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Asano W, Hantani R, Uhara T, Debaene F, Nomura A, Yamaguchi K, Adachi T, Otake K, Harada K, Hantani Y. Screening approaches for the identification of Nrf2-Keap1 protein-protein interaction inhibitors targeting hot spot residues. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100125. [PMID: 37935317 DOI: 10.1016/j.slasd.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/29/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023]
Abstract
Protein-protein interactions (PPIs) play a crucial role in most biological processes and are important targets in the development of therapeutic agents. However, small molecule drug discovery that targets PPIs remains very challenging. Targeting hot spot residues is considered the best option for inhibiting such interactions, but there are few examples of how knowledge of hot spots can be used in high throughput screening to find hit compounds. A substrate adaptor protein for a ubiquitin ligase complex, Kelch-like ECH-associated protein 1 (Keap1), negatively modulates the expression of genes involved in cellular protection against oxidative stress. Here, we focused on three arginine hot spot residues in the Keap1 substrate binding pocket (Arg380, Arg415, and Arg483), and screened the carboxylic acid library owned by Japan Tobacco Inc. for compounds that interact with the arginine residues in differential scanning fluorescence assays. Furthermore, we identified several small molecule compounds that specifically bind to the Keap1 Kelch domain hot spots by comparing binding to alanine mutant proteins (R380A, R415A, and R483A) with binding to the wild-type protein using surface plasmon resonance (SPR) screening. These compounds inhibited the protein-protein interaction between the Keap1 Kelch domain and the nuclear factor erythroid 2-related factor 2 (Nrf2) peptide, and the ubiquitination of Nrf2 catalyzed by the Cul3/RINGBox 1 E3 ligase. In addition, the binding mode of one compound (Compound 4) was determined by X-ray crystallography after validation of binding by isothermal titration calorimetry, native mass spectrometry, and nuclear magnetic resonance. Compound 4 had favorable thermodynamic properties, and noncovalently bound to Keap1 with a stoichiometry of 1:1. Our results suggest that Compound 4 could potentially be developed into effective therapeutic or preventive agents for a variety of diseases and conditions such as oxidative stress response, inflammation, and carcinogenesis. We believe that the use of a set of complementary biophysical techniques including the SPR assay with single alanine mutant of hot spots provides opportunities to identify hit compounds for developing inhibitors of PPIs.
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Affiliation(s)
- Wataru Asano
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Rie Hantani
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Toru Uhara
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - François Debaene
- Biophysics Dpt/ MS Platform, NovAliX, 16 rue d'Ankara, Strasbourg 67000, France
| | - Akihiro Nomura
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Keishi Yamaguchi
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tsuyoshi Adachi
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kazuki Otake
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kazuhito Harada
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yoshiji Hantani
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.
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2
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Gooran N, Kopra K. Fluorescence-Based Protein Stability Monitoring-A Review. Int J Mol Sci 2024; 25:1764. [PMID: 38339045 PMCID: PMC10855643 DOI: 10.3390/ijms25031764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.
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Affiliation(s)
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland;
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3
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Kumar V, Chunchagatta Lakshman PK, Prasad TK, Manjunath K, Bairy S, Vasu AS, Ganavi B, Jasti S, Kamariah N. Target-based drug discovery: Applications of fluorescence techniques in high throughput and fragment-based screening. Heliyon 2024; 10:e23864. [PMID: 38226204 PMCID: PMC10788520 DOI: 10.1016/j.heliyon.2023.e23864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024] Open
Abstract
Target-based discovery of first-in-class therapeutics demands an in-depth understanding of the molecular mechanisms underlying human diseases. Precise measurements of cellular and biochemical activities are critical to gain mechanistic knowledge of biomolecules and their altered function in disease conditions. Such measurements enable the development of intervention strategies for preventing or treating diseases by modulation of desired molecular processes. Fluorescence-based techniques are routinely employed for accurate and robust measurements of in-vitro activity of molecular targets and for discovering novel chemical molecules that modulate the activity of molecular targets. In the current review, the authors focus on the applications of fluorescence-based high throughput screening (HTS) and fragment-based ligand discovery (FBLD) techniques such as fluorescence polarization (FP), Förster resonance energy transfer (FRET), fluorescence thermal shift assay (FTSA) and microscale thermophoresis (MST) for the discovery of chemical probe to exploring target's role in disease biology and ultimately, serve as a foundation for drug discovery. Some recent advancements in these techniques for compound library screening against important classes of drug targets, such as G-protein-coupled receptors (GPCRs) and GTPases, as well as phosphorylation- and acetylation-mediated protein-protein interactions, are discussed. Overall, this review presents a landscape of how these techniques paved the way for the discovery of small-molecule modulators and biologics against these targets for therapeutic benefits.
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Affiliation(s)
| | | | - Thazhe Kootteri Prasad
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Kavyashree Manjunath
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Sneha Bairy
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Akshaya S. Vasu
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - B. Ganavi
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Subbarao Jasti
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Neelagandan Kamariah
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
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4
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Theuretzbacher U, Blasco B, Duffey M, Piddock LJV. Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections. Nat Rev Drug Discov 2023; 22:957-975. [PMID: 37833553 DOI: 10.1038/s41573-023-00791-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 10/15/2023]
Abstract
Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.
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Affiliation(s)
| | - Benjamin Blasco
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Maëlle Duffey
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland.
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5
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Davoine C, Traina A, Evrard J, Lanners S, Fillet M, Pochet L. Coumarins as factor XIIa inhibitors: Potency and selectivity improvements using a fragment-based strategy. Eur J Med Chem 2023; 259:115636. [PMID: 37478556 DOI: 10.1016/j.ejmech.2023.115636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Previously, we described weak coumarin inhibitors of factor XIIa, a promising target for artificial surface-induced thrombosis and various inflammatory diseases. In this work, we used fragment-based drug discovery approach to improve our coumarin series. First, we screened about 200 fragments for the S1 pocket. The S1 pocket of trypsin-like serine proteases, such as factor XIIa, is highly conserved and is known to drive a major part of the association energy. From the screening, we selected fragments displaying a micromolar activity and studied their selectivity on other serine proteases. Then, these fragments were merged to our coumarin templates, leading to the generation of nanomolar inhibitors. The mechanism of inhibition was further studied by mass spectrometry demonstrating the covalent binding through the formation of an acyl enzyme complex. The most potent compound was tested in plasma to evaluate its stability and efficacy on coagulation assays. It exhibited a plasmatic half-life of 1.9 h and a good selectivity for the intrinsic coagulation pathway over the extrinsic one.
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Affiliation(s)
- Clara Davoine
- Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium; Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Place Du 20 Août 7, 4000, Liège, Belgium
| | - Amandine Traina
- Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Jonathan Evrard
- Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Steve Lanners
- Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Place Du 20 Août 7, 4000, Liège, Belgium
| | - Lionel Pochet
- Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium.
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6
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Narayanan D, Tran KT, Pallesen JS, Solbak SMØ, Qin Y, Mukminova E, Luchini M, Vasilyeva KO, González Chichón D, Goutsiou G, Poulsen C, Haapanen N, Popowicz GM, Sattler M, Olagnier D, Gajhede M, Bach A. Development of Noncovalent Small-Molecule Keap1-Nrf2 Inhibitors by Fragment-Based Drug Discovery. J Med Chem 2022; 65:14481-14526. [PMID: 36263945 DOI: 10.1021/acs.jmedchem.2c00830] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeting the protein-protein interaction (PPI) between the transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) and its repressor, Kelch-like ECH-associated protein 1 (Keap1), constitutes a promising strategy for treating diseases involving oxidative stress and inflammation. Here, a fragment-based drug discovery (FBDD) campaign resulted in novel, high-affinity (Ki = 280 nM), and cell-active noncovalent small-molecule Keap1-Nrf2 PPI inhibitors. We screened 2500 fragments using orthogonal assays─fluorescence polarization (FP), thermal shift assay (TSA), and surface plasmon resonance (SPR)─and validated the hits by saturation transfer difference (STD) NMR, leading to 28 high-priority hits. Thirteen co-structures showed fragments binding mainly in the P4 and P5 subpockets of Keap1's Kelch domain, and three fluorenone-based fragments featuring a novel binding mode were optimized by structure-based drug discovery. We thereby disclose several fragment hits, including their binding modes, and show how FBDD can be performed to find new small-molecule Keap1-Nrf2 PPI inhibitors.
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Affiliation(s)
- Dilip Narayanan
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Kim T Tran
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jakob S Pallesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Sara M Ø Solbak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Yuting Qin
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Elina Mukminova
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Martina Luchini
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Kristina O Vasilyeva
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Dorleta González Chichón
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Georgia Goutsiou
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Cecilie Poulsen
- Department of Biomedicine, Faculty of Health, Aarhus University, 8000 Aarhus C, Denmark
| | - Nanna Haapanen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - David Olagnier
- Department of Biomedicine, Faculty of Health, Aarhus University, 8000 Aarhus C, Denmark
| | - Michael Gajhede
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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7
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Eguida M, Schmitt-Valencia C, Hibert M, Villa P, Rognan D. Target-Focused Library Design by Pocket-Applied Computer Vision and Fragment Deep Generative Linking. J Med Chem 2022; 65:13771-13783. [PMID: 36256484 DOI: 10.1021/acs.jmedchem.2c00931] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We here describe a computational approach (POEM: Pocket Oriented Elaboration of Molecules) to drive the generation of target-focused libraries while taking advantage of all publicly available structural information on protein-ligand complexes. A collection of 31 384 PDB-derived images with key shapes and pharmacophoric properties, describing fragment-bound microenvironments, is first aligned to the query target cavity by a computer vision method. The fragments of the most similar PDB subpockets are then directly positioned in the query cavity using the corresponding image transformation matrices. Lastly, suitable connectable atoms of oriented fragment pairs are linked by a deep generative model to yield fully connected molecules. POEM was applied to generate a library of 1.5 million potential cyclin-dependent kinase 8 inhibitors. By synthesizing and testing as few as 43 compounds, a few nanomolar inhibitors were quickly obtained with limited resources in just two iterative cycles.
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Affiliation(s)
- Merveille Eguida
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS-Université de Strasbourg, F-67400Illkirch, France
| | - Christel Schmitt-Valencia
- Plateforme de Chimie Biologique Intégrative de Strasbourg, UAR3286 CNRS-Université de Strasbourg, Institut du Médicament de Strasbourg, F-67400Illkirch, France
| | - Marcel Hibert
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS-Université de Strasbourg, F-67400Illkirch, France
| | - Pascal Villa
- Plateforme de Chimie Biologique Intégrative de Strasbourg, UAR3286 CNRS-Université de Strasbourg, Institut du Médicament de Strasbourg, F-67400Illkirch, France
| | - Didier Rognan
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS-Université de Strasbourg, F-67400Illkirch, France
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8
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Alibay I, Magarkar A, Seeliger D, Biggin PC. Evaluating the use of absolute binding free energy in the fragment optimisation process. Commun Chem 2022; 5:105. [PMID: 36697714 PMCID: PMC9814858 DOI: 10.1038/s42004-022-00721-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/10/2022] [Indexed: 02/01/2023] Open
Abstract
Key to the fragment optimisation process within drug design is the need to accurately capture the changes in affinity that are associated with a given set of chemical modifications. Due to the weakly binding nature of fragments, this has proven to be a challenging task, despite recent advancements in leveraging experimental and computational methods. In this work, we evaluate the use of Absolute Binding Free Energy (ABFE) calculations in guiding fragment optimisation decisions, retrospectively calculating binding free energies for 59 ligands across 4 fragment elaboration campaigns. We first demonstrate that ABFEs can be used to accurately rank fragment-sized binders with an overall Spearman's r of 0.89 and a Kendall τ of 0.67, although often deviating from experiment in absolute free energy values with an RMSE of 2.75 kcal/mol. We then also show that in several cases, retrospective fragment optimisation decisions can be supported by the ABFE calculations. Comparing against cheaper endpoint methods, namely Nwat-MM/GBSA, we find that ABFEs offer better ranking power and correlation metrics. Our results indicate that ABFE calculations can usefully guide fragment elaborations to maximise affinity.
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Affiliation(s)
- Irfan Alibay
- grid.4991.50000 0004 1936 8948Department of Biochemistry, The University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Aniket Magarkar
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach an de Riß, Germany
| | - Daniel Seeliger
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach an de Riß, Germany ,Present Address: Exscientia Inc, Office 400E, 2125 Biscayne Blvd, Miami, FL 33137 USA
| | - Philip Charles Biggin
- grid.4991.50000 0004 1936 8948Department of Biochemistry, The University of Oxford, South Parks Road, OX1 3QU Oxford, UK
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9
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Kozielski F, Sele C, Talibov VO, Lou J, Dong D, Wang Q, Shi X, Nyblom M, Rogstam A, Krojer T, Fisher Z, Knecht W. Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16. RSC Chem Biol 2022; 3:44-55. [PMID: 35128408 PMCID: PMC8729259 DOI: 10.1039/d1cb00135c] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022] Open
Abstract
Since the emergence of SARS-CoV-2 in 2019, Covid-19 has developed into a serious threat to our health, social and economic systems. Although vaccines have been developed in a tour-de-force and are now increasingly available, repurposing of existing drugs has been less successful. There is a clear need to develop new drugs against SARS-CoV-2 that can also be used against future coronavirus infections. Non-structural protein 10 (nsp10) is a conserved stimulator of two enzymes crucial for viral replication, nsp14 and nsp16, exhibiting exoribonuclease and methyltransferase activities. Interfering with RNA proofreading or RNA cap formation represents intervention strategies to inhibit replication. We applied fragment-based screening using nano differential scanning fluorometry and X-ray crystallography to identify ligands targeting SARS-CoV-2 nsp10. We identified four fragments located in two distinct sites: one can be modelled to where it would be located in the nsp14-nsp10 complex interface and the other in the nsp16-nsp10 complex interface. Microscale thermophoresis (MST) experiments were used to quantify fragment affinities for nsp10. Additionally, we showed by MST that the interaction by nsp14 and 10 is weak and thereby that complex formation could be disrupted by small molecules. The fragments will serve as starting points for the development of more potent analogues using fragment growing techniques and structure-based drug design.
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Affiliation(s)
- Frank Kozielski
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Céleste Sele
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
| | | | - Jiaqi Lou
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Danni Dong
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Qian Wang
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Xinyue Shi
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Maria Nyblom
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
| | - Annika Rogstam
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
| | - Tobias Krojer
- BioMAX beamline, MAX IV Laboratory Fotongatan 2 22484 Lund Sweden
| | - Zoë Fisher
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
- European Spallation Source ERIC P.O. Box 176 22100 Lund Sweden +46 721792250
| | - Wolfgang Knecht
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
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10
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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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11
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Holdgate GA, Bergsdorf C. Applications of Biophysics in Early Drug Discovery. SLAS DISCOVERY 2021; 26:945-946. [PMID: 34415216 DOI: 10.1177/24725552211035123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
| | - Christian Bergsdorf
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
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Moreira-Filho JT, Silva AC, Dantas RF, Gomes BF, Souza Neto LR, Brandao-Neto J, Owens RJ, Furnham N, Neves BJ, Silva-Junior FP, Andrade CH. Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. Front Immunol 2021; 12:642383. [PMID: 34135888 PMCID: PMC8203334 DOI: 10.3389/fimmu.2021.642383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022] Open
Abstract
Schistosomiasis is a parasitic disease caused by trematode worms of the genus Schistosoma and affects over 200 million people worldwide. The control and treatment of this neglected tropical disease is based on a single drug, praziquantel, which raises concerns about the development of drug resistance. This, and the lack of efficacy of praziquantel against juvenile worms, highlights the urgency for new antischistosomal therapies. In this review we focus on innovative approaches to the identification of antischistosomal drug candidates, including the use of automated assays, fragment-based screening, computer-aided and artificial intelligence-based computational methods. We highlight the current developments that may contribute to optimizing research outputs and lead to more effective drugs for this highly prevalent disease, in a more cost-effective drug discovery endeavor.
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Affiliation(s)
- José T. Moreira-Filho
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Arthur C. Silva
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Rafael F. Dantas
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Barbara F. Gomes
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lauro R. Souza Neto
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jose Brandao-Neto
- Diamond Light Source Ltd., Didcot, United Kingdom
- Research Complex at Harwell, Didcot, United Kingdom
| | - Raymond J. Owens
- The Rosalind Franklin Institute, Harwell, United Kingdom
- Division of Structural Biology, The Wellcome Centre for Human Genetic, University of Oxford, Oxford, United Kingdom
| | - Nicholas Furnham
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bruno J. Neves
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Floriano P. Silva-Junior
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carolina H. Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
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Emwas AH, Szczepski K, Poulson BG, Chandra K, McKay RT, Dhahri M, Alahmari F, Jaremko L, Lachowicz JI, Jaremko M. NMR as a "Gold Standard" Method in Drug Design and Discovery. Molecules 2020; 25:E4597. [PMID: 33050240 PMCID: PMC7594251 DOI: 10.3390/molecules25204597] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Studying disease models at the molecular level is vital for drug development in order to improve treatment and prevent a wide range of human pathologies. Microbial infections are still a major challenge because pathogens rapidly and continually evolve developing drug resistance. Cancer cells also change genetically, and current therapeutic techniques may be (or may become) ineffective in many cases. The pathology of many neurological diseases remains an enigma, and the exact etiology and underlying mechanisms are still largely unknown. Viral infections spread and develop much more quickly than does the corresponding research needed to prevent and combat these infections; the present and most relevant outbreak of SARS-CoV-2, which originated in Wuhan, China, illustrates the critical and immediate need to improve drug design and development techniques. Modern day drug discovery is a time-consuming, expensive process. Each new drug takes in excess of 10 years to develop and costs on average more than a billion US dollars. This demonstrates the need of a complete redesign or novel strategies. Nuclear Magnetic Resonance (NMR) has played a critical role in drug discovery ever since its introduction several decades ago. In just three decades, NMR has become a "gold standard" platform technology in medical and pharmacology studies. In this review, we present the major applications of NMR spectroscopy in medical drug discovery and development. The basic concepts, theories, and applications of the most commonly used NMR techniques are presented. We also summarize the advantages and limitations of the primary NMR methods in drug development.
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Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Kacper Szczepski
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Benjamin Gabriel Poulson
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Kousik Chandra
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Ryan T. McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada;
| | - Manel Dhahri
- Biology Department, Faculty of Science, Taibah University, Yanbu El-Bahr 46423, Saudi Arabia;
| | - Fatimah Alahmari
- Nanomedicine Department, Institute for Research and Medical, Consultations (IRMC), Imam Abdulrahman Bin Faisal University (IAU), Dammam 31441, Saudi Arabia;
| | - Lukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, Università di Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
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