve the affinity and selectivity profiles of covalent binders as compared to their non-covalent analogs. Recent advances have also enabled their use as chemical probes to disclose novel and also less tractable targets. Increasing interest in covalent drug discovery prompted the development of new computational tools, including covalent docking methods, that are available to predict the binding mode and affinity of covalent ligands. These tools integrate conventional non-covalent docking and scoring schemes by modeling the newly formed covalent bond and the interactions occurring at the reaction site. In this review, we provide a thorough analysis of state-of-the-art covalent docking programs by highlighting their main features and current limitations. Focusing on the implemented algorithms, we show the differences in handling the formation of the new covalent bond and their relative impact on the prediction. This analysis provides a comprehensive overview of the current technology and suggests future improvements in computer-aided covalent drug design. Finally, discussing successful retrospective and prospective covalent docking-based virtual screening applications, we intend to identify best practices for the drug discovery community.
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Affiliation(s)
- Andrea Scarpino
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Korutja 2, Budapest 1117, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Korutja 2, Budapest 1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Korutja 2, Budapest 1117, Hungary
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Scarpino A, Petri L, Knez D, Imre T, Ábrányi-Balogh P, Ferenczy GG, Gobec S, Keserű GM. WIDOCK: a reactive docking protocol for virtual screening of covalent inhibitors. J Comput Aided Mol Des 2021; 35:223-244. [PMID: 33458809 PMCID: PMC7904743 DOI: 10.1007/s10822-020-00371-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/30/2020] [Indexed: 12/28/2022]
Abstract
Here we present WIDOCK, a virtual screening protocol that supports the selection of diverse electrophiles as covalent inhibitors by incorporating ligand reactivity towards cysteine residues into AutoDock4. WIDOCK applies the reactive docking method (Backus et al. in Nature 534:570–574, 2016) and extends it into a virtual screening tool by introducing facile experimental or computational parametrization and a ligand focused evaluation scheme together with a retrospective and prospective validation against various therapeutically relevant targets. Parameters accounting for ligand reactivity are derived from experimental reaction kinetic data or alternatively from computed reaction barriers. The performance of this docking protocol was first evaluated by investigating compound series with diverse warhead chemotypes against KRASG12C, MurA and cathepsin B. In addition, WIDOCK was challenged on larger electrophilic libraries screened against OTUB2 and NUDT7. These retrospective analyses showed high sensitivity in retrieving experimental actives, by also leading to superior ROC curves, AUC values and better enrichments than the standard covalent docking tool available in AutoDock4 when compound collections with diverse warheads were investigated. Finally, we applied WIDOCK for the prospective identification of covalent human MAO-A inhibitors acting via a new mechanism by binding to Cys323. The inhibitory activity of several predicted compounds was experimentally confirmed and the labelling of Cys323 was proved by subsequent MS/MS measurements. These findings demonstrate the usefulness of WIDOCK as a warhead-sensitive, covalent virtual screening protocol.
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Affiliation(s)
- Andrea Scarpino
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, 1117, Budapest, Hungary
| | - László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, 1117, Budapest, Hungary
| | - Damijan Knez
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Tímea Imre
- MS Metabolomic Research Laboratory, Research Centre for Natural Sciences, Magyar tudósok krt 2, 1117, Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, 1117, Budapest, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, 1117, Budapest, Hungary
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, 1117, Budapest, Hungary.
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Rachman M, Bajusz D, Hetényi A, Scarpino A, Merő B, Egyed A, Buday L, Barril X, Keserű GM. Discovery of a novel kinase hinge binder fragment by dynamic undocking. RSC Med Chem 2020; 11:552-558. [PMID: 33479656 PMCID: PMC7593776 DOI: 10.1039/c9md00519f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/11/2020] [Indexed: 12/17/2022] Open
Abstract
A virtual screening workflow for fragment-sized kinase inhibitors is presented, along with a newly identified and validated hinge binder fragment.
One of the key motifs of type I kinase inhibitors is their interactions with the hinge region of ATP binding sites. These interactions contribute significantly to the potency of the inhibitors; however, only a tiny fraction of the available chemical space has been explored with kinase inhibitors reported in the last twenty years. This paper describes a workflow utilizing docking with rDock and dynamic undocking (DUck) for the virtual screening of fragment libraries in order to identify fragments that bind to the kinase hinge region. We have identified 8-amino-2H-isoquinolin-1-one (MR1), a novel and potent hinge binding fragment, which was experimentally tested on a diverse set of kinases, and is hereby suggested for future fragment growing or merging efforts against various kinases, particularly MELK. Direct binding of MR1 to MELK was confirmed by STD-NMR, and its binding to the ATP-pocket was confirmed by a new competitive binding assay based on microscale thermophoresis.
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Affiliation(s)
- Moira Rachman
- Facultat de Farmàcia and Institut de Biomedicina , Universitat de Barcelona , Av. Joan XXIII 27-31 , 08028 Barcelona , Spain.,Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary .
| | - Dávid Bajusz
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary .
| | - Anasztázia Hetényi
- Department of Medical Chemistry , University of Szeged , Dóm tér 8 , H-6720 Szeged , Hungary
| | - Andrea Scarpino
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary .
| | - Balázs Merő
- Signal Transduction and Functional Genomics Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary
| | - Attila Egyed
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary .
| | - László Buday
- Signal Transduction and Functional Genomics Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary
| | - Xavier Barril
- Facultat de Farmàcia and Institut de Biomedicina , Universitat de Barcelona , Av. Joan XXIII 27-31 , 08028 Barcelona , Spain.,Catalan Institution for Research and Advanced Studies (ICREA) , Passeig Lluís Companys 23 , 08010 Barcelona , Spain
| | - György M Keserű
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar Tudósok Körútja 2 , Budapest 1117 , Hungary .
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Rachman M, Scarpino A, Bajusz D, Pálfy G, Vida I, Perczel A, Barril X, Keserű GM. Front Cover: DUckCov: a Dynamic Undocking‐Based Virtual Screening Protocol for Covalent Binders (ChemMedChem 10/2019). ChemMedChem 2019. [DOI: 10.1002/cmdc.201900263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Moira Rachman
- Facultat de Farmàcia and Institut de BiomedicinaUniversitat de Barcelona Av. Joan XXIII 27–31 08028 Barcelona Spain
- Medicinal Chemistry Research GroupResearch Centre for Natural SciencesHungarian Academy of Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - Andrea Scarpino
- Medicinal Chemistry Research GroupResearch Centre for Natural SciencesHungarian Academy of Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research GroupResearch Centre for Natural SciencesHungarian Academy of Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and Biology & MTA-ELTE Protein Modelling Research GroupEötvös Loránd University Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - István Vida
- Laboratory of Structural Chemistry and Biology & MTA-ELTE Protein Modelling Research GroupEötvös Loránd University Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology & MTA-ELTE Protein Modelling Research GroupEötvös Loránd University Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - Xavier Barril
- Facultat de Farmàcia and Institut de BiomedicinaUniversitat de Barcelona Av. Joan XXIII 27–31 08028 Barcelona Spain
- Catalan Institution for Research and Advanced Studies (ICREA) Passeig Lluís Companys 23 08010 Barcelona Spain
| | - György M. Keserű
- Medicinal Chemistry Research GroupResearch Centre for Natural SciencesHungarian Academy of Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
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8
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Rachman M, Scarpino A, Bajusz D, Pálfy G, Vida I, Perczel A, Barril X, Keserű GM. DUckCov: a Dynamic Undocking-Based Virtual Screening Protocol for Covalent Binders. ChemMedChem 2019; 14:1011-1021. [PMID: 30786178 PMCID: PMC6593427 DOI: 10.1002/cmdc.201900078] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Indexed: 12/25/2022]
Abstract
Thanks to recent guidelines, the design of safe and effective covalent drugs has gained significant interest. Other than targeting non‐conserved nucleophilic residues, optimizing the noncovalent binding framework is important to improve potency and selectivity of covalent binders toward the desired target. Significant efforts have been made in extending the computational toolkits to include a covalent mechanism of protein targeting, like in the development of covalent docking methods for binding mode prediction. To highlight the value of the noncovalent complex in the covalent binding process, here we describe a new protocol using tethered and constrained docking in combination with Dynamic Undocking (DUck) as a tool to privilege strong protein binders for the identification of novel covalent inhibitors. At the end of the protocol, dedicated covalent docking methods were used to rank and select the virtual hits based on the predicted binding mode. By validating the method on JAK3 and KRas, we demonstrate how this fast iterative protocol can be applied to explore a wide chemical space and identify potent targeted covalent inhibitors.
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Affiliation(s)
- Moira Rachman
- Facultat de Farmàcia and Institut de Biomedicina, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028, Barcelona, Spain.,Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Andrea Scarpino
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and Biology & MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
| | - István Vida
- Laboratory of Structural Chemistry and Biology & MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology & MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
| | - Xavier Barril
- Facultat de Farmàcia and Institut de Biomedicina, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
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9
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Ábrányi-Balogh P, Petri L, Imre T, Szijj P, Scarpino A, Hrast M, Mitrović A, Fonovič UP, Németh K, Barreteau H, Roper DI, Horváti K, Ferenczy GG, Kos J, Ilaš J, Gobec S, Keserű GM. A road map for prioritizing warheads for cysteine targeting covalent inhibitors. Eur J Med Chem 2018; 160:94-107. [DOI: 10.1016/j.ejmech.2018.10.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/07/2018] [Accepted: 10/03/2018] [Indexed: 01/01/2023]
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10
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Affiliation(s)
- Andrea Scarpino
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
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11
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Abstract
Dietary, anthropometric, and chronic disease risk factors (CDRF) including blood lipids and blood pressure (BP), were measured in 91 vitamin-mineral supplement users (SU) and nonusers (NU) representing a wide range of athletic interests. Supplements were used by 46 (51%) subjects; 100% of female athletes and 51% of male athletes used supplements while none of a group of 15 control female subjects currently used supplements. Both dietary intake and energy expenditure were measured using 7-day records. Adiposity was determined from body weight, body mass index, and skinfolds. Total cholesterol, high-density lipoprotein cholesterol, serum ferritin, hemoglobin, hematocrit, zinc, copper, and vitamin C were based on 12-hour fasting blood samples. Dietary intake (excluding supplements) for SU tended to be greater than NU for vitamin C, thiamin, riboflavin, niacin, B6, B12, folate, calcium, iron and magnesium. Plasma vitamin C levels were significantly higher among SU than NU of both gender groups (p < 0.05). Although SU may exhibit additional healthy lifestyle practices, lipid profiles for many of these athletes were unfavorable with regard to CDRF.
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Affiliation(s)
- T L Bazzarre
- American Heart Association, National Center, Dallas, TX 75231-4596
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