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Pagba CV, Gupta AK, Dilsha K, Sadrpour P, Jakubec J, Prakash P, van der Hoeven D, Cho KJ, Gilbertson S, Gorfe AA. Biophysical and Biochemical Characterization of Structurally Diverse Small Molecule Hits for KRAS Inhibition. Chembiochem 2024; 25:e202300827. [PMID: 38349283 DOI: 10.1002/cbic.202300827] [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: 12/12/2023] [Revised: 02/12/2024] [Indexed: 03/08/2024]
Abstract
We describe six compounds as early hits for the development of direct inhibitors of KRAS, an important anticancer drug target. We show that these compounds bind to KRAS with affinities in the low micromolar range and exert different effects on its interactions with binding partners. Some of the compounds exhibit selective binding to the activated form of KRAS and inhibit signal transduction through both the MAPK or the phosphatidylinositide 3-kinase PI3K-protein kinase B (AKT) pathway in cells expressing mutant KRAS. Most inhibit intrinsic and/or SOS-mediated KRAS activation while others inhibit RAS-effector interaction. We propose these compounds as starting points for the development of non-covalent allosteric KRAS inhibitors.
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Affiliation(s)
- Cynthia V Pagba
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Amit K Gupta
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Kasuni Dilsha
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, TX 77204, USA
| | - Parisa Sadrpour
- Department of Biochemistry and Molecular Biology, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
| | - Jacob Jakubec
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Priyanka Prakash
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Dharini van der Hoeven
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge St., Houston, Texas, 77030, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
| | - Scott Gilbertson
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, TX 77204, USA
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
- Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, UTHealth MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, 6431 Fannin St., Houston, Texas, 77030, USA
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Yuan PX, Song SS, Zhan J, Chen C, Wang AJ, Feng JJ. Self-enhanced Electrochemiluminescence Luminophore Based on Pd Nanocluster-Anchored Metal Organic Frameworks via Ion Annihilation for Sensitive Cell Assay of Human Lung Cancer. Anal Chem 2023; 95:18572-18578. [PMID: 38064592 DOI: 10.1021/acs.analchem.3c04423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Electrochemiluminescence (ECL) has attracted significant interest in the analysis of cancer cells, where the ruthenium(II)-based emitter demonstrates urgency and feasibility to improve the ECL efficiency. In this work, the self-enhanced ECL luminophore was prepared by covalent anchoring of Pd nanoclusters on aminated metal organic frameworks (Pd NCs@MOFs), followed by linkage with bis(2,2'-bipyridine)-5-amino-1,10-phenanthroline ruthenium(II) (RuP). The resultant luminophore showed 214-fold self-magnification in the ECL efficiency over RuP alone, combined by promoting the interfacial photoelectron transfer. The enhanced mechanism through ion annihilation was critically proved by controlled experiments and density functional theory (DFT) calculations. Based on the above, a "signal off" ECL biosensor was built by assembly of tyrosine kinase 7 (PTK-7) aptamer (Apt) on the established sensing platform for analysis of human lung cancer cells (A549). The built sensor showed a lower detection limit of 8 cells mL-1, achieving the single-cell detection. This work reported a self-enhanced strategy for synthesis of advanced ECL emitters, combined by exploring the ECL biosensing devices in the single-cell analysis of cancers.
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Affiliation(s)
- Pei-Xin Yuan
- Key laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Shu-Shu Song
- Key laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Jiale Zhan
- Key laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Can Chen
- Key laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ai-Jun Wang
- Key laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Jiu-Ju Feng
- Key laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
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Bingham M, Pesnot T, Scott AD. Biophysical screening and characterisation in medicinal chemistry. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:61-104. [PMID: 37981351 DOI: 10.1016/bs.pmch.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
In the last two decades the use of biophysical assays and methods in medicinal chemistry has increased significantly, to meet the demands of the novel targets and modalities that drug discoverers are looking to tackle. The desire to obtain accurate affinities, kinetics, thermodynamics and structural data as early as possible in the drug discovery process has fuelled this innovation. This review introduces the principles underlying the techniques in common use and provides a perspective on the weaknesses and strengths of different methods. Case studies are used to further illustrate some of the applications in medicinal chemistry and a discussion of the emerging biophysical methods on the horizon is presented.
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Pujol-Vila F, Escudero P, Güell-Grau P, Pascual-Izarra C, Villa R, Alvarez M. Direct Color Observation of Light-Driven Molecular Conformation-Induced Stress. SMALL METHODS 2022; 6:e2101283. [PMID: 35174993 DOI: 10.1002/smtd.202101283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Although usually complex to handle, nanomechanical sensors are exceptional, label-free tools for monitoring molecular conformational changes, which makes them of paramount importance in understanding biomolecular interactions. Herein, a simple and inexpensive mechanical imaging approach based on low-stiffness cantilevers with structural coloration (mechanochromic cantilevers (MMC)) is demonstrated, able to monitor and quantify molecular conformational changes with similar sensitivity to the classical optical beam detection method of cantilever-based sensors (≈4.6 × 10-3 N m-1 ). This high sensitivity is achieved by using a white light and an RGB camera working in the reflection configuration. The sensor performance is demonstrated by monitoring the UV-light induced reversible conformational changes of azobenzene molecules coating. The trans-cis isomerization of the azobenzene molecules induces a deflection of the cantilevers modifying their diffracted color, which returns to the initial state by cis-trans relaxation. Interestingly, the mechanical imaging enables a simultaneous 2D mapping of the response thus enhancing the spatial resolution of the measurements. A tight correlation is found between the color output and the cantilever's deflection and curvature angle (sensitivities of 5 × 10-3 Hue µm-1 and 1.5 × 10-1 Hue (°)-1 ). These findings highlight the suitability of low-stiffness MMC as an enabling technology for monitoring molecular changes with unprecedented simplicity, high-throughput capability, and functionalities.
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Affiliation(s)
- Ferran Pujol-Vila
- Instituto de Microelectrónica de Barcelona (IMB-CNM, CSIC), Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Pedro Escudero
- Instituto de Microelectrónica de Barcelona (IMB-CNM, CSIC), Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Facultad de Ingeniería y Tecnologías de la Información y la Comunicación, Universidad Tecnológica Indoamérica, Ambato, 180103, Ecuador
| | - Pau Güell-Grau
- Instituto de Microelectrónica de Barcelona (IMB-CNM, CSIC), Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | | | - Rosa Villa
- Instituto de Microelectrónica de Barcelona (IMB-CNM, CSIC), Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Networking Research Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 50018, Madrid, Spain
| | - Mar Alvarez
- Instituto de Microelectrónica de Barcelona (IMB-CNM, CSIC), Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Networking Research Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 50018, Madrid, Spain
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5
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Le Breton G, Bonhomme O, Benichou E, Loison C. First Hyperpolarizability of Water in Bulk Liquid Phase: Long-Range Electrostatic Effects Included via the Second Hyperpolarizability. Phys Chem Chem Phys 2022; 24:19463-19472. [DOI: 10.1039/d2cp00803c] [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
The molecular first hyperpolarizability β contributes to second-order optical non-linear signals collected from molecular liquids. For the Second Harmonic Generation (SHG) response, the first hyperpolarizability β (2ω,ω,ω) often depends on...
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Le Breton G, Bonhomme O, Brevet PF, Benichou E, Loison C. First hyperpolarizability of water at the air-vapor interface: a QM/MM study questions standard experimental approximations. Phys Chem Chem Phys 2021; 23:24932-24941. [PMID: 34726679 DOI: 10.1039/d1cp02258j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Surface Second-Harmonic Generation (S-SHG) experiments provide a unique approach to probe interfaces. One important issue for S-SHG is how to interpret the S-SHG intensities at the molecular level. Established frameworks commonly assume that each molecule emits light according to an average molecular hyperpolarizability tensor β(-2ω,ω,ω). However, for water molecules, this first hyperpolarizability is known to be extremely sensitive to their environment. We have investigated the molecular first hyperpolarizability of water molecules within the liquid-vapor interface, using a quantum description with explicit, inhomogeneous electrostatic embedding. The resulting average molecular first hyperpolarizability tensor depends on the distance relative to the interface, and it practically respects the Kleinman symmetry everywhere in the liquid. Within this numerical approach, based on the dipolar approximation, the water layer contributing to the Surface Second Harmonic Generation (S-SHG) intensity is less than a nanometer. The results reported here question standard interpretations based on a single, averaged hyperpolarizability for all molecules at the interface. Not only the molecular first hyperpolarizability tensor significantly depends on the distance relative to the interface, but it is also correlated to the molecular orientation. Such hyperpolarizability fluctuations may impact the S-SHG intensity emitted by an aqueous interface.
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Affiliation(s)
- Guillaume Le Breton
- University of Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France.
| | - Oriane Bonhomme
- University of Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France.
| | - Pierre-François Brevet
- University of Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France.
| | - Emmanuel Benichou
- University of Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France.
| | - Claire Loison
- University of Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France.
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7
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Analytical challenges of glycosaminoglycans at biological interfaces. Anal Bioanal Chem 2021; 414:85-93. [PMID: 34647134 PMCID: PMC8514262 DOI: 10.1007/s00216-021-03705-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 11/15/2022]
Abstract
The analysis of glycosaminoglycans (GAGs) is a challenging task due to their high structural heterogeneity, which results in diverse GAG chains with similar chemical properties. Simultaneously, it is of high importance to understand their role and behavior in biological systems. It has been known for decades now that GAGs can interact with lipid molecules and thus contribute to the onset of atherosclerosis, but their interactions at and with biological interfaces, such as the cell membrane, are yet to be revealed. Here, analytical approaches that could yield important knowledge on the GAG-cell membrane interactions as well as the synthetic and analytical advances that make their study possible are discussed. Due to recent developments in laser technology, we particularly focus on nonlinear spectroscopic methods, especially vibrational sum-frequency generation spectroscopy, which has the potential to unravel the structural complexity of heterogeneous biological interfaces in contact with GAGs, in situ and in real time.
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Lundquist KP, Panchal V, Gotfredsen CH, Brenk R, Clausen MH. Fragment-Based Drug Discovery for RNA Targets. ChemMedChem 2021; 16:2588-2603. [PMID: 34101375 DOI: 10.1002/cmdc.202100324] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Indexed: 12/26/2022]
Abstract
Rapid development within the fields of both fragment-based drug discovery (FBDD) and medicinal targeting of RNA provides possibilities for combining technologies and methods in novel ways. This review provides an overview of fragment-based screening (FBS) against RNA targets, including a discussion of the most recently used screening and hit validation methods such as NMR spectroscopy, X-ray crystallography, and virtual screening methods. A discussion of fragment library design based on research from small-molecule RNA binders provides an overview on both the currently limited guidelines within RNA-targeting fragment library design, and future possibilities. Finally, future perspectives are provided on screening and hit validation methods not yet used in combination with both fragment screening and RNA targets.
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Affiliation(s)
- Kasper P Lundquist
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs. Lyngby, Denmark
| | - Vipul Panchal
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5020, Bergen, Norway
| | - Charlotte H Gotfredsen
- NMR Center ⋅ DTU, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs. Lyngby, Denmark
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5020, Bergen, Norway
| | - Mads H Clausen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs. Lyngby, Denmark
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9
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FitzGerald EA, Butko MT, Boronat P, Cederfelt D, Abramsson M, Ludviksdottir H, van Muijlwijk-Koezen JE, de Esch IJP, Dobritzsch D, Young T, Danielson UH. Discovery of fragments inducing conformational effects in dynamic proteins using a second-harmonic generation biosensor. RSC Adv 2021; 11:7527-7537. [PMID: 35423271 PMCID: PMC8694943 DOI: 10.1039/d0ra09844b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/28/2021] [Indexed: 01/13/2023] Open
Abstract
Biophysical screening of compound libraries for the identification of ligands that interact with a protein is efficient, but does typically not reveal if (or how) ligands may interfere with its functional properties. For this a biochemical/functional assay is required. But for proteins whose function is dependent on a conformational change, such assays are typically complex or have low throughput. Here we have explored a high-throughput second-harmonic generation (SHG) biosensor to detect fragments that induce conformational changes upon binding to a protein in real time and identify dynamic regions. Multiwell plate format SHG assays were developed for wild-type and six engineered single-cysteine mutants of acetyl choline binding protein (AChBP), a homologue to ligand gated ion channels (LGICs). They were conjugated with second harmonic-active labels via amine or maleimide coupling. To validate the assay, it was confirmed that the conformational changes induced in AChBP by nicotinic acetyl choline receptor (nAChR) agonists and antagonists were qualitatively different. A 1056 fragment library was subsequently screened against all variants and conformational modulators of AChBP were successfully identified, with hit rates from 9-22%, depending on the AChBP variant. A subset of four hits was selected for orthogonal validation and structural analysis. A time-resolved grating-coupled interferometry-based biosensor assay confirmed the interaction to be a reversible 1-step 1 : 1 interaction, and provided estimates of affinities and interaction kinetic rate constants (K D = 0.28-63 μM, k a = 0.1-6 μM-1 s-1, k d = 1 s-1). X-ray crystallography of two of the fragments confirmed their binding at a previously described conformationally dynamic site, corresponding to the regulatory site of LGICs. These results reveal that SHG has the sensitivity to identify fragments that induce conformational changes in a protein. A selection of fragment hits with a response profile different to known LGIC regulators was characterized and confirmed to bind to dynamic regions of the protein.
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Affiliation(s)
- Edward A FitzGerald
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
- Beactica Therapeutics Virdings allé 2 Uppsala 754 40 Sweden
| | | | - Pierre Boronat
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Daniela Cederfelt
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | - Mia Abramsson
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | | | - Jacqueline E van Muijlwijk-Koezen
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Iwan J P de Esch
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Doreen Dobritzsch
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | - Tracy Young
- Biodesy, Inc. 170 Harbor Way South San Francisco 94080 CA USA
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
- Science for Life Laboratory, Uppsala University Sweden
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10
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Abankwa D, Gorfe AA. Mechanisms of Ras Membrane Organization and Signaling: Ras Rocks Again. Biomolecules 2020; 10:E1522. [PMID: 33172116 PMCID: PMC7694788 DOI: 10.3390/biom10111522] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022] Open
Abstract
Ras is the most frequently mutated oncogene and recent drug development efforts have spurred significant new research interest. Here we review progress toward understanding how Ras functions in nanoscale, proteo-lipid signaling complexes on the plasma membrane, called nanoclusters. We discuss how G-domain reorientation is plausibly linked to Ras-nanoclustering and -dimerization. We then look at how these mechanistic features could cooperate in the engagement and activation of RAF by Ras. Moreover, we show how this structural information can be integrated with microscopy data that provide nanoscale resolution in cell biological experiments. Synthesizing the available data, we propose to distinguish between two types of Ras nanoclusters, an active, immobile RAF-dependent type and an inactive/neutral membrane anchor-dependent. We conclude that it is possible that Ras reorientation enables dynamic Ras dimerization while the whole Ras/RAF complex transits into an active state. These transient di/oligomer interfaces of Ras may be amenable to pharmacological intervention. We close by highlighting a number of open questions including whether all effectors form active nanoclusters and whether there is an isoform specific composition of Ras nanocluster.
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Affiliation(s)
- Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA
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11
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Marshall CB, KleinJan F, Gebregiworgis T, Lee KY, Fang Z, Eves BJ, Liu NF, Gasmi-Seabrook GMC, Enomoto M, Ikura M. NMR in integrated biophysical drug discovery for RAS: past, present, and future. JOURNAL OF BIOMOLECULAR NMR 2020; 74:531-554. [PMID: 32804298 DOI: 10.1007/s10858-020-00338-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Mutations in RAS oncogenes occur in ~ 30% of human cancers, with KRAS being the most frequently altered isoform. RAS proteins comprise a conserved GTPase domain and a C-terminal lipid-modified tail that is unique to each isoform. The GTPase domain is a 'switch' that regulates multiple signaling cascades that drive cell growth and proliferation when activated by binding GTP, and the signal is terminated by GTP hydrolysis. Oncogenic RAS mutations disrupt the GTPase cycle, leading to accumulation of the activated GTP-bound state and promoting proliferation. RAS is a key target in oncology, however it lacks classic druggable pockets and has been extremely challenging to target. RAS signaling has thus been targeted indirectly, by harnessing key downstream effectors as well as upstream regulators, or disrupting the proper membrane localization required for signaling, by inhibiting either lipid modification or 'carrier' proteins. As a small (20 kDa) protein with multiple conformers in dynamic equilibrium, RAS is an excellent candidate for NMR-driven characterization and screening for direct inhibitors. Several molecules have been discovered that bind RAS and stabilize shallow pockets through conformational selection, and recent compounds have achieved substantial improvements in affinity. NMR-derived insight into targeting the RAS-membrane interface has revealed a new strategy to enhance the potency of small molecules, while another approach has been development of peptidyl inhibitors that bind through large interfaces rather than deep pockets. Remarkable progress has been made with mutation-specific covalent inhibitors that target the thiol of a G12C mutant, and these are now in clinical trials. Here we review the history of RAS inhibitor development and highlight the utility of NMR and integrated biophysical approaches in RAS drug discovery.
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Affiliation(s)
- Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.
| | - Fenneke KleinJan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Ki-Young Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Zhenhao Fang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Ben J Eves
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Ningdi F Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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12
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Tran RJ, Sly KL, Conboy JC. Revealing the Kinetic Advantage of a Competitive Small-Molecule Immunoassay by Direct Detection. Anal Chem 2020; 92:13163-13171. [PMID: 32878441 DOI: 10.1021/acs.analchem.0c02286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small-molecule detection in an immunoassay format generally employs competition or labeling. A novel direct-detection label-free primary immunoassay utilizing second harmonic generation (SHG) has been developed and the utility of the method has been demonstrated for several small-molecule narcotics. Specifically, the binding of morphine, methadone, and cocaine to antimorphine, antimethadone, and anticocaine antibodies was measured by SHG, allowing binding affinities and rates of dissociation to be obtained. The SHG primary immunoassay has provided the first kinetic measurements of small-molecule hapten interactions with a receptor antibody. The kinetics reveal for the first time that competitive immunoassays achieve their selectivity by taking advantage of the kinetics of association and dissociation of the labeled and unlabeled target and nontarget small-molecule to the capture antibody. In particular, the induced fit of the target small-molecule to their antibody pairs prolongs their residence time, while the nontarget small-molecule dissociate rapidly in comparison.
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Affiliation(s)
- Renee J Tran
- Department of Chemistry, University of Utah, 315 South 1400 East RM. 2020, Salt Lake City, Utah 84112, United States
| | - Krystal L Sly
- Department of Chemistry, University of Utah, 315 South 1400 East RM. 2020, Salt Lake City, Utah 84112, United States
| | - John C Conboy
- Department of Chemistry, University of Utah, 315 South 1400 East RM. 2020, Salt Lake City, Utah 84112, United States
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13
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MacKerell AD, Jo S, Lakkaraju SK, Lind C, Yu W. Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots). Biochim Biophys Acta Gen Subj 2020; 1864:129519. [PMID: 31911242 DOI: 10.1016/j.bbagen.2020.129519] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/21/2019] [Accepted: 12/31/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Fragment-based ligand design is used for the development of novel ligands that target macromolecules, most notably proteins. Central to its success is the identification of fragment binding sites that are spatially adjacent such that fragments occupying those sites may be linked to create drug-like ligands. Current experimental and computational approaches that address this problem typically identify only a limited number of sites as well as use a limited number of fragment types. METHODS The site-identification by ligand competitive saturation (SILCS) approach is extended to the identification of fragment bindings sites, with the method termed SILCS-Hotspots. The approach involves precomputation of the SILCS FragMaps following which the identification of Hotspots, performed by identifying of all possible fragment binding sites on the full 3D structure of the protein followed by spatial clustering. RESULTS The SILCS-Hotspots approach identifies a large number of sites on the target protein, including many sites not accessible in experimental structures due to low binding affinities and binding sites on the protein interior. The identified sites are shown to recapitulate the location of known drug-like molecules in both allosteric and orthosteric binding sites on seven proteins including the androgen receptor, the CDK2 and Erk5 kinases, PTP1B phosphatase and three GPCRs; the β2-adrenergic, GPR40 fatty-acid binding and M2-muscarinic receptors. Analysis indicates the importance of considering all possible fragment binding sites, and not just those accessible to experimental methods, when identifying novel binding sites and performing ligand design versus just considering the most favorable sites. The approach is shown to identify a larger number of known binding sites of drug-like molecules versus the commonly used FTMap and Fpocket methods. GENERAL SIGNIFICANCE The present results indicate the potential utility of the SILCS-Hotspots approach for fragment-based rational design of ligands, including allosteric modulators.
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Affiliation(s)
- Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America.
| | - Sunhwan Jo
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202, United States of America
| | | | - Christoffer Lind
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
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