151
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Hamuro Y, Coales SJ. Hydrogen/Deuterium Exchange Mass Spectrometry for Weak Binders. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:735-739. [PMID: 35230104 DOI: 10.1021/jasms.1c00375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This note describes theoretical and experimental considerations to observe perturbation of a protein upon binding to a ligand with weak affinity by hydrogen/deuterium exchange mass spectrometry (HDX-MS). The most popular application of HDX-MS is to determine the binding site of a drug or drug lead in a protein target. However, when the affinity of a ligand is weak, driving the equilibrium to the formation of a complex is difficult, and thus, observing the perturbation upon binding is also challenging. Theoretical consideration indicates that the original concentration of a ligand over the dissociation constant ([L0]/KD) is roughly equal to the maximum protection factor expected for the experiment when the original concentration of a ligand is significantly larger than the original concentration of a protein and the dissociation constant ([L0] ≫ [P0] and [L0] ≫ KD). When HDX-MS analysis of a protein with a ligand of low affinity and low solubility is carried out, it may be challenging to achieve high enough ligand concentration to drive the equilibrium in favor of the complex due to the low solubility. There are two methods to alleviate this issue: (i) spiking a low affinity/low solubility ligand to exchange buffer to lower the required ligand concentration in aqueous protein stock solution and (ii) mixing a 1:1 ratio of aqueous protein-ligand stock solution and deuterated buffer to initiate the exchange reaction instead of the commonly used 1:9 ratio.
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Affiliation(s)
- Yoshitomo Hamuro
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, New Jersey 08852, United States
| | - Stephen J Coales
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, New Jersey 08852, United States
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152
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Shi B, Zhou Y, Li X. Recent advances in DNA-encoded dynamic libraries. RSC Chem Biol 2022; 3:407-419. [PMID: 35441147 PMCID: PMC8985084 DOI: 10.1039/d2cb00007e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/16/2022] [Indexed: 11/21/2022] Open
Abstract
The DNA-encoded chemical library (DEL) has emerged as a powerful technology platform in drug discovery and is also gaining momentum in academic research. The rapid development of DNA-/DEL-compatible chemistries has greatly expanded the chemical space accessible to DELs. DEL technology has been widely adopted in the pharmaceutical industry and a number of clinical drug candidates have been identified from DEL selections. Recent innovations have combined DELs with other legacy and emerging techniques. Among them, the DNA-encoded dynamic library (DEDL) introduces DNA encoding into the classic dynamic combinatorial libraries (DCLs) and also integrates the principle of fragment-based drug discovery (FBDD), making DEDL a novel approach with distinct features from static DELs. In this Review, we provide a summary of the recently developed DEDL methods and their applications. Future developments in DEDLs are expected to extend the application scope of DELs to complex biological systems with unique ligand-discovery capabilities.
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Affiliation(s)
- Bingbing Shi
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, Jining Medical University Jining Shandong 272067 P. R. China
| | - Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission Units 1503-1511 15/F. Building 17W Hong Kong SAR China
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153
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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154
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Arif SM, Floto RA, Blundell TL. Using Structure-guided Fragment-Based Drug Discovery to Target Pseudomonas aeruginosa Infections in Cystic Fibrosis. Front Mol Biosci 2022; 9:857000. [PMID: 35433835 PMCID: PMC9006449 DOI: 10.3389/fmolb.2022.857000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Cystic fibrosis (CF) is progressive genetic disease that predisposes lungs and other organs to multiple long-lasting microbial infections. Pseudomonas aeruginosa is the most prevalent and deadly pathogen among these microbes. Lung function of CF patients worsens following chronic infections with P. aeruginosa and is associated with increased mortality and morbidity. Emergence of multidrug-resistant, extensively drug-resistant and pandrug-resistant strains of P. aeruginosa due to intrinsic and adaptive antibiotic resistance mechanisms has failed the current anti-pseudomonal antibiotics. Hence new antibacterials are urgently needed to treat P. aeruginosa infections. Structure-guided fragment-based drug discovery (FBDD) is a powerful approach in the field of drug development that has succeeded in delivering six FDA approved drugs over the past 20 years targeting a variety of biological molecules. However, FBDD has not been widely used in the development of anti-pseudomonal molecules. In this review, we first give a brief overview of our structure-guided FBDD pipeline and then give a detailed account of FBDD campaigns to combat P. aeruginosa infections by developing small molecules having either bactericidal or anti-virulence properties. We conclude with a brief overview of the FBDD efforts in our lab at the University of Cambridge towards targeting P. aeruginosa infections.
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Affiliation(s)
| | - R. Andres Floto
- Molecular Immunity Unit, Department of Medicine University of Cambridge, MRC-Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Tom L. Blundell,
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155
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Revillo Imbernon J, Jacquemard C, Bret G, Marcou G, Kellenberger E. Comprehensive analysis of commercial fragment libraries. RSC Med Chem 2022; 13:300-310. [PMID: 35434627 PMCID: PMC8942207 DOI: 10.1039/d1md00363a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/22/2021] [Indexed: 12/26/2022] Open
Abstract
Screening of fragment libraries is a valuable approach to the drug discovery process. The quality of the library is one of the keys to success, and more particularly the design or choice of a library has to meet the specificities of the research program. In this study, we made an inventory of the commercial fragment libraries and we established a methodology which allows any library to be positioned in relation to the complete offer currently on the market, by addressing the following questions: does this chemical library look like another chemical library? What is the coverage of the current chemical space by this chemical library? What are the characteristic structural features of the fragments of this chemical library? We based our analysis on 2D and 3D chemical descriptors, framework class generation and the generative topographic map. We identified 59 270 scaffolds, which can be searched in a dedicated web site (https://gtmfrag.drugdesign.unistra.fr) and developed a model which accounts for fragment diversity while being easy to interpret (download at 10.5281/zenodo.5534434).
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Affiliation(s)
- Julia Revillo Imbernon
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
| | - Célien Jacquemard
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
| | - Guillaume Bret
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
| | - Gilles Marcou
- Laboratory of Chemoinformatics, UMR7177 CNRS Université de StrasbourgStrasbourgFrance
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
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156
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Hamilton DJ, Beemsterboer M, Carter CM, Elsayed J, Huiberts REM, Klein HF, O’Brien P, de Esch IJP, Wijtmans M. Puckering the planar landscape of fragments: design and synthesis of a 3D cyclobutane fragment library. ChemMedChem 2022; 17:e202200113. [PMID: 35277937 PMCID: PMC9315009 DOI: 10.1002/cmdc.202200113] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Indexed: 11/24/2022]
Abstract
Fragment‐based drug discovery (FBDD) has a growing need for unique screening libraries. The cyclobutane moiety was identified as an underrepresented yet attractive three‐dimensional (3D) scaffold. Synthetic strategies were developed via a key 3‐azido‐cyclobutanone intermediate, giving potential access to a range of functional groups with accessible growth vectors. A focused set of 33 novel 3D cyclobutane fragments was synthesised, comprising three functionalities: secondary amines, amides, and sulfonamides. This library was designed using Principal Component Analysis (PCA) and an expanded version of the rule of three (RO3), followed by Principal Moment of Inertia (PMI) analysis to achieve both chemical diversity and high 3D character. Cis and trans ring isomers of library members were generated to maximise the shape diversity obtained, while limiting molecular complexity through avoiding enantiomers. Property analyses of the cyclobutane library indicated that it fares favourably against existing synthetic 3D fragment libraries in terms of shape and physicochemical properties.
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Affiliation(s)
- David J. Hamilton
- Vrije Universiteit Amsterdam Chemistry and Pharmaceutical Sciences NETHERLANDS
| | | | - Caroline M. Carter
- Vrije Universiteit Amsterdam Chemistry and Pharmaceutical Sciences NETHERLANDS
| | - Jasmina Elsayed
- Vrije Universiteit Amsterdam Chemistry and Pharmaceutical Sciences NETHERLANDS
| | | | - Hanna F. Klein
- University of York Department of Chemistry UNITED KINGDOM
| | - Peter O’Brien
- University of York Department of Chemistry UNITED KINGDOM
| | - Iwan J. P. de Esch
- Vrije Universiteit Amsterdam Chemistry and Pharmaceutical Sciences NETHERLANDS
| | - Maikel Wijtmans
- Vrije Universiteit Amsterdam Chemistry & Pharamceutical Sciences De Boelelaan 1083 1081 HV Amsterdam NETHERLANDS
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157
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The current toolbox for APOBEC drug discovery. Trends Pharmacol Sci 2022; 43:362-377. [PMID: 35272863 PMCID: PMC9018551 DOI: 10.1016/j.tips.2022.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/03/2022] [Accepted: 02/09/2022] [Indexed: 12/14/2022]
Abstract
Mutational processes driving genome evolution and heterogeneity contribute to immune evasion and therapy resistance in viral infections and cancer. APOBEC3 (A3) enzymes promote such mutations by catalyzing the deamination of cytosines to uracils in single-stranded DNA. Chemical inhibition of A3 enzymes may yield an antimutation therapeutic strategy to improve the durability of current drug therapies that are prone to resistance mutations. A3 small-molecule drug discovery efforts to date have been restricted to a single high-throughput biochemical activity assay; however, the arsenal of discovery assays has significantly expanded in recent years. The assays used to study A3 enzymes are reviewed here with an eye towards their potential for small-molecule discovery efforts.
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158
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Alarcon-Barrera JC, Kostidis S, Ondo-Mendez A, Giera M. Recent advances in metabolomics analysis for early drug development. Drug Discov Today 2022; 27:1763-1773. [PMID: 35218927 DOI: 10.1016/j.drudis.2022.02.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/25/2022] [Accepted: 02/21/2022] [Indexed: 12/25/2022]
Abstract
The pharmaceutical industry adapted proteomics and other 'omics technologies for drug research early following their initial introduction. Although metabolomics lacked behind in this development, it has now become an accepted and widely applied approach in early drug development. Over the past few decades, metabolomics has evolved from a pure exploratory tool to a more mature and quantitative biochemical technology. Several metabolomics-based platforms are now applied during the early phases of drug discovery. Metabolomics analysis assists in the definition of the physiological response and target engagement (TE) markers as well as elucidation of the mode of action (MoA) of drug candidates under investigation. In this review, we highlight recent examples and novel developments of metabolomics analyses applied during early drug development.
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Affiliation(s)
- Juan Carlos Alarcon-Barrera
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, the Netherlands; Clinical Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
| | - Sarantos Kostidis
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Alejandro Ondo-Mendez
- Clinical Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
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159
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Kaminski JW, Vera L, Stegmann DP, Vering J, Eris D, Smith KML, Huang CY, Meier N, Steuber J, Wang M, Fritz G, Wojdyla JA, Sharpe ME. Fast fragment- and compound-screening pipeline at the Swiss Light Source. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:328-336. [PMID: 35234147 PMCID: PMC8900825 DOI: 10.1107/s2059798322000705] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/19/2022] [Indexed: 11/10/2022]
Abstract
Over the last two decades, fragment-based drug discovery (FBDD) has emerged as an effective and efficient method to identify new chemical scaffolds for the development of lead compounds. X-ray crystallography can be used in FBDD as a tool to validate and develop fragments identified as binders by other methods. However, it is also often used with great success as a primary screening technique. In recent years, technological advances at macromolecular crystallography beamlines in terms of instrumentation, beam intensity and robotics have enabled the development of dedicated platforms at synchrotron sources for FBDD using X-ray crystallography. Here, the development of the Fast Fragment and Compound Screening (FFCS) platform, an integrated next-generation pipeline for crystal soaking, handling and data collection which allows crystallography-based screening of protein crystals against hundreds of fragments and compounds, at the Swiss Light Source is reported.
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160
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Mureddu LG, Vuister GW. Fragment-Based Drug Discovery by NMR. Where Are the Successes and Where can It Be Improved? Front Mol Biosci 2022; 9:834453. [PMID: 35252355 PMCID: PMC8895297 DOI: 10.3389/fmolb.2022.834453] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Over the last century, the definitions of pharmaceutical drug and drug discovery have changed considerably. Evolving from an almost exclusively serendipitous approach, drug discovery nowadays involves several distinct, yet sometimes interconnected stages aimed at obtaining molecules able to interact with a defined biomolecular target, and triggering a suitable biological response. At each of the stages, a wide range of techniques are typically employed to obtain the results required to move the project into the next stage. High Throughput Screening (HTS) and Fragment Based Drug Design (FBDD) are the two main approaches used to identify drug-like candidates in the early stages of drug discovery. Nuclear Magnetic Resonance (NMR) spectroscopy has many applications in FBDD and is used extensively in industry as well as in academia. In this manuscript, we discuss the paths of both successful and unsuccessful molecules where NMR had a crucial part in their development. We specifically focus on the techniques used and describe strengths and weaknesses of each stage by examining several case studies. More precisely, we examine the development history from the primary screening to the final lead optimisation of AZD3839 interacting with BACE-1, ABT-199 interacting with BCL2/XL and S64315 interacting with MCL-1. Based on these studies, we derive observations and conclusions regarding the FBDD process by NMR and discuss its potential improvements.
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Affiliation(s)
| | - Geerten W. Vuister
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
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161
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Tetramethylammonium Fluoride: Fundamental Properties and Applications in C-F Bond-Forming Reactions and as a Base. Catalysts 2022. [DOI: 10.3390/catal12020233] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nucleophilic ionic sources of fluoride are essential reagents in the synthetic toolbox to access high added-value fluorinated building blocks unattainable by other means. In this review, we provide a concise description and rationale of the outstanding features of one of these reagents, tetramethylammonium fluoride (TMAF), as well as disclosing the different methods for its preparation, and how its physicochemical properties and solvation effects in different solvents are intimately associated with its reactivity. Furthermore, herein we also comprehensively describe its historic and recent utilization, up to December 2021, in C-F bond-forming reactions with special emphasis on nucleophilic aromatic substitution fluorinations with a potential sustainable application in industrial settings, as well as its use as a base capable of rendering unprecedented transformations.
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162
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Engineered protein-small molecule conjugates empower selective enzyme inhibition. Cell Chem Biol 2022; 29:328-338.e4. [PMID: 34363759 PMCID: PMC8807807 DOI: 10.1016/j.chembiol.2021.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/17/2021] [Accepted: 07/14/2021] [Indexed: 11/20/2022]
Abstract
Potent, specific ligands drive precision medicine and fundamental biology. Proteins, peptides, and small molecules constitute effective ligand classes. Yet greater molecular diversity would aid the pursuit of ligands to elicit precise biological activity against challenging targets. We demonstrate a platform to discover protein-small molecule (PriSM) hybrids to combine unique pharmacophore activities and shapes with constrained, efficiently engineerable proteins. In this platform, a fibronectin protein library is displayed on yeast with a single cysteine coupled to acetazolamide via a maleimide-poly(ethylene glycol) linker. Magnetic and flow cytometric sorts enrich specific binders to carbonic anhydrase isoforms. Isolated PriSMs exhibit potent, specific inhibition of carbonic anhydrase isoforms with efficacy superior to that of acetazolamide or protein alone, including an 80-fold specificity increase and 9-fold potency gain. PriSMs are engineered with multiple linker lengths, protein conjugation sites, and sequences against two different isoforms, which reveal platform flexibility and impacts of molecular designs. PriSMs advance the molecular diversity of efficiently engineerable ligands.
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163
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Jackl MK, Seo H, Karges J, Kalaj M, Cohen SM. Salicylate metal-binding isosteres as fragments for metalloenzyme inhibition. Chem Sci 2022; 13:2128-2136. [PMID: 35308862 PMCID: PMC8849047 DOI: 10.1039/d1sc06011b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/12/2022] [Indexed: 01/22/2023] Open
Abstract
Metalloenzyme inhibitors typically share a common need to possess a metal-binding pharmacophore (MBP) for binding the active site metal ions. However, MBPs can suffer from physicochemical liabilities, impeding the pharmacological properties and drug-likeliness of inhibitors. To circumvent this, problematic features of the MBP can be identified and exchanged with isosteric replacements. Herein, the carboxylic and hydroxyl group of the salicylic acid MBP were replaced and a total of 27 salicylate metal-binding isosteres (MBIs) synthesized. Of these 27 MBIs, at least 12 represent previously unreported compounds, and the metal-binding abilities of >20 of the MBIs have not been previously reported. These salicylate MBIs were examined for their metal-binding features in model complexes, physicochemical properties, and biological activity. It was observed that salicylate MBIs can demonstrate a range of attractive physicochemical properties and bind to the metal in a variety of expected and unexpected binding modes. The biological activity of these novel MBIs was evaluated by measuring inhibition against two Zn2+-dependent metalloenzymes, human glyoxalase 1 (GLO1) and matrix metalloproteinase 3 (MMP-3), as well as a dinuclear Mn2+-dependent metalloenzyme, influenza H1N1 N-terminal endonuclease (PAN). It was observed that salicylate MBIs could maintain or improve enzyme inhibition and selectivity. To probe salicylate MBIs as fragments for fragment-based drug discovery (FBDD), an MBI that showed good inhibitory activity against GLO1 was derivatized and a rudimentary structure-activity relationship was developed. The resulting elaborated fragments showed GLO1 inhibition with low micromolar activity.
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Affiliation(s)
- Moritz K Jackl
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Hyeonglim Seo
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Johannes Karges
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Mark Kalaj
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
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164
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Mahato S. Recent Development of Small Molecules for SARS-CoV-2 and the Opportunity for Fragment-Based Drug Discovery. Med Chem 2022; 18:847-858. [DOI: 10.2174/1573406418666220214091107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/10/2021] [Accepted: 12/03/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
The ongoing pandemic of Covid-19 caused by SARS-CoV-2 is a major threat to global public health, drawing attention to develop new therapeutics for treatment. Much research work is focused on identifying or repurposing new small molecules to serve as potential inhibitors by interacting with viral or host-cell molecular targets and understanding the nature of the virus in the host cells. Identifying small molecules as potent inhibitors at an early stage is advantageous to make a molecule with higher potency and then find a lead compound for the development of drug discovery. Small molecules can show their inhibition property by targeting either SARS-CoV-2 main protease (Mpro) enzyme, papain-like protease (PLpro) enzyme, or helicase (Hel), or blocking the spike (S) protein angiotensin-converting enzyme 2 (ACE2) receptor. A very recent outbreak of a new variant (B.1.617.2—termed as Delta variant) of SARS-CoV-2 worldwide posed a greater challenge as it is resistant to clinically undergoing vaccine trials. Thus, the development of new drug molecules is of potential interest to combat SARS-CoV-2 disease, and for that, fragment-based drug discovery (FBDD) approach could be one of the ways to bring out an effective solution. Two cysteine protease enzymes would be an attractive choice of target for fragment-based drug discovery to tune the molecular structure at an early stage with suitable functionality. In this short review, the recent development of small-molecule as inhibitors against Covid-19 are discussed and the opportunity for FBDD is envisioned optimistically to provide an outlook regarding Covid-19 that may pave the way in the direction of the Covid-19 drug development paradigm.
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Affiliation(s)
- Sujit Mahato
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat, Gujarat-395007, INDIA
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165
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Dragovich PS, Haap W, Mulvihill MM, Plancher JM, Stepan AF. Small-Molecule Lead-Finding Trends across the Roche and Genentech Research Organizations. J Med Chem 2022; 65:3606-3615. [PMID: 35138850 DOI: 10.1021/acs.jmedchem.1c02106] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The origin of small-molecule leads that were pursued across the independent research organizations Roche and Genentech from 2009 to 2020 is described. The identified chemical series are derived from a variety of lead-finding methods, which include public information, high-throughput screening (both full file and focused), fragment-based design, DNA-encoded library technology, use of legacy internal data, in-licensing, and de novo design (often structure-based). The translation of the lead series into in vivo tool compounds and development candidates is discussed as are the associated biological target classes and corresponding therapeutic areas. These analyses identify important trends regarding the various lead-finding approaches, which will likely impact their future application in the Roche and Genentech research groups. They also highlight commonalities and differences across the two independent research organizations. Several caveats associated with the employed data collection and analysis methodologies are included to enhance the interpretation of the presented information.
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Affiliation(s)
- Peter S Dragovich
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Wolfgang Haap
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Melinda M Mulvihill
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jean-Marc Plancher
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Antonia F Stepan
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
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166
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Discovery of novel TMPRSS2 inhibitors for COVID-19 using in silico fragment-based drug design, molecular docking, molecular dynamics, and quantum mechanics studies. INFORMATICS IN MEDICINE UNLOCKED 2022; 29:100870. [PMID: 35128036 PMCID: PMC8806845 DOI: 10.1016/j.imu.2022.100870] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/29/2022] [Accepted: 01/29/2022] [Indexed: 01/18/2023] Open
Abstract
The global expansion of COVID-19 and the mutations of severe acute respiratory syndrome coronavirus necessitate quick development of treatment and vaccination. Because the androgen-responsive serine protease TMPRSS2 is involved in cleaving the SARS-CoV-2 spike protein allowing the virus to enter the cell, therefore, direct TMPRSS2 inhibition will inhibit virus activation and disease progression which make it an important target for drug discovery. In this study, a homology model of TMPRSS2 protein was initially developed. Then, we used the fragment-based drug design (FBDD) technique to develop effective TMPRSS2 inhibitors. Over a half-million fragments from the enamine database were screened for their binding ability to target protein, and then best-scoring fragments were linked to building new molecules with a good binding affinity. XP docking and MM-GBSA studies revealed 10 new formed molecules with docking score ≤ -14.982 kcal/mol compared to ambroxol (control) with a docking score of -6.464 kcal/mol. Finally, molecular dynamics (MD) and density functional theory (DFT) were calculated for the top 3 molecules.
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167
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Miao J, Yuan H, Rao J, Zou J, Yang K, Peng G, Cao S, Chen H, Song Y. Identification of a small compound that specifically inhibits Zika virus in vitro and in vivo by targeting the NS2B-NS3 protease. Antiviral Res 2022; 199:105255. [PMID: 35143853 DOI: 10.1016/j.antiviral.2022.105255] [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: 07/13/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/02/2022]
Abstract
Zika virus (ZIKV) has rapid become a global threat, but no ZIKV-specific vaccines or drugs are currently available. In this study, inhibitors of ZIKV NS2B-NS3 protease were screened from a library containing 4,452 compound fragments. One of the compounds, 6-bromo-1,2-naphthalenedione, exhibited high specific inhibition against ZIKV NS2B-NS3 protease, but had no inhibitory effects against other viral proteases. A microscale thermophoresis (MST) assay confirmed that the compound bound to ZIKV NS2B-NS3 protein with a binding constant (Kd) of 12.26 μM. Indirect immunofluorescence assays, Western blots, and plaque assays indicated that the compound inhibited virus replication in cells. Virus titer was reduced by more than 75% when the compound was present at 1 μM. A time-of-addition assay showed that inhibition occurred at the virus replication stage, but not at the adsorption or invasion stages. The half cytotoxicity concentration (CC50) of the compound on HeLa, Vero, and BHK-21 cells were 445.44 μM, 123.87 μM, and 123.64 μM, respectively. In vivo tests using infected AG129 mice demonstrated that treatment with the compound reduced mortality by up to 60%. Mice treated with the compound showed a reduction in histopathological lesions in brain, testis, and ovary. Viral RNA, IL-1β, and IL-6 mRNA levels decreased significantly in these tissues. In summary, this study has identified a small compound with high and specific inhibitory effects on ZIKV. The compound can be used as a therapeutic agent and is also an ideal starting point for drug optimization.
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Affiliation(s)
- Juan Miao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Honggen Yuan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jingwei Rao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiahui Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kelu Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shengbo Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunfeng Song
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China.
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168
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Sharifi Tabar M, Francis H, Yeo D, Bailey CG, Rasko JEJ. Mapping oncogenic protein interactions for precision medicine. Int J Cancer 2022; 151:7-19. [PMID: 35113472 PMCID: PMC9306658 DOI: 10.1002/ijc.33954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 11/10/2022]
Abstract
Normal protein‐protein interactions (normPPIs) occur with high fidelity to regulate almost every physiological process. In cancer, this highly organised and precisely regulated network is disrupted, hijacked or reprogrammed resulting in oncogenic protein‐protein interactions (oncoPPIs). OncoPPIs, which can result from genomic alterations, are a hallmark of many types of cancers. Recent technological advances in the field of mass spectrometry (MS)‐based interactomics, structural biology and drug discovery have prompted scientists to identify and characterise oncoPPIs. Disruption of oncoPPI interfaces has become a major focus of drug discovery programs and has resulted in the use of PPI‐specific drugs clinically. However, due to several technical hurdles, studies to build a reference oncoPPI map for various cancer types have not been undertaken. Therefore, there is an urgent need for experimental workflows to overcome the existing challenges in studying oncoPPIs in various cancers and to build comprehensive reference maps. Here, we discuss the important hurdles for characterising oncoPPIs and propose a three‐phase multidisciplinary workflow to identify and characterise oncoPPIs. Systematic identification of cancer‐type‐specific oncogenic interactions will spur new opportunities for PPI‐focused drug discovery projects and precision medicine.
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Affiliation(s)
- Mehdi Sharifi Tabar
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, Sydney, NSW, Australia
| | - Habib Francis
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, Sydney, NSW, Australia
| | - Dannel Yeo
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW, Australia.,Li Ka Shing Cell & Gene Therapy Program, The University of Sydney, Camperdown, NSW, Australia.,Cell & Molecular Therapies, Royal Prince Alfred Hospital, Sydney Local Health District, Camperdown, NSW, Australia
| | - Charles G Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, Sydney, NSW, Australia
| | - John E J Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, Sydney, NSW, Australia.,Li Ka Shing Cell & Gene Therapy Program, The University of Sydney, Camperdown, NSW, Australia.,Cell & Molecular Therapies, Royal Prince Alfred Hospital, Sydney Local Health District, Camperdown, NSW, Australia
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169
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Smilova MD, Curran PR, Radoux CJ, von Delft F, Cole JC, Bradley AR, Marsden BD. Fragment Hotspot Mapping to Identify Selectivity-Determining Regions between Related Proteins. J Chem Inf Model 2022; 62:284-294. [PMID: 35020376 PMCID: PMC8790751 DOI: 10.1021/acs.jcim.1c00823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Selectivity is a
crucial property in small molecule development.
Binding site comparisons within a protein family are a key piece of
information when aiming to modulate the selectivity profile of a compound.
Binding site differences can be exploited to confer selectivity for
a specific target, while shared areas can provide insights into polypharmacology.
As the quantity of structural data grows, automated methods are needed
to process, summarize, and present these data to users. We present
a computational method that provides quantitative and data-driven
summaries of the available binding site information from an ensemble
of structures of the same protein. The resulting ensemble maps identify
the key interactions important for ligand binding in the ensemble.
The comparison of ensemble maps of related proteins enables the identification
of selectivity-determining regions within a protein family. We applied
the method to three examples from the well-researched human bromodomain
and kinase families, demonstrating that the method is able to identify
selectivity-determining regions that have been used to introduce selectivity
in past drug discovery campaigns. We then illustrate how the resulting
maps can be used to automate comparisons across a target protein family.
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Affiliation(s)
- Mihaela D Smilova
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K
| | - Peter R Curran
- The Cambridge Crystallographic Data Centre (CCDC), Cambridge CB2 1EZ, U.K.,Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Chris J Radoux
- Exscientia Ltd., The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, U.K
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K.,Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.,Research Complex at Harwell. Harwell Science and Innovation Campus, Didcot OX11 0FA, U.K.,Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Jason C Cole
- The Cambridge Crystallographic Data Centre (CCDC), Cambridge CB2 1EZ, U.K
| | - Anthony R Bradley
- Exscientia Ltd., The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, U.K
| | - Brian D Marsden
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K.,Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford OX3 7DQ, U.K
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170
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Sachdeo RA, Anthwal T, Nain S. Fragment based drug design. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2018-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Rational approaches towards drug development have emerged as one of the most promising ways among the tedious conventional procedures with the aim of redefining the drug discovery process. The need of current medical system is demanding a much precise, faster and reliable approaches in parallel to faster growing technology for development of drugs with more intrinsic action and fewer side effects. Systematic and well-defined diagnostic studies have revealed the specific causes of disease and related targets for drug development. Designing a drug as per the specific target, studying it in-silico prior to its development has been proved as an added benefit to the studies. Many approaches like structure based drug design, fragment based drug design and ligand based drug design are been in practice for the drug discovery and development with the similar fundamental theory. Fragment based drug design utilizes a library of fragments designed specifically for the concerned target and these fragments are studied further before screening with virtual methods as well as with biophysical methods. The process follows a well-defined pathway which moulds a fragment into a perfect drug candidate. In this chapter we have tried to cover all the basic aspects of fragment based drug design and related technologies.
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Affiliation(s)
- Rahul Ashok Sachdeo
- Department of Pharmaceutical Chemistry , Government College of Pharmacy , Karad , Maharashtra , 415124 , India
| | - Tulika Anthwal
- Department of Pharmacy , Banasthali Vidyapith , Banasthali , Rajasthan , 304022 , India
| | - Sumitra Nain
- Department of Pharmacy , Banasthali Vidyapith , Banasthali , Rajasthan , 304022 , India
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171
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Chen L, Zhang J, Lin Z, Zhang Z, Mao M, Wu J, Li Q, Zhang Y, Fan C. Pharmaceutical applications of framework nucleic acids. Acta Pharm Sin B 2022; 12:76-91. [PMID: 35127373 PMCID: PMC8799870 DOI: 10.1016/j.apsb.2021.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 01/21/2023] Open
Abstract
DNA is a biological polymer that encodes and stores genetic information in all living organism. Particularly, the precise nucleobase pairing inside DNA is exploited for the self-assembling of nanostructures with defined size, shape and functionality. These DNA nanostructures are known as framework nucleic acids (FNAs) for their skeleton-like features. Recently, FNAs have been explored in various fields ranging from physics, chemistry to biology. In this review, we mainly focus on the recent progress of FNAs in a pharmaceutical perspective. We summarize the advantages and applications of FNAs for drug discovery, drug delivery and drug analysis. We further discuss the drawbacks of FNAs and provide an outlook on the pharmaceutical research direction of FNAs in the future.
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Affiliation(s)
- Liang Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jie Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhun Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ziyan Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Miao Mao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiacheng Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yuanqing Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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172
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Srdanović S, Hegedüs Z, Warriner SL, Wilson AJ. Towards Identification of Protein-Protein Interaction Stabilizers via Inhibitory Peptide-Fragment Hybrids Using Templated Fragment Ligation. RSC Chem Biol 2022; 3:546-550. [PMID: 35656480 PMCID: PMC9092428 DOI: 10.1039/d2cb00025c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/25/2022] [Indexed: 11/21/2022] Open
Abstract
Using the hDMX/14-3-3 interaction, acylhydrazone-based ligand-directed fragment ligation was used to identify protein-protein interaction (PPI) inhibitory peptide-fragment hybrids. Separation of the peptide-fragment hybrids into the components yielded fragments that stabilized...
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Affiliation(s)
- Sonja Srdanović
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
| | - Zsofia Hegedüs
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Stuart L Warriner
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
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173
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Eliandro da Silva, Jr. P, Melo SMGD, Helder de Paula M, Vessecchi R, Opatz T, Day J, Ganesan A, da Silva Emery F. Growth vector elaboration of fragments: regioselective functionalization of 5-hydroxy-6-azaindazole and 3-hydroxy-2,6-naphtyridine. Org Biomol Chem 2022; 20:7483-7490. [DOI: 10.1039/d2ob00968d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article discusses the reactivity of an 6-azaindazole (1) and a 2,6-naphthyridine (2), proposed to be “heteroaromatic rings of the future” which would be useful for fragment-based drug discovery (FBDD)...
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174
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Martín-Guerrero SM, Markovinovic A, Mórotz GM, Salam S, Noble W, Miller CCJ. Targeting ER-Mitochondria Signaling as a Therapeutic Target for Frontotemporal Dementia and Related Amyotrophic Lateral Sclerosis. Front Cell Dev Biol 2022; 10:915931. [PMID: 35693938 PMCID: PMC9184680 DOI: 10.3389/fcell.2022.915931] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are two major neurodegenerative diseases. FTD is the second most common cause of dementia and ALS is the most common form of motor neuron disease. These diseases are now known to be linked. There are no cures or effective treatments for FTD or ALS and so new targets for therapeutic intervention are required but this is hampered by the large number of physiological processes that are damaged in FTD/ALS. Many of these damaged functions are now known to be regulated by signaling between the endoplasmic reticulum (ER) and mitochondria. This signaling is mediated by "tethering" proteins that serve to recruit ER to mitochondria. One tether strongly associated with FTD/ALS involves an interaction between the ER protein VAPB and the mitochondrial protein PTPIP51. Recent studies have shown that ER-mitochondria signaling is damaged in FTD/ALS and that this involves breaking of the VAPB-PTPIP51 tethers. Correcting disrupted tethering may therefore correct many other downstream damaged features of FTD/ALS. Here, we review progress on this topic with particular emphasis on targeting of the VAPB-PTPIP51 tethers as a new drug target.
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Affiliation(s)
- Sandra M Martín-Guerrero
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Andrea Markovinovic
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Gábor M Mórotz
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Shaakir Salam
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Wendy Noble
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Christopher C J Miller
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
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175
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Lan X, Zhang Y, Jia X, Dong S, Liu Y, Zhang M, Guo J, Cao J, Guo Y, Xiao G, Wang W. Screening and identification of Lassa virus endonuclease-targeting inhibitors from a fragment-based drug discovery library. Antiviral Res 2021; 197:105230. [PMID: 34965446 DOI: 10.1016/j.antiviral.2021.105230] [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: 09/09/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/02/2022]
Abstract
Lassa virus (LASV) belongs to the Old World genus Mammarenavirus, family Arenaviridae, and order Bunyavirales. Arenavirus contains a segmented negative-sense RNA genome, which is in line with the bunyavirus and orthomyxoviruses. The segmented negative-sense RNA viruses utilize a cap-snatching strategy to provide primers cleavaged from the host capped mRNA for viral mRNA transcription. As a similar strategy and the conformational conservation shared with these viruses, the endonuclease (EN) would serve as an attractive target for developing broad-spectrum inhibitors. Using the LASV minigenome (MG) system, we screened a fragment-based drug discovery library and found that two hits, F1204 and F1781, inhibited LASV MG activity. Both hits also inhibited the prototype arenavirus Lymphocytic choriomeningitis virus (LCMV) MG activity. Furthermore, both hits effectively inhibited authentic LCMV and severe fever with thrombocytopenia syndrome virus (SFTSV) infections. Similarly, both hits could inhibit the activity of LASV, LCMV, and SFTSV EN. The combination of either compound with an arenavirus entry inhibitor had significant synergistic antiviral effects. Moreover, both hits were found to be capable of binding to LASV EN with a binding affinity at the micromolar level. These findings provide a basis for developing the hits as potential candidates for the treatment of segmented negative-sense RNA virus infections.
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Affiliation(s)
- Xiaohao Lan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; College of Pharmacy and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300450, China
| | - Yueli Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; College of Pharmacy and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300450, China
| | - Xiaoying Jia
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Siqi Dong
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Mengmeng Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; College of Pharmacy and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300450, China
| | - Jiao Guo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Junyuan Cao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Guo
- College of Pharmacy and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300450, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - Wei Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China.
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176
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Shi Y, El-Deeb IM, Masic V, Hartley-Tassell L, Maggioni A, Itzstein MV, Ve T. Discovery of Cofactor Competitive Inhibitors against the Human Methyltransferase Fibrillarin. Pharmaceuticals (Basel) 2021; 15:26. [PMID: 35056083 PMCID: PMC8779173 DOI: 10.3390/ph15010026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 11/21/2022] Open
Abstract
Fibrillarin (FBL) is an essential and evolutionarily highly conserved S-adenosyl methionine (SAM) dependent methyltransferase. It is the catalytic component of a multiprotein complex that facilitates 2'-O-methylation of ribosomal RNAs (rRNAs), a modification essential for accurate and efficient protein synthesis in eukaryotic cells. It was recently established that human FBL (hFBL) is critical for Nipah, Hendra, and respiratory syncytial virus infections. In addition, overexpression of hFBL contributes towards tumorgenesis and is associated with poor survival in patients with breast cancer, suggesting that hFBL is a potential target for the development of both antiviral and anticancer drugs. An attractive strategy to target cofactor-dependent enzymes is the selective inhibition of cofactor binding, which has been successful for the development of inhibitors against several protein methyltransferases including PRMT5, DOT1L, and EZH2. In this work, we solved crystal structures of the methyltransferase domain of hFBL in apo form and in complex with the cofactor SAM. Screening of a fluorinated fragment library, via X-ray crystallography and 19F NMR spectroscopy, yielded seven hit compounds that competed with cofactor binding, two of which resulted in co-crystal structures. One of these structures revealed unexpected conformational variability in the cofactor binding site, which allows it to accommodate a compound significantly different from SAM. Our structural data provide critical information for the design of selective cofactor competitive inhibitors targeting hFBL, and preliminary elaboration of hit compounds has led to additional cofactor site binders.
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Affiliation(s)
- Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Ibrahim M El-Deeb
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | | | - Andrea Maggioni
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
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177
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Piticchio SG, Martínez-Cartró M, Scaffidi S, Rachman M, Rodriguez-Arevalo S, Sanchez-Arfelis A, Escolano C, Picaud S, Krojer T, Filippakopoulos P, von Delft F, Galdeano C, Barril X. Discovery of Novel BRD4 Ligand Scaffolds by Automated Navigation of the Fragment Chemical Space. J Med Chem 2021; 64:17887-17900. [PMID: 34898210 DOI: 10.1021/acs.jmedchem.1c01108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fragment-based drug discovery (FBDD) is a very effective hit identification method. However, the evolution of fragment hits into suitable leads remains challenging and largely artisanal. Fragment evolution is often scaffold-centric, meaning that its outcome depends crucially on the chemical structure of the starting fragment. Considering that fragment screening libraries cover only a small proportion of the corresponding chemical space, hits should be seen as probes highlighting privileged areas of the chemical space rather than actual starting points. We have developed an automated computational pipeline to mine the chemical space around any specific fragment hit, rapidly finding analogues that share a common interaction motif but are structurally novel and diverse. On a prospective application on the bromodomain-containing protein 4 (BRD4), starting from a known fragment, the platform yields active molecules with nonobvious scaffold changes. The procedure is fast and inexpensive and has the potential to uncover many hidden opportunities in FBDD.
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Affiliation(s)
- Serena G Piticchio
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Míriam Martínez-Cartró
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Salvatore Scaffidi
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Moira Rachman
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Sergio Rodriguez-Arevalo
- Laboratory of Medicinal Chemistry (Associated Unit to CSIC), Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Ainoa Sanchez-Arfelis
- Laboratory of Medicinal Chemistry (Associated Unit to CSIC), Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Carmen Escolano
- Laboratory of Medicinal Chemistry (Associated Unit to CSIC), Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Tobias Krojer
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Frank von Delft
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom.,Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom.,Centre for Medicines Discovery, University of Oxford, Oxford OX1 3QU, United Kingdom.,Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Carles Galdeano
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Xavier Barril
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
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178
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Herrera-España AD, Aguiar-Pech JA, Alvarez-Sánchez ME, Arana-Argáez VE, Palomar-Gómez CK, Jiménez-Ross AG, Cáceres-Castillo D, Carballo RM, Torres-Romero JC. Lupeol acetate isolated from Chrysophyllum cainito L. fruit as a template for the synthesis of N-alkyl-arylsulfonamide derivatives and their synergistic effects with metronidazole against Trichomonas vaginalis. Nat Prod Res 2021; 36:5508-5516. [PMID: 34930096 DOI: 10.1080/14786419.2021.2018429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Pentacyclic triterpenes are found in a great variety of natural products and constitute an organic template for the development of new derivative compounds with therapeutic applications. In the present work, lupeol acetate isolated from Chrysophyllum cainito L. fruit was used as a template for the synthesis of novel N-alkyl-arylsulfonamide derivatives, and their synergistic effects with metronidazole against strains of Trichomonas vaginalis were tested. A library of 18 derivatives was synthesized. Ten compounds exhibited an IC50 < 100 μM against a metronidazole-sensitive strain of T. vaginalis. Only seven of these compounds (12, 15, 18-22) also showed activity against metronidazole-resistant strains. The compounds 20 (N-cyclohexyl-p-chlorobenzenesulfonamidolupeol acetate) and 22 (N-cyclohexyl-p-nitrobenzenesulfonamidolupeol acetate) exhibited a similar IC50 against both susceptible and resistant T. vaginalis strains and enhanced the efficacy of metronidazole in a partial and total synergistic way, respectively. These data provided evidence of the trichomonicidal effect of N-alkyl-arylsulfonamide derivatives of lupeol acetate, representing highly promising novel antiparasitic agents.
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Affiliation(s)
- Angel D Herrera-España
- División de Ciencias de la Salud, Universidad de Quintana Roo (UQROO), Chetumal, Quintana Roo, México
| | - Julio A Aguiar-Pech
- Department Facultad de Química, Universidad Autónoma de Yucatán (UADY), Mérida, Yucatán, México
| | - M Elizbeth Alvarez-Sánchez
- Department Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), Ciudad de, México, México
| | - Victor E Arana-Argáez
- Department Facultad de Química, Universidad Autónoma de Yucatán (UADY), Mérida, Yucatán, México
| | - Cynthia K Palomar-Gómez
- Department Facultad de Química, Universidad Autónoma de Yucatán (UADY), Mérida, Yucatán, México
| | - Armin G Jiménez-Ross
- Department Facultad de Química, Universidad Autónoma de Yucatán (UADY), Mérida, Yucatán, México
| | - David Cáceres-Castillo
- Department Facultad de Química, Universidad Autónoma de Yucatán (UADY), Mérida, Yucatán, México
| | - Rubén M Carballo
- Department Facultad de Química, Universidad Autónoma de Yucatán (UADY), Mérida, Yucatán, México
| | - Julio C Torres-Romero
- Department Facultad de Química, Universidad Autónoma de Yucatán (UADY), Mérida, Yucatán, México
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179
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Selection of Promising Novel Fragment Sized S. aureus SrtA Noncovalent Inhibitors Based on QSAR and Docking Modeling Studies. Molecules 2021; 26:molecules26247677. [PMID: 34946760 PMCID: PMC8709105 DOI: 10.3390/molecules26247677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/22/2022] Open
Abstract
Sortase A (SrtA) of Staphylococcus aureus has been identified as a promising target to a new type of antivirulent drugs, and therefore, the design of lead molecules with a low nanomolar range of activity and suitable drug-like properties is important. In this work, we aimed at identifying new fragment-sized starting points to design new noncovalent S. aureus SrtA inhibitors by making use of the dedicated molecular motif, 5-arylpyrrolidine-2-carboxylate, which has been previously shown to be significant for covalent binding SrtA inhibitors. To this end, an in silico approach combining QSAR and molecular docking studies was used. The known SrtA inhibitors from the ChEMBL database with diverse scaffolds were first employed to derive descriptors and interpret their significance and correlation to activity. Then, the classification and regression QSAR models were built, which were used for rough ranking of the virtual library of the synthetically feasible compounds containing the dedicated motif. Additionally, the virtual library compounds were docked into the “activated” model of SrtA (PDB:2KID). The consensus ranking of the virtual library resulted in the most promising structures, which will be subject to further synthesis and experimental testing in order to establish new fragment-like molecules for further development into antivirulent drugs.
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180
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Fragment-to-lead tailored in silico design. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:44-57. [PMID: 34916022 DOI: 10.1016/j.ddtec.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/25/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
Fragment-based drug discovery (FBDD) emerged as a disruptive technology and became established during the last two decades. Its rationality and low entry costs make it appealing, and the numerous examples of approved drugs discovered through FBDD validate the approach. However, FBDD still faces numerous challenges. Perhaps the most important one is the transformation of the initial fragment hits into viable leads. Fragment-to-lead (F2L) optimization is resource-intensive and is therefore limited in the possibilities that can be actively pursued. In silico strategies play an important role in F2L, as they can perform a deeper exploration of chemical space, prioritize molecules with high probabilities of being active and generate non-obvious ideas. Here we provide a critical overview of current in silico strategies in F2L optimization and highlight their remarkable impact. While very effective, most solutions are target- or fragment- specific. We propose that fully integrated in silico strategies, capable of automatically and systematically exploring the fast-growing available chemical space can have a significant impact on accelerating the release of fragment originated drugs.
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181
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Ballante F, Kooistra AJ, Kampen S, de Graaf C, Carlsson J. Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You? Pharmacol Rev 2021; 73:527-565. [PMID: 34907092 DOI: 10.1124/pharmrev.120.000246] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome and are important therapeutic targets. During the last decade, the number of atomic-resolution structures of GPCRs has increased rapidly, providing insights into drug binding at the molecular level. These breakthroughs have created excitement regarding the potential of using structural information in ligand design and initiated a new era of rational drug discovery for GPCRs. The molecular docking method is now widely applied to model the three-dimensional structures of GPCR-ligand complexes and screen for chemical probes in large compound libraries. In this review article, we first summarize the current structural coverage of the GPCR superfamily and the understanding of receptor-ligand interactions at atomic resolution. We then present the general workflow of structure-based virtual screening and strategies to discover GPCR ligands in chemical libraries. We assess the state of the art of this research field by summarizing prospective applications of virtual screening based on experimental structures. Strategies to identify compounds with specific efficacy and selectivity profiles are discussed, illustrating the opportunities and limitations of the molecular docking method. Our overview shows that structure-based virtual screening can discover novel leads and will be essential in pursuing the next generation of GPCR drugs. SIGNIFICANCE STATEMENT: Extraordinary advances in the structural biology of G protein-coupled receptors have revealed the molecular details of ligand recognition by this large family of therapeutic targets, providing novel avenues for rational drug design. Structure-based docking is an efficient computational approach to identify novel chemical probes from large compound libraries, which has the potential to accelerate the development of drug candidates.
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Affiliation(s)
- Flavio Ballante
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Albert J Kooistra
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Stefanie Kampen
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Chris de Graaf
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
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182
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Vilca-Melendez S, Uthaug MV, Griffin JL. 1H Nuclear Magnetic Resonance: A Future Approach to the Metabolic Profiling of Psychedelics in Human Biofluids? Front Psychiatry 2021; 12:742856. [PMID: 34966300 PMCID: PMC8710695 DOI: 10.3389/fpsyt.2021.742856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/18/2021] [Indexed: 11/25/2022] Open
Abstract
While psychedelics may have therapeutic potential for treating mental health disorders such as depression, further research is needed to better understand their biological effects and mechanisms of action when considering the development of future novel therapy approaches. Psychedelic research could potentially benefit from the integration of metabonomics by proton nuclear magnetic resonance (1H NMR) spectroscopy which is an analytical chemistry-based approach that can measure the breakdown of drugs into their metabolites and their metabolic consequences from various biofluids. We have performed a systematic review with the primary aim of exploring published literature where 1H NMR analysed psychedelic substances including psilocin, lysergic acid diethylamide (LSD), LSD derivatives, N,N-dimethyltryptamine (DMT), 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT) and bufotenin. The second aim was to assess the benefits and limitations of 1H NMR spectroscopy-based metabolomics as a tool in psychedelic research and the final aim was to explore potential future directions. We found that the most current use of 1H NMR in psychedelic research has been for the structural elucidation and analytical characterisation of psychedelic molecules and that no papers used 1H NMR in the metabolic profiling of biofluids, thus exposing a current research gap and the underuse of 1H NMR. The efficacy of 1H NMR spectroscopy was also compared to mass spectrometry, where both metabonomics techniques have previously shown to be appropriate for biofluid analysis in other applications. Additionally, potential future directions for psychedelic research were identified as real-time NMR, in vivo 1H nuclear magnetic resonance spectroscopy (MRS) and 1H NMR studies of the gut microbiome. Further psychedelic studies need to be conducted that incorporate the use of 1H NMR spectroscopy in the analysis of metabolites both in the peripheral biofluids and in vivo to determine whether it will be an effective future approach for clinical and naturalistic research.
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Affiliation(s)
- Sylvana Vilca-Melendez
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Malin V. Uthaug
- The Centre for Psychedelic Research, Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of Neuropsychology and Psychopharmacology, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Julian L. Griffin
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
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183
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Novel series of triazole containing coumarin and isatin based hybrid molecules as acetylcholinesterase inhibitors. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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184
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Chávez-Hernández AL, Juárez-Mercado KE, Saldívar-González FI, Medina-Franco JL. Towards the De Novo Design of HIV-1 Protease Inhibitors Based on Natural Products. Biomolecules 2021; 11:biom11121805. [PMID: 34944448 PMCID: PMC8698858 DOI: 10.3390/biom11121805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 01/14/2023] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) continues to be a public health problem. In 2020, 680,000 people died from HIV-related causes, and 1.5 million people were infected. Antiretrovirals are a way to control HIV infection but not to cure AIDS. As such, effective treatment must be developed to control AIDS. Developing a drug is not an easy task, and there is an enormous amount of work and economic resources invested. For this reason, it is highly convenient to employ computer-aided drug design methods, which can help generate and identify novel molecules. Using the de novo design, novel molecules can be developed using fragments as building blocks. In this work, we develop a virtual focused compound library of HIV-1 viral protease inhibitors from natural product fragments. Natural products are characterized by a large diversity of functional groups, many sp3 atoms, and chiral centers. Pseudo-natural products are a combination of natural products fragments that keep the desired structural characteristics from different natural products. An interactive version of chemical space visualization of virtual compounds focused on HIV-1 viral protease inhibitors from natural product fragments is freely available in the supplementary material.
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185
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Cantrelle F, Boll E, Brier L, Moschidi D, Belouzard S, Landry V, Leroux F, Dewitte F, Landrieu I, Dubuisson J, Deprez B, Charton J, Hanoulle X. NMR Spectroscopy of the Main Protease of SARS‐CoV‐2 and Fragment‐Based Screening Identify Three Protein Hotspots and an Antiviral Fragment. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- François‐Xavier Cantrelle
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Emmanuelle Boll
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Lucile Brier
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Danai Moschidi
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Sandrine Belouzard
- Univ. Lille CNRS INSERM, CHU Lille Institut Pasteur de Lille U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille 1 rue du Professeur Calmette F-59019 Lille France
| | - Valérie Landry
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Florence Leroux
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Frédérique Dewitte
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Isabelle Landrieu
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Jean Dubuisson
- Univ. Lille CNRS INSERM, CHU Lille Institut Pasteur de Lille U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille 1 rue du Professeur Calmette F-59019 Lille France
| | - Benoit Deprez
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Julie Charton
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Xavier Hanoulle
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
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186
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Cantrelle F, Boll E, Brier L, Moschidi D, Belouzard S, Landry V, Leroux F, Dewitte F, Landrieu I, Dubuisson J, Deprez B, Charton J, Hanoulle X. NMR Spectroscopy of the Main Protease of SARS-CoV-2 and Fragment-Based Screening Identify Three Protein Hotspots and an Antiviral Fragment. Angew Chem Int Ed Engl 2021; 60:25428-25435. [PMID: 34570415 PMCID: PMC8653025 DOI: 10.1002/anie.202109965] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/16/2021] [Indexed: 11/17/2022]
Abstract
The main protease (3CLp) of the SARS-CoV-2, the causative agent for the COVID-19 pandemic, is one of the main targets for drug development. To be active, 3CLp relies on a complex interplay between dimerization, active site flexibility, and allosteric regulation. The deciphering of these mechanisms is a crucial step to enable the search for inhibitors. In this context, using NMR spectroscopy, we studied the conformation of dimeric 3CLp from the SARS-CoV-2 and monitored ligand binding, based on NMR signal assignments. We performed a fragment-based screening that led to the identification of 38 fragment hits. Their binding sites showed three hotspots on 3CLp, two in the substrate binding pocket and one at the dimer interface. F01 is a non-covalent inhibitor of the 3CLp and has antiviral activity in SARS-CoV-2 infected cells. This study sheds light on the complex structure-function relationships of 3CLp and constitutes a strong basis to assist in developing potent 3CLp inhibitors.
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Affiliation(s)
- François‐Xavier Cantrelle
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Emmanuelle Boll
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Lucile Brier
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Danai Moschidi
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Sandrine Belouzard
- Univ. LilleCNRSINSERM, CHU LilleInstitut Pasteur de LilleU1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille1 rue du Professeur CalmetteF-59019LilleFrance
| | - Valérie Landry
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Florence Leroux
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Frédérique Dewitte
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Isabelle Landrieu
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Jean Dubuisson
- Univ. LilleCNRSINSERM, CHU LilleInstitut Pasteur de LilleU1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille1 rue du Professeur CalmetteF-59019LilleFrance
| | - Benoit Deprez
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Julie Charton
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Xavier Hanoulle
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
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187
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Gally JM, Pahl A, Czodrowski P, Waldmann H. Pseudonatural Products Occur Frequently in Biologically Relevant Compounds. J Chem Inf Model 2021; 61:5458-5468. [PMID: 34669418 PMCID: PMC8611719 DOI: 10.1021/acs.jcim.1c01084] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
A new methodology
for classifying fragment combinations and characterizing
pseudonatural products (PNPs) is described. The source code is based
on open-source tools and is organized as a Python package. Tasks can
be executed individually or within the context of scalable, robust
workflows. First, structures are standardized and duplicate entries
are filtered out. Then, molecules are probed for the presence of predefined
fragments. For molecules with more than one match, fragment combinations
are classified. The algorithm considers the pairwise relative position
of fragments within the molecule (fused atoms, linkers, intermediary
rings), resulting in 18 different possible fragment combination categories.
Finally, all combinations for a given molecule are assembled into
a fragment combination graph, with fragments as nodes and combination
types as edges. This workflow was applied to characterize PNPs in
the ChEMBL database via comparison of fragment combination graphs
with natural product (NP) references, represented by the Dictionary
of Natural Products. The Murcko fragments extracted from 2000 structures
previously described were used to define NP fragments. The results
indicate that ca. 23% of the biologically relevant compounds listed
in ChEMBL comply to the PNP definition and that, therefore, PNPs occur
frequently among known biologically relevant small molecules. The
majority (>95%) of PNPs contain two to four fragments, mainly (>95%)
distributed in five different combination types. These findings may
provide guidance for the design of new PNPs.
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Affiliation(s)
- José-Manuel Gally
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Axel Pahl
- Compound Management and Screening Center, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Paul Czodrowski
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
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188
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Matricon P, Vo DD, Gao ZG, Kihlberg J, Jacobson KA, Carlsson J. Fragment-based design of selective GPCR ligands guided by free energy simulations. Chem Commun (Camb) 2021; 57:12305-12308. [PMID: 34734588 PMCID: PMC8603191 DOI: 10.1039/d1cc03202j] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/12/2021] [Indexed: 01/14/2023]
Abstract
Fragment-based drug discovery relies on successful optimization of weakly binding ligands for affinity and selectivity. Herein, we explored strategies for structure-based evolution of fragments binding to a G protein-coupled receptor. Molecular dynamics simulations combined with rigorous free energy calculations guided synthesis of nanomolar ligands with up to >1000-fold improvements of binding affinity and close to 40-fold subtype selectivity.
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Affiliation(s)
- Pierre Matricon
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala SE-751 24, Sweden.
| | - Duc Duy Vo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala SE-751 24, Sweden.
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Uppsala SE-751 23, Sweden
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala SE-751 24, Sweden.
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189
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Seo H, Prosser KE, Kalaj M, Karges J, Dick BL, Cohen SM. Evaluating Metal-Ligand Interactions of Metal-Binding Isosteres Using Model Complexes. Inorg Chem 2021; 60:17161-17172. [PMID: 34699201 DOI: 10.1021/acs.inorgchem.1c02433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioisosteres are a useful approach to address pharmacokinetic liabilities and improve drug-like properties. Specific to developing metalloenzyme inhibitors, metal-binding pharmacophores (MBPs) have been combined with bioisosteres, to produce metal-binding isosteres (MBIs) as alternative scaffolds for use in fragment-based drug discovery (FBDD). Picolinic acid MBIs have been reported and evaluated for their metal-binding ability, pharmacokinetic properties, and enzyme inhibitory activity. However, their structural, electronic, and spectroscopic properties with metal ions other than Zn(II) have not been reported, which might reveal similarities and differences between MBIs and the parent MBPs. To this end, [M(TPA)(MBI)]+ (M = Ni(II) and Co(II), TPA = tris(2-pyridylmethyl)amine) is presented as a bioinorganic model system for investigating picolinic acid, four heterocyclic MBIs, and 2,2'-bipyridine. These complexes were characterized by X-ray crystallography as well as NMR, IR, and UV-vis spectroscopies, and their magnetic moments were accessed. In addition, [(TpPh,Me)Co(MBI)] (TpPh,Me = hydrotris(3,5-phenylmethylpyrazolyl)borate) was used as a second model compound, and the limitations and attributes of the two model systems are discussed. These results demonstrate that bioinorganic model complexes are versatile tools for metalloenzyme inhibitor design and can provide insights into the broader use of MBIs.
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Affiliation(s)
- Hyeonglim Seo
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Kathleen E Prosser
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Mark Kalaj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Johannes Karges
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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190
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Norton D, Bonnette WG, Callahan JF, Carr MG, Griffiths-Jones CM, Heightman TD, Kerns JK, Nie H, Rich SJ, Richardson C, Rumsey W, Sanchez Y, Verdonk ML, Willems HMG, Wixted WE, Wolfe L, Woolford AJA, Wu Z, Davies TG. Fragment-Guided Discovery of Pyrazole Carboxylic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2 Related Factor 2 (KEAP1:NRF2) Protein-Protein Interaction. J Med Chem 2021; 64:15949-15972. [PMID: 34705450 DOI: 10.1021/acs.jmedchem.1c01351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The NRF2-mediated cytoprotective response is central to cellular homoeostasis, and there is increasing interest in developing small-molecule activators of this pathway as therapeutics for diseases involving chronic oxidative stress. The protein KEAP1, which regulates NRF2, is a key point for pharmacological intervention, and we recently described the use of fragment-based drug discovery to develop a tool compound that directly disrupts the protein-protein interaction between NRF2 and KEAP1. We now present the identification of a second, chemically distinct series of KEAP1 inhibitors, which provided an alternative chemotype for lead optimization. Pharmacophoric information from our original fragment screen was used to identify new hit matter through database searching and to evolve this into a new lead with high target affinity and cell-based activity. We highlight how knowledge obtained from fragment-based approaches can be used to focus additional screening campaigns in order to de-risk projects through the rapid identification of novel chemical series.
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Affiliation(s)
- David Norton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - William G Bonnette
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - James F Callahan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Maria G Carr
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Tom D Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Jeffrey K Kerns
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Hong Nie
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Sharna J Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - William Rumsey
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Yolanda Sanchez
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Marcel L Verdonk
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - William E Wixted
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Lawrence Wolfe
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | | | - Zining Wu
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Thomas G Davies
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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191
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Candish L, Collins KD, Cook GC, Douglas JJ, Gómez-Suárez A, Jolit A, Keess S. Photocatalysis in the Life Science Industry. Chem Rev 2021; 122:2907-2980. [PMID: 34558888 DOI: 10.1021/acs.chemrev.1c00416] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the pursuit of new pharmaceuticals and agrochemicals, chemists in the life science industry require access to mild and robust synthetic methodologies to systematically modify chemical structures, explore novel chemical space, and enable efficient synthesis. In this context, photocatalysis has emerged as a powerful technology for the synthesis of complex and often highly functionalized molecules. This Review aims to summarize the published contributions to the field from the life science industry, including research from industrial-academic partnerships. An overview of the synthetic methodologies developed and strategic applications in chemical synthesis, including peptide functionalization, isotope labeling, and both DNA-encoded and traditional library synthesis, is provided, along with a summary of the state-of-the-art in photoreactor technology and the effective upscaling of photocatalytic reactions.
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Affiliation(s)
- Lisa Candish
- Drug Discovery Sciences, Pharmaceuticals, Bayer AG, 42113 Wuppertal, Germany
| | - Karl D Collins
- Bayer Foundation, Public Affairs, Science and Sustainability, Bayer AG, 51368 Leverkusen, Germany
| | - Gemma C Cook
- Discovery High-Throughput Chemistry, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, U.K
| | - James J Douglas
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, U.K
| | - Adrián Gómez-Suárez
- Organic Chemistry, Bergische Universität Wuppertal, 42119 Wuppertal, Germany
| | - Anais Jolit
- Medicinal Chemistry Department, Neuroscience Discovery Research, AbbVie Deutschland GmbH & Co. KG, 67061 Ludwigshafen, Germany
| | - Sebastian Keess
- Medicinal Chemistry Department, Neuroscience Discovery Research, AbbVie Deutschland GmbH & Co. KG, 67061 Ludwigshafen, Germany
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192
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Chessari G, Grainger R, Holvey RS, Ludlow RF, Mortenson PN, Rees DC. C-H functionalisation tolerant to polar groups could transform fragment-based drug discovery (FBDD). Chem Sci 2021; 12:11976-11985. [PMID: 34667563 PMCID: PMC8457390 DOI: 10.1039/d1sc03563k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/30/2021] [Indexed: 12/28/2022] Open
Abstract
We have analysed 131 fragment-to-lead (F2L) examples targeting a wide variety of protein families published by academic and industrial laboratories between 2015-2019. Our assessment of X-ray structural data identifies the most common polar functional groups involved in fragment-protein binding are: N-H (hydrogen bond donors on aromatic and aliphatic N-H, amides and anilines; totalling 35%), aromatic nitrogen atoms (hydrogen bond acceptors; totalling 23%), and carbonyl oxygen group atoms (hydrogen bond acceptors on amides, ureas and ketones; totalling 22%). Furthermore, the elaboration of each fragment into its corresponding lead is analysed to identify the nominal synthetic growth vectors. In ∼80% of cases, growth originates from an aromatic or aliphatic carbon on the fragment and more than 50% of the total bonds formed are carbon-carbon bonds. This analysis reveals that growth from carbocentric vectors is key and therefore robust C-H functionalisation methods that tolerate the innate polar functionality on fragments could transform fragment-based drug discovery (FBDD). As a further resource to the community, we have provided the full data of our analysis as well as an online overlay page of the X-ray structures of the fragment hit and leads: https://astx.com/interactive/F2L-2021/.
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Affiliation(s)
- Gianni Chessari
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Rachel Grainger
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Rhian S Holvey
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | | | - Paul N Mortenson
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - David C Rees
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
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193
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Badir SO, Lipp A, Krumb M, Cabrera-Afonso MJ, Kammer LM, Wu VE, Huang M, Csakai A, Marcaurelle LA, Molander GA. Photoredox-mediated hydroalkylation and hydroarylation of functionalized olefins for DNA-encoded library synthesis. Chem Sci 2021; 12:12036-12045. [PMID: 34667569 PMCID: PMC8457374 DOI: 10.1039/d1sc03191k] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/04/2021] [Indexed: 12/29/2022] Open
Abstract
DNA-encoded library (DEL) technology features a time- and cost-effective interrogation format for the discovery of therapeutic candidates in the pharmaceutical industry. To develop DEL platforms, the implementation of water-compatible transformations that facilitate the incorporation of multifunctional building blocks (BBs) with high C(sp3) carbon counts is integral for success. In this report, a decarboxylative-based hydroalkylation of DNA-conjugated trifluoromethyl-substituted alkenes enabled by single-electron transfer (SET) and subsequent hydrogen atom termination through electron donor-acceptor (EDA) complex activation is detailed. In a further photoredox-catalyzed hydroarylation protocol, the coupling of functionalized, electronically unbiased olefins is achieved under air and within minutes of blue light irradiation through the intermediacy of reactive (hetero)aryl radical species with full retention of the DNA tag integrity. Notably, these processes operate under mild reaction conditions, furnishing complex structural scaffolds with a high density of pendant functional groups.
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Affiliation(s)
- Shorouk O Badir
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Alexander Lipp
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Matthias Krumb
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - María Jesús Cabrera-Afonso
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Lisa Marie Kammer
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Victoria E Wu
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Minxue Huang
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Adam Csakai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Lisa A Marcaurelle
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Gary A Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
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194
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Brüschweiler S, Fuchs JE, Bader G, McConnell DB, Konrat R, Mayer M. A Step toward NRF2-DNA Interaction Inhibitors by Fragment-Based NMR Methods. ChemMedChem 2021; 16:3576-3587. [PMID: 34524728 PMCID: PMC9293343 DOI: 10.1002/cmdc.202100458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/30/2021] [Indexed: 12/30/2022]
Abstract
The NRF2 transcription factor is a key regulator in cellular oxidative stress response, and acts as a tumor suppressor. Aberrant activation of NRF2 has been implicated in promoting chemo-resistance, tumor growth, and metastasis by activating its downstream target genes. Hence, inhibition of NRF2 promises to be an attractive therapeutic strategy to suppress cell proliferation and enhance cell apoptosis in cancer. Direct targeting of NRF2 with small-molecules to discover protein-DNA interaction inhibitors is challenging as it is a largely intrinsically disordered protein. To discover molecules that bind to NRF2 at the DNA binding interface, we performed an NMR-based fragment screen against its DNA-binding domain. We discovered several weakly binding fragment hits that bind to a region overlapping with the DNA binding site. Using SAR by catalogue we developed an initial structure-activity relationship for the most interesting initial hit series. By combining NMR chemical shift perturbations and data-driven docking, binding poses which agreed with NMR information and the observed SAR were elucidated. The herein discovered NRF2 hits and proposed binding modes form the basis for future structure-based optimization campaigns on this important but to date 'undrugged' cancer driver.
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Affiliation(s)
- Sven Brüschweiler
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Julian E Fuchs
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
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195
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Singh R, Bhatia H, Prakash P, Debroye E, Dey S, Dehaen W. Tandem Nenitzescu Reaction/Nucleophilic Aromatic Substitution to Form Novel Pyrido Fused Indole Frameworks. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Rashmi Singh
- Department of Chemistry Indian Institute of Technology (Indian School of Mines), Dhanbad Dhanbad 826004 India
- Molecular Design and Synthesis Department of Chemistry KU Leuven Celestijnenlaan 200F 3001 Leuven Belgium
| | - Harshita Bhatia
- Molecular Imaging and Photonics Department of Chemistry KU Leuven Celestijnenlaan 200F 3001 Leuven Belgium
| | - Prabhat Prakash
- Materials Engineering Indian Institute of Technology Gandhinagar Palaj, Gandhinagar 382355 Gujarat India
| | - Elke Debroye
- Molecular Imaging and Photonics Department of Chemistry KU Leuven Celestijnenlaan 200F 3001 Leuven Belgium
| | - Swapan Dey
- Department of Chemistry Indian Institute of Technology (Indian School of Mines), Dhanbad Dhanbad 826004 India
| | - Wim Dehaen
- Molecular Design and Synthesis Department of Chemistry KU Leuven Celestijnenlaan 200F 3001 Leuven Belgium
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196
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Bolcato G, Cescon E, Pavan M, Bissaro M, Bassani D, Federico S, Spalluto G, Sturlese M, Moro S. A Computational Workflow for the Identification of Novel Fragments Acting as Inhibitors of the Activity of Protein Kinase CK1δ. Int J Mol Sci 2021; 22:ijms22189741. [PMID: 34575906 PMCID: PMC8471300 DOI: 10.3390/ijms22189741] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 11/24/2022] Open
Abstract
Fragment-Based Drug Discovery (FBDD) has become, in recent years, a consolidated approach in the drug discovery process, leading to several drug candidates under investigation in clinical trials and some approved drugs. Among these successful applications of the FBDD approach, kinases represent a class of targets where this strategy has demonstrated its real potential with the approved kinase inhibitor Vemurafenib. In the Kinase family, protein kinase CK1 isoform δ (CK1δ) has become a promising target in the treatment of different neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis. In the present work, we set up and applied a computational workflow for the identification of putative fragment binders in large virtual databases. To validate the method, the selected compounds were tested in vitro to assess the CK1δ inhibition.
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Affiliation(s)
- Giovanni Bolcato
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy; (G.B.); (M.P.); (M.B.); (D.B.); (M.S.)
| | - Eleonora Cescon
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgeri 1, 34127 Trieste, Italy; (E.C.); (S.F.); (G.S.)
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy; (G.B.); (M.P.); (M.B.); (D.B.); (M.S.)
| | - Maicol Bissaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy; (G.B.); (M.P.); (M.B.); (D.B.); (M.S.)
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy; (G.B.); (M.P.); (M.B.); (D.B.); (M.S.)
| | - Stephanie Federico
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgeri 1, 34127 Trieste, Italy; (E.C.); (S.F.); (G.S.)
| | - Giampiero Spalluto
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgeri 1, 34127 Trieste, Italy; (E.C.); (S.F.); (G.S.)
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy; (G.B.); (M.P.); (M.B.); (D.B.); (M.S.)
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy; (G.B.); (M.P.); (M.B.); (D.B.); (M.S.)
- Correspondence:
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197
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Jeridi S, Rak A, Gupta A, Soule P. Fast Mek1 Hit Identification with TRIC Technology Correlates Well with Other Biophysical Methods. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:1014-1019. [PMID: 34238039 DOI: 10.1177/24725552211026267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The variety and complexity of drug targets are expanding rapidly. At the same time, there is significant interest in exploring a larger chemical space to identify new candidates. Fragment-based screening (FBS) has emerged as a popular alternative to traditional high-throughput screening campaigns to identify such drug candidates. FBS identifies hit fragments that exhibit weak interactions with the target of interest, thereby enabling the rational design of small-molecule compounds from the identified hit fragments, which serve as building blocks. This strategy reduces the number of molecules to screen while also allowing the exploration of a greater chemical space.Here we use temperature-related intensity change (TRIC) technology to perform FBS against the target MAPK/ERK kinase-1 (Mek1). TRIC describes the change in fluorescence intensity of a fluorescently labeled molecule upon a change in temperature. This intensity variation is dependent on the physicochemical environment in the vicinity of the dye and strongly affected by binding events. Thus, the detection of binding events is independent of mass, making TRIC an ideal tool for FBS.Using only 150 pmol of labeled Mek1, the authors screened 193 fragments from a prescreened library in less than 1 h of measurement time, leading to 66 hits. Among those hits, they identified more than 80% of the published top hits found using orthogonal techniques. Furthermore, TRIC allowed the identification of fragments that were of poor solubility but could be mistaken as false-positive hits in other methods.
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Affiliation(s)
- Semir Jeridi
- Application Team, NanoTemper Technologies GmbH, Munich, Germany
| | - Alexey Rak
- Structure-Design-Informatics, Sanofi R&D, Vitry sur Seine, France
| | - Amit Gupta
- Product Management, NanoTemper Technologies GmbH, Munich, Germany
| | - Pierre Soule
- Application Team, NanoTemper Technologies GmbH, Munich, Germany
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Metz A, Wollenhaupt J, Glöckner S, Messini N, Huber S, Barthel T, Merabet A, Gerber HD, Heine A, Klebe G, Weiss MS. Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking. Acta Crystallogr D Struct Biol 2021; 77:1168-1182. [PMID: 34473087 PMCID: PMC8411975 DOI: 10.1107/s2059798321008196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/09/2021] [Indexed: 11/10/2022] Open
Abstract
In recent years, crystallographic fragment screening has matured into an almost routine experiment at several modern synchrotron sites. The hits of the screening experiment, i.e. small molecules or fragments binding to the target protein, are revealed along with their 3D structural information. Therefore, they can serve as useful starting points for further structure-based hit-to-lead development. However, the progression of fragment hits to tool compounds or even leads is often hampered by a lack of chemical feasibility. As an attractive alternative, compound analogs that embed the fragment hit structurally may be obtained from commercial catalogs. Here, a workflow is reported based on filtering and assessing such potential follow-up compounds by template docking. This means that the crystallographic binding pose was integrated into the docking calculations as a central starting parameter. Subsequently, the candidates are scored on their interactions within the binding pocket. In an initial proof-of-concept study using five starting fragments known to bind to the aspartic protease endothiapepsin, 28 follow-up compounds were selected using the designed workflow and their binding was assessed by crystallography. Ten of these compounds bound to the active site and five of them showed significantly increased affinity in isothermal titration calorimetry of up to single-digit micromolar affinity. Taken together, this strategy is capable of efficiently evolving the initial fragment hits without major synthesis efforts and with full control by X-ray crystallography.
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Affiliation(s)
- Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Steffen Glöckner
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Niki Messini
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Simon Huber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Ahmed Merabet
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Hans-Dieter Gerber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
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199
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Zhou Y, Shen W, Peng J, Deng Y, Li X. Identification of isoform/domain-selective fragments from the selection of DNA-encoded dynamic library. Bioorg Med Chem 2021; 45:116328. [PMID: 34364223 DOI: 10.1016/j.bmc.2021.116328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 12/18/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged to be a powerful ligand screening technology in drug discovery. Recently, we reported a DNA-encoded dynamic library (DEDL) approach that combines the principle of traditional dynamic combinatorial library (DCL) with DEL. DEDL has shown excellent potential in fragment-based ligand discovery with a variety of protein targets. Here, we further tested the utility of DEDL in identifying low molecular weight fragments that are selective for different isoforms or domains of the same protein family. A 10,000-member DEDL was selected against sirtuin-1, 2, and 5 (SIRT1, 2, 5) and the BD1 and BD2 domains of bromodomain 4 (BRD4), respectively. Albeit with modest potency, a series of isoform/domain-selective fragments were identified and the corresponding inhibitors were derived by fragment linking.
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Affiliation(s)
- Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Wenyin Shen
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Jianzhao Peng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Yuqing Deng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region; Laboratory for Synthetic Chemistry and Chemical Biology, Health@InnoHK, Innovation and Technology Commission, Hong Kong Special Administrative Region
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200
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Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chem Rev 2021; 122:7327-7385. [PMID: 34449207 DOI: 10.1021/acs.chemrev.1c00293] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Small molecule drug discovery has been propelled by the continual development of novel scientific methodologies to occasion therapeutic advances. Although established biophysical methods can be used to obtain information regarding the molecular mechanisms underlying drug action, these approaches are often inefficient, low throughput, and ineffective in the analysis of heterogeneous systems including dynamic oligomeric assemblies and proteins that have undergone extensive post-translational modification. Native mass spectrometry can be used to probe protein-small molecule interactions with unprecedented speed and sensitivity, providing unique insights into polydisperse biomolecular systems that are commonly encountered during the drug discovery process. In this review, we describe potential and proven applications of native MS in the study of interactions between small, drug-like molecules and proteins, including large multiprotein complexes and membrane proteins. Approaches to quantify the thermodynamic and kinetic properties of ligand binding are discussed, alongside a summary of gas-phase ion activation techniques that have been used to interrogate the structure of protein-small molecule complexes. We additionally highlight some of the key areas in modern drug design for which native mass spectrometry has elicited significant advances. Future developments and applications of native mass spectrometry in drug discovery workflows are identified, including potential pathways toward studying protein-small molecule interactions on a whole-proteome scale.
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Affiliation(s)
- Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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