1
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Fotsch C, Basu D, Case R, Chen Q, Koneru PC, Lo MC, Ngo R, Sharma P, Vaish A, Yi X, Zech SG, Hodder P. Creating a more strategic small molecule biophysical hit characterization workflow. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100159. [PMID: 38723666 DOI: 10.1016/j.slasd.2024.100159] [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: 01/10/2024] [Revised: 03/16/2024] [Accepted: 05/06/2024] [Indexed: 05/21/2024]
Abstract
To confirm target engagement of hits from our high-throughput screening efforts, we ran biophysical assays on several hundreds of hits from 15 different high-throughput screening campaigns. Analyzing the biophysical assay results from these screening campaigns led us to conclude that we could be more strategic in our biophysical analysis of hits by first confirming activity in a thermal shift assay (TSA) and then confirming activity in either a surface plasmon resonance (SPR) assay or a temperature-related intensity change (TRIC) assay. To understand how this new workflow shapes the quality of the final hits, we compared TSA/SPR or TSA/TRIC confirmed and unconfirmed hits to one another using four measures of compound quality: quantitative estimate of drug-likeness (QED), Pan-Assay Interference Compounds (PAINS), promiscuity, and aqueous solubility. In general, we found that the biophysically confirmed hits performed better in the compound quality metrics than the unconfirmed hits, demonstrating that our workflow not only confirmed target engagement of the hits but also enriched for higher quality hits.
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Affiliation(s)
- Christopher Fotsch
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA.
| | - Debaleena Basu
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Ryan Case
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Qing Chen
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
| | - Pratibha C Koneru
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Mei-Chu Lo
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Rachel Ngo
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Pooja Sharma
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
| | - Amit Vaish
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
| | - Xiang Yi
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Stephan G Zech
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
| | - Peter Hodder
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
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2
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Pal S, Nare Z, Rao VA, Smith BO, Morrison I, Fitzgerald EA, Scott A, Bingham MJ, Pesnot T. Accelerating BRPF1b hit identification with BioPhysical and Active Learning Screening (BioPALS). ChemMedChem 2024; 19:e202300590. [PMID: 38372199 DOI: 10.1002/cmdc.202300590] [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: 10/29/2023] [Revised: 01/25/2024] [Accepted: 02/12/2024] [Indexed: 02/20/2024]
Abstract
We report the development of BioPhysical and Active Learning Screening (BioPALS); a rapid and versatile hit identification protocol combining AI-powered virtual screening with a GCI-driven biophysical confirmation workflow. Its application to the BRPF1b bromodomain afforded a range of novel micromolar binders with favorable ADMET properties. In addition to the excellent in silico/in vitro confirmation rate demonstrated with BRPF1b, binding kinetics were determined, and binding topologies predicted for all hits. BioPALS is a lean, data-rich, and standardized approach to hit identification applicable to a wide range of biological targets.
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Affiliation(s)
- Sandeep Pal
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Zandile Nare
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Vincenzo A Rao
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Brian O Smith
- University of Glasgow, School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, G12 8QQ, Glasgow, UK
| | - Ian Morrison
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | | | - Andrew Scott
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Matilda J Bingham
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Thomas Pesnot
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
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3
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Zhao Y, Mikes A, Tóth G, Aigbirhio F. Detection of Small-Molecule Interactions with Fibrillar Tau Protein Aggregates Using Microscale Thermophoresis. Methods Mol Biol 2024; 2754:205-217. [PMID: 38512669 DOI: 10.1007/978-1-0716-3629-9_12] [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] [Indexed: 03/23/2024]
Abstract
Aggregated fibrillar tau protein is a pathological hallmark of several neurodegenerative diseases. Small molecules that bind to tau fibrils may be applied for their detection and quantification. This is of great importance as they can potentially be used for earlier diagnosis of disease and disease progression. Microscale thermophoresis (MST) enables the detection of biomolecular interactions in an aqueous environment in which no immobilization of either reaction partner is required. Here, an MST assay methodology is described for the detection of the interaction between a variety of small molecules and tau fibrils. The results of this study demonstrate that MST is a practical methodology to quantify interactions between small molecules and tau fibrillar aggregates.
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Affiliation(s)
- Yanyan Zhao
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
| | - Anna Mikes
- NAP B - Drug Discovery Research Group - Neurodegenerative Diseases, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gergely Tóth
- NAP B - Drug Discovery Research Group - Neurodegenerative Diseases, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
- Cantabio Pharmaceuticals Inc., Palo Alto, CA, USA
| | - Franklin Aigbirhio
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
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4
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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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5
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Du L, Wilson BAP, Li N, Shah R, Dalilian M, Wang D, Smith EA, Wamiru A, Goncharova EI, Zhang P, O’Keefe BR. Discovery and Synthesis of a Naturally Derived Protein Kinase Inhibitor that Selectively Inhibits Distinct Classes of Serine/Threonine Kinases. JOURNAL OF NATURAL PRODUCTS 2023; 86:2283-2293. [PMID: 37843072 PMCID: PMC10616853 DOI: 10.1021/acs.jnatprod.3c00394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Indexed: 10/17/2023]
Abstract
The DNAJB1-PRKACA oncogenic gene fusion results in an active kinase enzyme, J-PKAcα, that has been identified as an attractive antitumor target for fibrolamellar hepatocellular carcinoma (FLHCC). A high-throughput assay was used to identify inhibitors of J-PKAcα catalytic activity by screening the NCI Program for Natural Product Discovery (NPNPD) prefractionated natural product library. Purification of the active agent from a single fraction of an Aplidium sp. marine tunicate led to the discovery of two unprecedented alkaloids, aplithianines A (1) and B (2). Aplithianine A (1) showed potent inhibition against J-PKAcα with an IC50 of ∼1 μM in the primary screening assay. In kinome screening, 1 inhibited wild-type PKA with an IC50 of 84 nM. Further mechanistic studies including cocrystallization and X-ray diffraction experiments revealed that 1 inhibited PKAcα catalytic activity by competitively binding to the ATP pocket. Human kinome profiling of 1 against a panel of 370 kinases revealed potent inhibition of select serine/threonine kinases in the CLK and PKG families with IC50 values in the range ∼11-90 nM. An efficient, four-step total synthesis of 1 has been accomplished, enabling further evaluation of aplithianines as biologically relevant kinase inhibitors.
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Affiliation(s)
- Lin Du
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Brice A. P. Wilson
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ning Li
- Center
for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Rohan Shah
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Masoumeh Dalilian
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Leidos
Biomedical Research, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Dongdong Wang
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Emily A. Smith
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Leidos
Biomedical Research, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Antony Wamiru
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Leidos
Biomedical Research, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ekaterina I. Goncharova
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Leidos
Biomedical Research, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ping Zhang
- Center
for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Barry R. O’Keefe
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Natural
Products Branch, Development Therapeutics Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702, United States
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6
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Acquah FA, Mooers BHM. Targeting RNA Structure to Inhibit Editing in Trypanosomes. Int J Mol Sci 2023; 24:10110. [PMID: 37373258 PMCID: PMC10298474 DOI: 10.3390/ijms241210110] [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: 05/01/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Mitochondrial RNA editing in trypanosomes represents an attractive target for developing safer and more efficient drugs for treating infections with trypanosomes because this RNA editing pathway is not found in humans. Other workers have targeted several enzymes in this editing system, but not the RNA. Here, we target a universal domain of the RNA editing substrate, which is the U-helix formed between the oligo-U tail of the guide RNA and the target mRNA. We selected a part of the U-helix that is rich in G-U wobble base pairs as the target site for the virtual screening of 262,000 compounds. After chemoinformatic filtering of the top 5000 leads, we subjected 50 representative complexes to 50 nanoseconds of molecular dynamics simulations. We identified 15 compounds that retained stable interactions in the deep groove of the U-helix. The microscale thermophoresis binding experiments on these five compounds show low-micromolar to nanomolar binding affinities. The UV melting studies show an increase in the melting temperatures of the U-helix upon binding by each compound. These five compounds can serve as leads for drug development and as research tools to probe the role of the RNA structure in trypanosomal RNA editing.
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Affiliation(s)
- Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Laboratory of Biomolecular Structure and Function, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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7
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Pundir M, De Rosa MC, Lobanova L, Abdulmawjood S, Chen X, Papagerakis S, Papagerakis P. Structural properties and binding mechanism of DNA aptamers sensing saliva melatonin for diagnosis and monitoring of circadian clock and sleep disorders. Anal Chim Acta 2023; 1251:340971. [PMID: 36925277 DOI: 10.1016/j.aca.2023.340971] [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: 11/14/2022] [Revised: 01/25/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023]
Abstract
Circadian desynchrony with the external light-dark cycle influences the rhythmic secretion of melatonin which is among the first signs of circadian rhythm sleep disorders. An accurate dim light melatonin onset (established indicator of circadian rhythm sleep disorders) measurement requires lengthy assays, and antibody affinities alterations, especially in patients with circadian rhythm disorders whose melatonin salivary levels vary significantly, making antibodies detection mostly inadequate. In contrast, aptamers with their numerous advantages (e.g., target selectivity, structural flexibility in tuning binding affinities, small size, etc.) can become preferable biorecognition molecules for salivary melatonin detection with high sensitivity and specificity. This study thoroughly characterizes the structural property and binding mechanism of a single-stranded DNA aptamer full sequence (MLT-C-1) and its truncated versions (MLT-A-2, MLT-A-4) to decipher its optimal characteristics for saliva melatonin detection. We use circular dichroism spectroscopy to determine aptamers' conformational changes under different ionic strengths and showed that aptamers display a hairpin loop structure where few base pairs in the stem play a significant role in melatonin binding and formation of aptamer stabilized structure. Through microscale thermophoresis, aptamers demonstrated a high binding affinity in saliva samples (MLT-C-1F Kd = 12.5 ± 1.7 nM; MLT-A-4F Kd = 11.2 ± 1.6 nM; MLT-A-2F Kd = 2.4 ± 2.8 nM; limit-of-detection achieved in pM, highest sensitivity attained for MLT-A-2F aptamer with the lowest detection limit of 1.35 pM). Our data suggest that aptamers are promising as biorecognition molecules and provide the baseline parameters for the development of an aptamer-based point-of-care diagnostic system for melatonin detection and accurate profiling of its fluctuations in saliva.
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Affiliation(s)
- Meenakshi Pundir
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada; Laboratory of Oral, Head and Neck Cancer - Personalized Diagnostics and Therapeutics, Department of Surgery, College of Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada
| | - Maria C De Rosa
- Department of Chemistry, Faculty of Science, Carleton University, 1125 Colonel by Drive, Ottawa, Ontario, K1S 5B6, Canada.
| | - Liubov Lobanova
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada
| | - Shahad Abdulmawjood
- Department of Chemistry, Faculty of Science, Carleton University, 1125 Colonel by Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Xiongbiao Chen
- Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada; Department of Mechanical Engineering, School of Engineering, University of Saskatchewan, 57 Campus Dr, S7K 5A9, Saskatoon, Canada.
| | - Silvana Papagerakis
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Laboratory of Oral, Head and Neck Cancer - Personalized Diagnostics and Therapeutics, Department of Surgery, College of Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Michigan, 1500 E Medical Center Dr, Ann Arbor, MI, 48109, United States.
| | - Petros Papagerakis
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada.
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8
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Wilson BAP, Li N, Martinez Fiesco JA, Dalilian M, Wang D, Smith EA, Wamiru A, Shah R, Goncharova EI, Beutler JA, Grkovic T, Zhang P, O’Keefe BR. Biochemical Discovery, Intracellular Evaluation, and Crystallographic Characterization of Synthetic and Natural Product Adenosine 3',5'-Cyclic Monophosphate-Dependent Protein Kinase A (PKA) Inhibitors. ACS Pharmacol Transl Sci 2023; 6:633-650. [PMID: 37082750 PMCID: PMC10111623 DOI: 10.1021/acsptsci.3c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Indexed: 04/22/2023]
Abstract
The recent demonstration that adenosine 3',5'-cyclic monophosphate (cAMP)-dependent protein kinase A (PKA) plays an oncogenic role in a number of important cancers has led to a renaissance in drug development interest targeting this kinase. We therefore have established a suite of biochemical, cell-based, and structural biology assays for identifying and evaluating new pharmacophores for PKA inhibition. This discovery process started with a 384-well high-throughput screen of more than 200,000 substances, including fractionated natural product extracts. Identified active compounds were further prioritized in biochemical, biophysical, and cell-based assays. Priority lead compounds were assessed in detail to fully characterize several previously unrecognized PKA pharmacophores including the generation of new X-ray crystallography structures demonstrating unique interactions between PKA and bound inhibitor molecules.
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Affiliation(s)
- Brice A. P. Wilson
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ning Li
- Center
for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Juliana A. Martinez Fiesco
- Center
for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Masoumeh Dalilian
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Dongdong Wang
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Emily A. Smith
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Antony Wamiru
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Rohan Shah
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ekaterina I. Goncharova
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Advanced
Biomedical Computational Science, Frederick
National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - John A. Beutler
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Tanja Grkovic
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Natural
Products Branch, Developmental Therapeutics Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702, United States
| | - Ping Zhang
- Center
for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Barry R. O’Keefe
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Natural
Products Branch, Developmental Therapeutics Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702, United States
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9
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Mayer DB, Braun D, Franosch T. Thermophoretic motion of a charged single colloidal particle. Phys Rev E 2023; 107:044602. [PMID: 37198806 DOI: 10.1103/physreve.107.044602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 03/13/2023] [Indexed: 05/19/2023]
Abstract
We calculate the thermophoretic drift of a charged single colloidal particle with hydrodynamically slipping surface immersed in an electrolyte solution in response to a small temperature gradient. Here we rely on a linearized hydrodynamic approach for the fluid flow and the motion of the electrolyte ions while keeping the full nonlinearity of the Poisson-Boltzmann equation of the unperturbed system to account for possible large surface charging. The partial differential equations are transformed into a coupled set of ordinary differential equations in linear response. Numerical solutions are elaborated for parameter regimes of small and large Debye shielding and different hydrodynamic boundary conditions encoded in a varying slip length. Our results are in good agreement with predictions from recent theoretical work and successfully describe experimental observations on thermophoresis of DNA. We also compare our numerical results with experimental data on polystyrene beads.
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Affiliation(s)
- Daniel B Mayer
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Dieter Braun
- Systems Biophysics, Physics Department, Nanosystems Initiative Munich and Center for NanoScience, Ludwig-Maximilians-Universität München, Amalienstrasse 54, D-80799 München, Germany
| | - Thomas Franosch
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
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10
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Computational Design, Synthesis, and Biophysical Evaluation of β-Amido Boronic Acids as SARS-CoV-2 M pro Inhibitors. Molecules 2023; 28:molecules28052356. [PMID: 36903597 PMCID: PMC10005264 DOI: 10.3390/molecules28052356] [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: 01/31/2023] [Revised: 02/16/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
The COVID-19 pandemic has given a strong impetus to the search for antivirals active on SARS-associated coronaviruses. Over these years, numerous vaccines have been developed and many of these are effective and clinically available. Similarly, small molecules and monoclonal antibodies have also been approved by the FDA and EMA for the treatment of SARS-CoV-2 infection in patients who could develop the severe form of COVID-19. Among the available therapeutic tools, the small molecule nirmatrelvir was approved in 2021. It is a drug capable of binding to the Mpro protease, an enzyme encoded by the viral genome and essential for viral intracellular replication. In this work, by virtual screening of a focused library of β-amido boronic acids, we have designed and synthesized a focused library of compounds. All of them were biophysically tested by microscale thermophoresis, attaining encouraging results. Moreover, they also displayed Mpro protease inhibitory activity, as demonstrated by performing enzymatic assays. We are confident that this study will pave the way for the design of new drugs potentially useful for the treatment of SARS-CoV-2 viral infection.
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11
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Targeted systematic evolution of an RNA platform neutralizing DNMT1 function and controlling DNA methylation. Nat Commun 2023; 14:99. [PMID: 36609400 PMCID: PMC9823104 DOI: 10.1038/s41467-022-35222-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/23/2022] [Indexed: 01/09/2023] Open
Abstract
DNA methylation is a fundamental epigenetic modification regulating gene expression. Aberrant DNA methylation is the most common molecular lesion in cancer cells. However, medical intervention has been limited to the use of broadly acting, small molecule-based demethylating drugs with significant side-effects and toxicities. To allow for targeted DNA demethylation, we integrated two nucleic acid-based approaches: DNMT1 interacting RNA (DiR) and RNA aptamer strategy. By combining the RNA inherent capabilities of inhibiting DNMT1 with an aptamer platform, we generated a first-in-class DNMT1-targeted approach - aptaDiR. Molecular modelling of RNA-DNMT1 complexes coupled with biochemical and cellular assays enabled the identification and characterization of aptaDiR. This RNA bio-drug is able to block DNA methylation, impair cancer cell viability and inhibit tumour growth in vivo. Collectively, we present an innovative RNA-based approach to modulate DNMT1 activity in cancer or diseases characterized by aberrant DNA methylation and suggest the first alternative strategy to overcome the limitations of currently approved non-specific hypomethylating protocols, which will greatly improve clinical intervention on DNA methylation.
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12
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The Inhibitory Properties of a Novel, Selective LMTK3 Kinase Inhibitor. Int J Mol Sci 2023; 24:ijms24010865. [PMID: 36614307 PMCID: PMC9821308 DOI: 10.3390/ijms24010865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 01/05/2023] Open
Abstract
Recently, the oncogenic role of lemur tyrosine kinase 3 (LMTK3) has been well established in different tumor types, highlighting it as a viable therapeutic target. In the present study, using in vitro and cell-based assays coupled with biophysical analyses, we identify a highly selective small molecule LMTK3 inhibitor, namely C36. Biochemical/biophysical and cellular studies revealed that C36 displays a high in vitro selectivity profile and provides notable therapeutic effect when tested in the National Cancer Institute (NCI)-60 cancer cell line panel. We also report the binding affinity between LMTK3 and C36 as demonstrated via microscale thermophoresis (MST). In addition, C36 exhibits a mixed-type inhibition against LMTK3, consistent with the inhibitor overlapping with both the adenosine 5'-triphosphate (ATP)- and substrate-binding sites. Treatment of different breast cancer cell lines with C36 led to decreased proliferation and increased apoptosis, further reinforcing the prospective value of LMTK3 inhibitors for cancer therapy.
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13
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Bobone S, Storti C, Calligari P, Stella L. Fluorescence Anisotropy and Polarization in the Characterization of Biomolecular Association Processes and Their Application to Study SH2 Domain Binding Affinity. Methods Mol Biol 2023; 2705:93-112. [PMID: 37668971 DOI: 10.1007/978-1-0716-3393-9_6] [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] [Indexed: 09/06/2023]
Abstract
Fluorescence anisotropy (or polarization) is a powerful technique to study biomolecular association processes, by following the rotational motions of one of the two partners in the interaction, labeled with a fluorophore. It can be used to determine dissociation constants in solution, down to nM values, and unlabeled ligands can be characterized, too, by using competition experiments. In this chapter, we introduce the basic principles of the technique, compare it with other experimental approaches, and discuss the experimental details with specific examples regarding SH2 domain/phosphopeptide association processes. The experimental protocols to be used in binding experiments and displacement studies are described, as well as the caveats to be considered in performing accurate measurements.
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Affiliation(s)
- Sara Bobone
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Claudia Storti
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Paolo Calligari
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy.
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14
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Zimmermann R, Schwickert M, Meidner JL, Nidoieva Z, Helm M, Schirmeister T. An Optimized Microscale Thermophoresis Method for High-Throughput Screening of DNA Methyltransferase 2 Ligands. ACS Pharmacol Transl Sci 2022; 5:1079-1085. [PMID: 36407957 PMCID: PMC9667538 DOI: 10.1021/acsptsci.2c00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Indexed: 11/28/2022]
Abstract
Developing methyltransferase inhibitors is challenging, since most of the currently used assays are time-consuming and cost-intensive. Therefore, efficient, fast, and reliable methods for screenings and affinity determinations are of utmost importance. Starting from a literature-known fluorescent S-adenosylhomocysteine derivative, 5-FAM-triazolyl-adenosyl-Dab, developed for a fluorescence polarization assay to investigate the histone methyltransferase mixed-lineage leukemia 1, we herein describe the applicability of this compound as a fluorescent tracer for the investigation of DNA-methyltransferase 2 (DNMT2), a human RNA methyltransferase. Based on these findings, we established a microscale thermophoresis (MST) assay for DNMT2. This displacement assay can circumvent various problems inherent to this method. Furthermore, we optimized a screening method via MST which even indicates if the detected binding is competitive and gives the opportunity to estimate the potency of a ligand, both of which are not possible with a direct binding assay.
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Affiliation(s)
| | | | | | - Zarina Nidoieva
- Institute
of Pharmaceutical and Biomedical
Sciences, Johannes Gutenberg University
Mainz Staudinger Weg 5, D-55128 Mainz, Germany
| | - Mark Helm
- Institute
of Pharmaceutical and Biomedical
Sciences, Johannes Gutenberg University
Mainz Staudinger Weg 5, D-55128 Mainz, Germany
| | - Tanja Schirmeister
- Institute
of Pharmaceutical and Biomedical
Sciences, Johannes Gutenberg University
Mainz Staudinger Weg 5, D-55128 Mainz, Germany
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15
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Mabonga L, Ikwegbue PC, Masamba P, Kappo AP. Molecular interaction between small nuclear ribonucleoprotein polypeptide G and heat shock protein 70.14: a microscale thermophoresis exposition towards developing anti-cancer drugs. Am J Transl Res 2022; 14:6150-6162. [PMID: 36247303 PMCID: PMC9556510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Targeting protein-protein interactions (PPIs) linked to protein quality control (PQC) pathways as potential anti-cancer drug targets have unanimously widened biological insights and the therapeutic potential of PPIs as smart-drug discovery tools in cancer. PPIs between disease-relevant proteins associated with protein homeostasis in PQC pathways have been linked to improved mechanistic understanding associated with conformational abnormalities and impairment, cellular proteotoxicity, induced apoptosis, and pathogenesis in different types of cancers. In this context, PPIs between small nuclear ribonucleoprotein polypeptide G (SNRPG) and heat shock protein 70.14 (Hsp70.14) have attracted attention as potential smart drug discovery tools in cancer diagnostics and therapeutics. Validated evidence of high-quality biological data has shown the presence of the two proteins in different types of cancers including breast cancer. The links between SNRPG and Hsp70.14 in cancer-cell networks remain elusive, overlooked, and uncharacterized. METHODOLOGY In this study, we explored the interaction between the two oncogenic proteins using the MST-based assays. RESULTS The results revealed a low KD in the nanomolar concentration range of 2.4673 × 10-7 demonstrating a great affinity for SNRPG binding to Hsp70.14. CONCLUSIONS The results suggest a possible involvement between the two proteins in hostile tumour microenvironments. Furthermore, these findings offer a different therapeutic perspective that could pave the way for the creation of novel small molecule inhibitors as drugs for the treatment of cancer.
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Affiliation(s)
- Lloyd Mabonga
- Department of Biochemistry and Microbiology, University of ZululandKwaDlangezwa 3886, South Africa
| | - Paul Chukwudi Ikwegbue
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape TownCape Town, South Africa
| | - Priscilla Masamba
- Molecular Biophysics and Structural Biology (MBSB) Group, Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park Kingsway CampusSouth Africa
| | - Abidemi Paul Kappo
- Molecular Biophysics and Structural Biology (MBSB) Group, Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park Kingsway CampusSouth Africa
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16
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El Deeb S, Al-Harrasi A, Khan A, Al-Broumi M, Al-Thani G, Alomairi M, Elumalai P, Sayed RA, Ibrahim AE. Microscale thermophoresis as a powerful growing analytical technique for the investigation of biomolecular interaction and the determination of binding parameters. Methods Appl Fluoresc 2022; 10. [PMID: 35856854 DOI: 10.1088/2050-6120/ac82a6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/20/2022] [Indexed: 11/12/2022]
Abstract
The in vitro panel of technologies to address biomolecular interactions are in play, however microscale thermophoresis is continuously increasing in use to represent a key player in this arena. This review highlights the usefulness of microscale thermophoresis in the determination of molecular and biomolecular affinity interactions. This work reviews the literature from January 2016 to January 2022 about microscale thermophoresis. It gives a summarized overview about both the state-of the art and the development in the field of microscale thermophoresis. The principle of microscale thermophoresis is also described supported with self-created illustrations. Moreover, some recent advances are mentioned that showing application of the technique in investigating biomolecular interactions in different fields. Finally, advantages as well as drawbacks of the technique in comparison with other competing techniques are summarized.
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Affiliation(s)
- Sami El Deeb
- Technische Universitat Braunschweig, Braunschweig, Braunschweig, Niedersachsen, 38106, GERMANY
| | | | - Ajmal Khan
- University of Nizwa, Nizwa, Nizwa, 616, OMAN
| | | | | | | | | | - Rania A Sayed
- Pharmaceutical analytical chemistry department, Zagazig University, Zagazig, Zagazig, 44519, EGYPT
| | - Adel Ehab Ibrahim
- Pharmaceutical Analytical Chemistry, Port Said University, Port Said, Port Said, 42526, EGYPT
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17
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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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18
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Tsang NY, Li WF, Varhegyi E, Rong L, Zhang HJ. Ebola Entry Inhibitors Discovered from Maesa perlarius. Int J Mol Sci 2022; 23:ijms23052620. [PMID: 35269770 PMCID: PMC8910447 DOI: 10.3390/ijms23052620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/08/2022] [Accepted: 02/23/2022] [Indexed: 11/21/2022] Open
Abstract
Ebola virus disease (EVD), a disease caused by infection with Ebola virus (EBOV), is characterized by hemorrhagic fever and a high case fatality rate. With limited options for the treatment of EVD, anti-Ebola viral therapeutics need to be urgently developed. In this study, over 500 extracts of medicinal plants collected in the Lingnan region were tested against infection with Ebola-virus-pseudotyped particles (EBOVpp), leading to the discovery of Maesa perlarius as an anti-EBOV plant lead. The methanol extract (MPBE) of the stems of this plant showed an inhibitory effect against EBOVpp, with an IC50 value of 0.52 µg/mL, which was confirmed by testing the extract against infectious EBOV in a biosafety level 4 laboratory. The bioassay-guided fractionation of MPBE resulted in three proanthocyanidins (procyanidin B2 (1), procyanidin C1 (2), and epicatechin-(4β→8)-epicatechin-(4β→8)-epicatechin-(4β→8)-epicatechin (3)), along with two flavan-3-ols ((+)-catechin (4) and (−)-epicatechin (5)). The IC50 values of the compounds against pseudovirion-bearing EBOV-GP ranged from 0.83 to 36.0 µM, with 1 as the most potent inhibitor. The anti-EBOV activities of five synthetic derivatives together with six commercially available analogues, including EGCG ((−)-epigallocatechin-3-O-gallate (8)), were further investigated. Molecular docking analysis and binding affinity measurement suggested the EBOV glycoprotein could be a potential molecular target for 1 and its related compounds.
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Affiliation(s)
- Nga Yi Tsang
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong, China; (N.Y.T.); (W.-F.L.)
| | - Wan-Fei Li
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong, China; (N.Y.T.); (W.-F.L.)
| | - Elizabeth Varhegyi
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, 909 South Wolcott Ave, Chicago, IL 60612, USA;
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, 909 South Wolcott Ave, Chicago, IL 60612, USA;
- Correspondence: (L.R.); (H.-J.Z.); Tel.: +1-312-3550203 (L.R.); +852-34112956 (H.-J.Z.)
| | - Hong-Jie Zhang
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong, China; (N.Y.T.); (W.-F.L.)
- Correspondence: (L.R.); (H.-J.Z.); Tel.: +1-312-3550203 (L.R.); +852-34112956 (H.-J.Z.)
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19
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Peptide Linked Diacetylene Amphiphiles for Detection of Epitope Specific Antibodies. CHEMOSENSORS 2022; 10. [DOI: 10.3390/chemosensors10020062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Antibodies produced in response to adaptive immunity provide a receptor with multiple sites for binding to a distinct epitope of an antigen. Determining antibody levels to specific antigens has important clinical applications in assessing immune status or deficiency, monitoring infectious or autoimmune diseases, and diagnosing allergies. Leveraging that a specific antibody will bind to a distinct small peptide epitope without requiring the entire antigen to be present, we demonstrate in this work a proof-of-concept assay to detect the presence of an antibody by using peptide epitopes linked to an amphiphile to generate a vesicle-based sensing system. By affording multiple copies of the epitope site on the vesicle, we revealed that the vesicles visibly aggregate in response to an antibody specific for that epitope due to multivalent binding provided by the antibody. We also uncovered the role of peptide surface density in providing accessible epitopes on the vesicles for antibody binding. In summary, using a peptide derived from the coat protein of human influenza virus directly linked to a diacetylene-containing amphiphile afforded peptide-laden vesicles that proved capable of detecting the presence of antibodies specific for human influenza hemagglutinin.
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20
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Fragment-based exploration of the 14-3-3/Amot-p130 interface. Curr Res Struct Biol 2022; 4:21-28. [PMID: 35036934 PMCID: PMC8743172 DOI: 10.1016/j.crstbi.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 02/06/2023] Open
Abstract
The modulation of protein-protein interactions (PPIs) has developed into a well-established field of drug discovery. Despite the advances achieved in the field, many PPIs are still deemed as ‘undruggable’ targets and the design of PPIs stabilizers remains a significant challenge. The application of fragment-based methods for the identification of drug leads and to evaluate the ‘tractability’ of the desired protein target has seen a remarkable development in recent years. In this study, we explore the molecular characteristics of the 14-3-3/Amot-p130 PPI and the conceptual possibility of targeting this interface using X-ray crystallography fragment-based screening. We report the first structural elucidation of the 14-3-3 binding motif of Amot-p130 and the characterization of the binding mode and affinities involved. We made use of fragments to probe the ‘ligandability’ of the 14-3-3/Amot-p130 composite binding pocket. Here we disclose initial hits with promising stabilizing activity and an early-stage selectivity toward the Amot-p130 motifs over other representatives 14-3-3 partners. Our findings highlight the potential of using fragments to characterize and explore proteins' surfaces and might provide a starting point toward the development of small molecules capable of acting as molecular glues. Phosphorylation of Ser 175 mediates binding of Amot-p130 to 14-3-3. The crystal structure of the 14-3-3σΔC/Amot-p130 peptide complex describes the interface. A fragment-based exploration of the interface assesses ‘ligandability’. Fragments binding at the 14-3-3/Amot-p130 interface display an initial stabilizing activity.
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Key Words
- 14-3-3 /protein-protein interactions stabilizers
- AIP4, Atrophin-1 interacting protein 4
- Amot, Angiomotin
- Amot-p130
- AmotL1/2, Angiomotin-like 1/2
- FBDD, Fragment-based drug discovery
- FP, Fluorescence polarization
- Fragment-based drug discovery
- Lats 1/2, Large tumor suppressor 1/2
- Ligandability
- MST, Microscale thermophoresis
- PPI, Protein-protein interaction
- PTMs, post-translational modifications
- X-ray crystallography
- YAP1, Yes-associated protein 1
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21
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Bartoschik T, Zoephel A, Rumpel K, Ciulli A, Heffern C. MST and TRIC Technology to Reliably Study PROTAC Binary and Ternary Binding in Drug Development. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2365:115-133. [PMID: 34432241 DOI: 10.1007/978-1-0716-1665-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
PROTACs have shown promise as a new class of therapy, with a unique mechanism of action orthogonal to traditional small molecules that are used to regulate protein activity. Their novel MOA utilizing the body's natural protein degradation machinery degrades a protein of interest rather than inhibiting its function. This strategy has several advantages over conventional small-molecule inhibitors, e.g., higher sensitivity, less off-target effects, and greater target space. However, unlocking the potential of PROTACs necessitates drug discovery techniques that can support the complexity of the novel MOA. In this chapter, we describe the application of MicroScale Thermophoresis (MST) and Temperature-Related Intensity Change (TRIC) to characterize both the binary and ternary binding of PROTACs with target proteins and ubiquitin ligases along with an efficient determination of the cooperativity of the ternary complex formation. The assay development and experimental procedure to characterize the well-described BET PROTAC MZ1 show how MST and TRIC can be applied as a fast and highly sensitive method for PROTAC discovery.
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Affiliation(s)
| | | | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Alessio Ciulli
- School of Life Sciences, University of Dundee, Scotland, UK
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22
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Farina B, Pirone L, D’Abrosca G, Della Valle M, Russo L, Isernia C, Sassano M, Del Gatto A, Di Gaetano S, Zaccaro L, Malgieri G, Pedone EM, Fattorusso R. Screening a Molecular Fragment Library to Modulate the PED/PEA15-Phospholipase D1 Interaction in Cellular Lysate Environments. ACS Chem Biol 2021; 16:2798-2807. [PMID: 34825823 DOI: 10.1021/acschembio.1c00688] [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
The overexpression of PED/PEA15, the phosphoprotein enriched in diabetes/phosphoprotein enriched in the astrocytes 15 protein (here referred simply to as PED), observed in some forms of type II diabetes, reduces the transport of insulin-stimulated glucose by binding to the phospholipase D1 (PLD1). The inhibition of the PED/PLD1 interaction was shown to restore basal glucose transport, indicating PED as a pharmacological target for the development of drugs capable of improving insulin sensitivity and glucose tolerance. We here report the identification and selection of PED ligands by means of NMR screening of a library of small organic molecules, NMR characterization of the PED/PLD1 interaction in lysates of cells expressing PLD1, and modulation of such interactions using BPH03, the best selected ligand. Overall, we complement the available literature data by providing detailed information on the structural determinants of the PED/PLD1 interaction in a cellular lysate environment and indicate BPH03 as a precious scaffold for the development of novel compounds that are able to modulate such interactions with possible therapeutic applications in type II diabetes.
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Affiliation(s)
- Biancamaria Farina
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Luciano Pirone
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Gianluca D’Abrosca
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maria Della Valle
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Carla Isernia
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Marica Sassano
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Annarita Del Gatto
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Sonia Di Gaetano
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Laura Zaccaro
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Gaetano Malgieri
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Emilia M. Pedone
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
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23
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Mabonga L, Masamba P, Basson AK, Kappo AP. Microscale thermophoresis analysis of the molecular interaction between small nuclear ribonucleoprotein polypeptide G and the RING finger domain of RBBP6 towards anti-cancer drug discovery. Am J Transl Res 2021; 13:12775-12785. [PMID: 34956492 PMCID: PMC8661184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/16/2021] [Indexed: 06/14/2023]
Abstract
Regulatory core-splicing proteins are now becoming highly promising therapeutic targets for the development of anti-cancer drugs. SNRPG and RBBP6 are two good examples of regulatory core-splicing proteins involved in tumorigenesis and tumor development whose multi-functional role is primarily mediated by protein-protein interactions. Over the years, skepticism abutting from the two onco-proteins has been mounting. Suggestive evidence using yeast 2-hybrid technique observed possible involvement between SNRPG and the RING finger domain of RBBP6. However, the putative interaction remains elusive and yet to be characterized. In this study, we developed the first MST-based assay to confirm the interaction between SNRPG and the RING finger domain of RBBP6. The results demonstrated a strong binding affinity between SNRPG and the RING finger domain of RBBP6 with a KD in the low nanomolar concentration range of 3.1596 nM. The results are congruent with previous findings suggesting possible involvement between the two proteins in cancer-cell networks, thereby providing a new mechanistic insight into the interaction between SNRPG and the RING finger domain of RBBP6. The interaction is therapeutically relevant and represents a great milestone in the anti-cancer drug discovery space. Identification of small molecule inhibitors to modulate the binding affinity between the two proteins would therefore be a major breakthrough in the development of new PPI-focused anti-cancer drugs.
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Affiliation(s)
- Lloyd Mabonga
- Department of Biochemistry and Microbiology, University of ZululandKwaDlangezwa 3886, South Africa
| | - Priscilla Masamba
- Molecular Biophysics and Structural Biology (MBSB) Group, Department of Biochemistry, Faculty of Science, University of Johannesburg, Kingsway CampusAuckland Park 2006, South Africa
| | - Albertus Kotze Basson
- Department of Biochemistry and Microbiology, University of ZululandKwaDlangezwa 3886, South Africa
| | - Abidemi Paul Kappo
- Molecular Biophysics and Structural Biology (MBSB) Group, Department of Biochemistry, Faculty of Science, University of Johannesburg, Kingsway CampusAuckland Park 2006, South Africa
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24
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Burastero O, Niebling S, Defelipe LA, Günther C, Struve A, Garcia Alai MM. eSPC: an online data-analysis platform for molecular biophysics. Acta Crystallogr D Struct Biol 2021; 77:1241-1250. [PMID: 34605428 PMCID: PMC8489228 DOI: 10.1107/s2059798321008998] [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: 04/30/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
All biological processes rely on the formation of protein-ligand, protein-peptide and protein-protein complexes. Studying the affinity, kinetics and thermodynamics of binding between these pairs is critical for understanding basic cellular mechanisms. Many different technologies have been designed for probing interactions between biomolecules, each based on measuring different signals (fluorescence, heat, thermophoresis, scattering and interference, among others). Evaluation of the data from binding experiments and their fitting is an essential step towards the quantification of binding affinities. Here, user-friendly online tools to analyze biophysical data from steady-state fluorescence spectroscopy, microscale thermophoresis and differential scanning fluorimetry experiments are presented. The modules of the data-analysis platform (https://spc.embl-hamburg.de/) contain classical thermodynamic models and clear user guidelines for the determination of equilibrium dissociation constants (Kd) and thermal unfolding parameters such as melting temperatures (Tm).
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Affiliation(s)
- Osvaldo Burastero
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2620, Ciudad Autónoma de Buenos Aires, Argentina
- IQUIBICEN–UBA/CONICET, Intendente Güiraldes 2620, Ciudad Autónoma de Buenos Aires, Argentina
| | - Stephan Niebling
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lucas A. Defelipe
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian Günther
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology, Notkestrasse 85, 22607 Hamburg, Germany
| | - Angelica Struve
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maria M. Garcia Alai
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology, Notkestrasse 85, 22607 Hamburg, Germany
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25
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Bang YJ, Hu Z, Li Y, Gattu S, Ruhn KA, Raj P, Herz J, Hooper LV. Serum amyloid A delivers retinol to intestinal myeloid cells to promote adaptive immunity. Science 2021; 373:eabf9232. [PMID: 34529485 DOI: 10.1126/science.abf9232] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Ye-Ji Bang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zehan Hu
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yun Li
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sureka Gattu
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kelly A Ruhn
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joachim Herz
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Center for Translational Neurodegeneration Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lora V Hooper
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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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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Al Hamoui Dit Banni G, Nasreddine R, Fayad S, Colas C, Marchal A, Nehmé R. Investigation of lipase-ligand interactions in porcine pancreatic extracts by microscale thermophoresis. Anal Bioanal Chem 2021; 413:3667-3681. [PMID: 33797603 DOI: 10.1007/s00216-021-03314-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/19/2022]
Abstract
The evaluation of binding affinities between large biomolecules and small ligands is challenging and requires highly sensitive techniques. Microscale thermophoresis (MST) is an emerging biophysical technique used to overcome this limitation. This work describes the first MST binding method to evaluate binding affinities of small ligands to lipases from crude porcine pancreatic extracts. The conditions of the MST assay were thoroughly optimized to successfully evaluate the dissociation constant (Kd) between pancreatic lipases (PL) and triterpenoid compounds purified from oakwood. More precisely, the fluorescent labeling of PL (PL*) using RED-NHS dye was achieved via a buffer exchange procedure. The MST buffer was composed of 20 mM NaH2PO4 + 77 mM NaCl (pH 6.6) with 0.05% Triton-X added to efficiently prevent protein aggregation and adsorption, even when using only standard, uncoated MST capillaries. Storage at -20 °C ensured stability of PL* and its fluorescent signal. MST results showed that crude pancreatic extracts were suitable as a source of PL for the evaluation of binding affinities of small ligands. Quercotriterpenoside-I (QTT-I) demonstrated high PL* binding affinity (31 nM) followed by 3-O-galloylbarrinic acid (3-GBA) (500 nM) and bartogenic acid (BA) (1327 nM). To enrich the 50 kDa lipase responsible for the majority of hydrolysis activity in the crude pancreatic extracts, ammonium sulfate precipitation was attempted and its efficiency confirmed using capillary electrophoresis (CE)-based activity assays and HRMS. Moreover, to accurately explain enzyme modulation mechanism, it is imperative to complement binding assays with catalytic activity ones.
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Affiliation(s)
- Ghassan Al Hamoui Dit Banni
- Institut de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d'Orléans, 45067, Orléans, France
| | - Rouba Nasreddine
- Institut de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d'Orléans, 45067, Orléans, France
| | - Syntia Fayad
- Institut des Sciences de la Vigne et du Vin (ISVV), EA 5477, Unité de recherche Œnologie, USC 1366 INRA, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Cyril Colas
- Institut de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d'Orléans, 45067, Orléans, France.,Centre de Biophysique Moléculaire, CNRS-Université d'Orléans, UPR 4311, 45071, Orléans CEDEX 2, France
| | - Axel Marchal
- Institut des Sciences de la Vigne et du Vin (ISVV), EA 5477, Unité de recherche Œnologie, USC 1366 INRA, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Reine Nehmé
- Institut de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d'Orléans, 45067, Orléans, France.
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Panter F, Bader CD, Müller R. Synergizing the potential of bacterial genomics and metabolomics to find novel antibiotics. Chem Sci 2021; 12:5994-6010. [PMID: 33995996 PMCID: PMC8098685 DOI: 10.1039/d0sc06919a] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development based on natural products has faced a long lasting decline since the 1970s, while both the speed and the extent of antimicrobial resistance (AMR) development have been severely underestimated. The discovery of antimicrobial natural products of bacterial and fungal origin featuring new chemistry and previously unknown mode of actions is increasingly challenged by rediscovery issues. Natural products that are abundantly produced by the corresponding wild type organisms often featuring strong UV signals have been extensively characterized, especially the ones produced by extensively screened microbial genera such as streptomycetes. Purely synthetic chemistry approaches aiming to replace the declining supply from natural products as starting materials to develop novel antibiotics largely failed to provide significant numbers of antibiotic drug leads. To cope with this fundamental issue, microbial natural products science is being transformed from a 'grind-and-find' study to an integrated approach based on bacterial genomics and metabolomics. Novel technologies in instrumental analytics are increasingly employed to lower detection limits and expand the space of detectable substance classes, while broadening the scope of accessible and potentially bioactive natural products. Furthermore, the almost exponential increase in publicly available bacterial genome data has shown that the biosynthetic potential of the investigated strains by far exceeds the amount of detected metabolites. This can be judged by the discrepancy between the number of biosynthetic gene clusters (BGC) encoded in the genome of each microbial strain and the number of secondary metabolites actually detected, even when considering the increased sensitivity provided by novel analytical instrumentation. In silico annotation tools for biosynthetic gene cluster classification and analysis allow fast prioritization in BGC-to-compound workflows, which is highly important to be able to process the enormous underlying data volumes. BGC prioritization is currently accompanied by novel molecular biology-based approaches to access the so-called orphan BGCs not yet correlated with a secondary metabolite. Integration of metabolomics, in silico genomics and molecular biology approaches into the mainstream of natural product research will critically influence future success and impact the natural product field in pharmaceutical, nutritional and agrochemical applications and especially in anti-infective research.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
| | - Chantal D Bader
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
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29
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Jiang H, Cole PA. N-Terminal Protein Labeling with N-Hydroxysuccinimide Esters and Microscale Thermophoresis Measurements of Protein-Protein Interactions Using Labeled Protein. Curr Protoc 2021; 1:e14. [PMID: 33484499 PMCID: PMC7839251 DOI: 10.1002/cpz1.14] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein labeling strategies have been explored for decades to study protein structure, function, and regulation. Fluorescent labeling of a protein enables the study of protein-protein interactions through biophysical methods such as microscale thermophoresis (MST). MST measures the directed motion of a fluorescently labeled protein in response to microscopic temperature gradients, and the protein's thermal mobility can be used to determine binding affinity. However, the stoichiometry and site specificity of fluorescent labeling are hard to control, and heterogeneous labeling can generate inaccuracies in binding measurements. Here, we describe an easy-to-apply protocol for high-stoichiometric, site-specific labeling of a protein at its N-terminus with N-hydroxysuccinimide (NHS) esters as a means to measure protein-protein interaction affinity by MST. This protocol includes guidelines for NHS ester labeling, fluorescent-labeled protein purification, and MST measurement using a labeled protein. As an example of the entire workflow, we additionally provide a protocol for labeling a ubiquitin E3 enzyme and testing ubiquitin E2-E3 enzyme binding affinity. These methods are highly adaptable and can be extended for protein interaction studies in various biological and biochemical circumstances. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Labeling a protein of interest at its N-terminus with NHS esters through stepwise reaction Alternate Protocol: Labeling a protein of interest at its N-terminus with NHS esters through a one-pot reaction Basic Protocol 2: Purifying the N-terminal fluorescent-labeled protein and determining its concentration and labeling efficiency Basic Protocol 3: Using MST to determine the binding affinity of an N-terminal fluorescent-labeled protein to a binding partner. Basic Protocol 4: NHS ester labeling of ubiquitin E3 ligase WWP2 and measurement of the binding affinity between WWP2 and an E2 conjugating enzyme by the MST binding assay.
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Affiliation(s)
- Hanjie Jiang
- Division of Genetics, Brigham and Women’s Hospital,
Department of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard
Medical School, Boston, Massachusetts 02115, United States
- Department of Pharmacology and Molecular Sciences, Johns
Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Philip A. Cole
- Division of Genetics, Brigham and Women’s Hospital,
Department of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard
Medical School, Boston, Massachusetts 02115, United States
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30
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Feoli A, Pisapia V, Viviano M, Castellano S, Bartoschik T, Sbardella G. Development of a Microscale Thermophoresis-Based Method for Screening and Characterizing Inhibitors of the Methyl-Lysine Reader Protein MRG15. SLAS DISCOVERY 2020; 26:77-87. [PMID: 32808584 DOI: 10.1177/2472555220949166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
MRG15 is a transcription factor containing the methyl-lysine reader chromodomain. Despite its involvement in different physiological and pathological states, to date the role of this protein has not been fully elucidated due to the lack of a specific and potent chemical probe.In this work, we report the development of a microscale thermophoresis (MST)-based assay for the study of MRG15-ligand binding interactions. After the development, the assay was validated using a small focused library and UNC1215 as the reference compound, to yield the identification of 10 MRG15 ligands with affinities ranging from 37.8 nM to 59.1 µM.Hence, our method is robust, convenient, and fast and could be applied to other methylation reader domain-containing proteins for the identification of new chemical probes.
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Affiliation(s)
- Alessandra Feoli
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Vincenzo Pisapia
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy.,PhD Program in Drug Discovery and Development, University of Salerno, Fisciano, SA, Italy.,NanoTemper Technologies GmbH, Munich, Germany
| | - Monica Viviano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Sabrina Castellano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | | | - Gianluca Sbardella
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
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31
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Honarnejad S, van Boeckel S, van den Hurk H, van Helden S. Hit Discovery for Public Target Programs in the European Lead Factory: Experiences and Output from Assay Development and Ultra-High-Throughput Screening. SLAS DISCOVERY 2020; 26:192-204. [PMID: 32734803 PMCID: PMC8637381 DOI: 10.1177/2472555220942765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The European Lead Factory (ELF) consortium provides European academics and small and medium enterprises access to ~0.5 million unique compounds, a state-of-the-art ultra-high-throughput screening (u-HTS) platform, and industrial early drug discovery (DD) expertise with the aim of delivering innovative DD starting points. From 2013 to 2018, 154 proposals for eight target classes in seven therapeutic areas were submitted to the ELF consortium, 88 of which were accepted by the selection committee. During this period, 76 primary assays based on seven different readout technologies were optimized and mainly miniaturized to 1536-well plates. In total, 72 u-HTS campaigns were carried out, and follow-up work including hit triage through orthogonal, deselection, selectivity, and biophysical assays were finalized. This ambitious project showed that besides the quality of the compound library and the primary assay, the success of centralized u-HTS of large compound libraries across many target classes, various assay types, and different readout technologies is also largely dependent on the capacity and flexibility of the automation on one hand and the hit-triaging phase on the other, particularly because of undesired compound-assay interference. Thus far, the delivered hit lists from the ELF consortium have resulted in spinoffs, patents, in vivo proof of concepts, preclinical development programs, peer-reviewed publications, PhD theses, and much more, demonstrating early success indications.
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Affiliation(s)
- Saman Honarnejad
- Pivot Park Screening Centre B.V., Oss, North Brabant, The Netherlands
| | - Stan van Boeckel
- Pivot Park Screening Centre B.V., Oss, North Brabant, The Netherlands
| | | | - Steven van Helden
- Pivot Park Screening Centre B.V., Oss, North Brabant, The Netherlands
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32
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Romain M, Thiroux B, Tardy M, Quesnel B, Thuru X. Measurement of Protein-Protein Interactions through Microscale Thermophoresis (MST). Bio Protoc 2020; 10:e3574. [PMID: 33659544 DOI: 10.21769/bioprotoc.3574] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 11/02/2022] Open
Abstract
The binding interactions of PD-1 and PD-L1 have been studied by surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) over the past few years, but these investigations resulted in controversy regarding the values of the dissociation constant (Kd) ( Freeman et al., 2000 ). MST is a powerful new method for the quantitative analysis of protein-protein interactions (PPIs) with low sample consumption. The technique is based on the movement of molecules along microscopic temperature gradients, and it detects changes in their hydration shell, charge or size. One binding partner is fluorescently labeled, while the other binding partner remains label-free. We used a protocol that allows the determination of the binding affinity by MST without purification of the target protein from the cell lysate. The application of this MST method to PD-1-eGFP and PD-L1-eGFP expressed in CHO-K1 cells allowed us, for the first time, to determine the affinity of the complex formed between PD-1 and its ligand PD-L1 during tumor escape. The protocol has a variety of potential applications for studying the interactions of proteins with small molecules.
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Affiliation(s)
- Magnez Romain
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Bryan Thiroux
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Morgane Tardy
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Bruno Quesnel
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Xavier Thuru
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000 Lille, France
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33
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Gao K, Oerlemans R, Groves MR. Theory and applications of differential scanning fluorimetry in early-stage drug discovery. Biophys Rev 2020; 12:85-104. [PMID: 32006251 PMCID: PMC7040159 DOI: 10.1007/s12551-020-00619-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Differential scanning fluorimetry (DSF) is an accessible, rapid, and economical biophysical technique that has seen many applications over the years, ranging from protein folding state detection to the identification of ligands that bind to the target protein. In this review, we discuss the theory, applications, and limitations of DSF, including the latest applications of DSF by ourselves and other researchers. We show that DSF is a powerful high-throughput tool in early drug discovery efforts. We place DSF in the context of other biophysical methods frequently used in drug discovery and highlight their benefits and downsides. We illustrate the uses of DSF in protein buffer optimization for stability, refolding, and crystallization purposes and provide several examples of each. We also show the use of DSF in a more downstream application, where it is used as an in vivo validation tool of ligand-target interaction in cell assays. Although DSF is a potent tool in buffer optimization and large chemical library screens when it comes to ligand-binding validation and optimization, orthogonal techniques are recommended as DSF is prone to false positives and negatives.
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Affiliation(s)
- Kai Gao
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Rick Oerlemans
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Matthew R Groves
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands.
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34
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Molnar KS, Dunyak BM, Su B, Izrayelit Y, McGlasson-Naumann B, Hamilton PD, Qian M, Covey DF, Gestwicki JE, Makley LN, Andley UP. Mechanism of Action of VP1-001 in cryAB(R120G)-Associated and Age-Related Cataracts. Invest Ophthalmol Vis Sci 2019; 60:3320-3331. [PMID: 31369034 PMCID: PMC6676924 DOI: 10.1167/iovs.18-25647] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Purpose We previously identified an oxysterol, VP1-001 (also known as compound 29), that partially restores the transparency of lenses with cataracts. To understand the mechanism of VP1-001, we tested the ability of its enantiomer, ent-VP1-001, to bind and stabilize αB-crystallin (cryAB) in vitro and to produce a similar therapeutic effect in cryAB(R120G) mutant and aged wild-type mice with cataracts. VP1-001 and ent-VP1-001 have identical physicochemical properties. These experiments are designed to critically evaluate whether stereoselective binding to cryAB is required for activity. Methods We compared the binding of VP1-001 and ent-VP1-001 to cryAB using in silico docking, differential scanning fluorimetry (DSF), and microscale thermophoresis (MST). Compounds were delivered by six topical administrations to mouse eyes over 2 weeks, and the effects on cataracts and lens refractive measures in vivo were examined. Additionally, lens epithelial and fiber cell morphologies were assessed via transmission electron microscopy. Results Docking studies suggested greater binding of VP1-001 into a deep groove in the cryAB dimer compared with ent-VP1-001. Consistent with this prediction, DSF and MST experiments showed that VP1-001 bound cryAB, whereas ent-VP1-001 did not. Accordingly, topical treatment of lenses with ent-VP1-001 had no effect, whereas VP1-001 produced a statistically significant improvement in lens clarity and favorable changes in lens morphology. Conclusions The ability of VP1-001 to bind native cryAB dimers is important for its ability to reverse lens opacity in mouse models of cataracts.
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Affiliation(s)
- Kathleen S Molnar
- ViewPoint Therapeutics, South San Francisco, California, United States
| | - Bryan M Dunyak
- ViewPoint Therapeutics, South San Francisco, California, United States
| | - Bonnie Su
- ViewPoint Therapeutics, South San Francisco, California, United States
| | | | - Brittney McGlasson-Naumann
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Paul D Hamilton
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Mingxing Qian
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Douglas F Covey
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Diseases, University of California at San Francisco, San Francisco, California, United States
| | - Leah N Makley
- ViewPoint Therapeutics, South San Francisco, California, United States
| | - Usha P Andley
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
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35
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Niether D, Wiegand S. Thermophoresis of biological and biocompatible compounds in aqueous solution. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:503003. [PMID: 31491783 DOI: 10.1088/1361-648x/ab421c] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
With rising popularity of microscale thermophoresis for the characterisation of protein-ligand binding reactions and possible applications in microfluidic devices, there is a growing interest in considering thermodiffusion in the context of life sciences. But although the understanding of thermodiffusion in non-polar mixtures has grown rapidly in recent years, predictions for associated mixtures like aqueous solutions remain challenging. This review aims to give an overview of the literature on thermodiffusion in aqueous systems, show the difficulties in theoretical description that arise from the non-ideal behaviour of water-mixtures, and highlight the relevance of thermodiffusion in a biological context. We find that the thermodiffusion in aqueous systems is dominated by contributions from heat of transfer, hydrogen bond interactions and charge effects. However, the separation of these effects is often difficult, especially in case of biological systems where a systematic exclusion of contributions may not be feasible.
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Affiliation(s)
- D Niether
- ICS-3 Soft Condensed Matter, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
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36
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Kirsch P, Hartman AM, Hirsch AKH, Empting M. Concepts and Core Principles of Fragment-Based Drug Design. Molecules 2019; 24:molecules24234309. [PMID: 31779114 PMCID: PMC6930586 DOI: 10.3390/molecules24234309] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/11/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
In this review, a general introduction to fragment-based drug design and the underlying concepts is given. General considerations and methodologies ranging from library selection/construction over biophysical screening and evaluation methods to in-depth hit qualification and subsequent optimization strategies are discussed. These principles can be generally applied to most classes of drug targets. The examples given for fragment growing, merging, and linking strategies at the end of the review are set in the fields of enzyme-inhibitor design and macromolecule–macromolecule interaction inhibition. Building upon the foundation of fragment-based drug discovery (FBDD) and its methodologies, we also highlight a few new trends in FBDD.
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Affiliation(s)
- Philine Kirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123 Saarbrücken, Germany
| | - Alwin M. Hartman
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-681-988-062-031
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M. Beck E, Parnell E, Cowley A, Porter A, Gillespie J, Robinson J, Robinson L, Pannifer AD, Hamon V, Jones P, Morrison A, McElroy S, Timmerman M, Rutjes H, Mahajan P, Wiejak J, Luchowska-Stańska U, Morgan D, Barker G, Rehmann H, Yarwood SJ. Identification of A Novel Class of Benzofuran Oxoacetic Acid-Derived Ligands that Selectively Activate Cellular EPAC1. Cells 2019; 8:cells8111425. [PMID: 31726720 PMCID: PMC6912754 DOI: 10.3390/cells8111425] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/20/2022] Open
Abstract
Cyclic AMP promotes EPAC1 and EPAC2 activation through direct binding to a specific cyclic nucleotide-binding domain (CNBD) within each protein, leading to activation of Rap GTPases, which control multiple cell responses, including cell proliferation, adhesion, morphology, exocytosis, and gene expression. As a result, it has become apparent that directed activation of EPAC1 and EPAC2 with synthetic agonists may also be useful for the future treatment of diabetes and cardiovascular diseases. To identify new EPAC agonists we have developed a fluorescent-based, ultra-high-throughput screening (uHTS) assay that measures the displacement of binding of the fluorescent cAMP analogue, 8-NBD-cAMP to the EPAC1 CNBD. Triage of the output of an approximately 350,000 compound screens using this assay identified a benzofuran oxaloacetic acid EPAC1 binder (SY000) that displayed moderate potency using orthogonal assays (competition binding and microscale thermophoresis). We next generated a limited library of 91 analogues of SY000 and identified SY009, with modifications to the benzofuran ring associated with a 10-fold increase in potency towards EPAC1 over SY000 in binding assays. In vitro EPAC1 activity assays confirmed the agonist potential of these molecules in comparison with the known EPAC1 non-cyclic nucleotide (NCN) partial agonist, I942. Rap1 GTPase activation assays further demonstrated that SY009 selectively activates EPAC1 over EPAC2 in cells. SY009 therefore represents a novel class of NCN EPAC1 activators that selectively activate EPAC1 in cellulae.
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Affiliation(s)
- Elizabeth M. Beck
- European Screening Centre Newhouse, University of Dundee, Biocity Scotland, Bo’Ness Road, Newhouse, Lanarkshire ML1 5UH, UK; (E.M.B.); (A.C.); (A.P.); (J.G.); (J.R.); (L.R.); (A.D.P.); (V.H.); (P.J.); (A.M.); (S.M.)
| | - Euan Parnell
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | - Angela Cowley
- European Screening Centre Newhouse, University of Dundee, Biocity Scotland, Bo’Ness Road, Newhouse, Lanarkshire ML1 5UH, UK; (E.M.B.); (A.C.); (A.P.); (J.G.); (J.R.); (L.R.); (A.D.P.); (V.H.); (P.J.); (A.M.); (S.M.)
| | - Alison Porter
- European Screening Centre Newhouse, University of Dundee, Biocity Scotland, Bo’Ness Road, Newhouse, Lanarkshire ML1 5UH, UK; (E.M.B.); (A.C.); (A.P.); (J.G.); (J.R.); (L.R.); (A.D.P.); (V.H.); (P.J.); (A.M.); (S.M.)
| | - Jonathan Gillespie
- European Screening Centre Newhouse, University of Dundee, Biocity Scotland, Bo’Ness Road, Newhouse, Lanarkshire ML1 5UH, UK; (E.M.B.); (A.C.); (A.P.); (J.G.); (J.R.); (L.R.); (A.D.P.); (V.H.); (P.J.); (A.M.); (S.M.)
| | - John Robinson
- European Screening Centre Newhouse, University of Dundee, Biocity Scotland, Bo’Ness Road, Newhouse, Lanarkshire ML1 5UH, UK; (E.M.B.); (A.C.); (A.P.); (J.G.); (J.R.); (L.R.); (A.D.P.); (V.H.); (P.J.); (A.M.); (S.M.)
| | - Lindsay Robinson
- European Screening Centre Newhouse, University of Dundee, Biocity Scotland, Bo’Ness Road, Newhouse, Lanarkshire ML1 5UH, UK; (E.M.B.); (A.C.); (A.P.); (J.G.); (J.R.); (L.R.); (A.D.P.); (V.H.); (P.J.); (A.M.); (S.M.)
| | - Andrew D. Pannifer
- European Screening Centre Newhouse, University of Dundee, Biocity Scotland, Bo’Ness Road, Newhouse, Lanarkshire ML1 5UH, UK; (E.M.B.); (A.C.); (A.P.); (J.G.); (J.R.); (L.R.); (A.D.P.); (V.H.); (P.J.); (A.M.); (S.M.)
| | - Veronique Hamon
- European Screening Centre Newhouse, University of Dundee, Biocity Scotland, Bo’Ness Road, Newhouse, Lanarkshire ML1 5UH, UK; (E.M.B.); (A.C.); (A.P.); (J.G.); (J.R.); (L.R.); (A.D.P.); (V.H.); (P.J.); (A.M.); (S.M.)
| | - Philip Jones
- European Screening Centre Newhouse, University of Dundee, Biocity Scotland, Bo’Ness Road, Newhouse, Lanarkshire ML1 5UH, UK; (E.M.B.); (A.C.); (A.P.); (J.G.); (J.R.); (L.R.); (A.D.P.); (V.H.); (P.J.); (A.M.); (S.M.)
| | - Angus Morrison
- European Screening Centre Newhouse, University of Dundee, Biocity Scotland, Bo’Ness Road, Newhouse, Lanarkshire ML1 5UH, UK; (E.M.B.); (A.C.); (A.P.); (J.G.); (J.R.); (L.R.); (A.D.P.); (V.H.); (P.J.); (A.M.); (S.M.)
| | - Stuart McElroy
- European Screening Centre Newhouse, University of Dundee, Biocity Scotland, Bo’Ness Road, Newhouse, Lanarkshire ML1 5UH, UK; (E.M.B.); (A.C.); (A.P.); (J.G.); (J.R.); (L.R.); (A.D.P.); (V.H.); (P.J.); (A.M.); (S.M.)
| | - Martin Timmerman
- Pivot Park Screening Centre, Kloosterstraat 9, 5349 AB Oss, The Netherlands; (M.T.); (H.R.)
| | - Helma Rutjes
- Pivot Park Screening Centre, Kloosterstraat 9, 5349 AB Oss, The Netherlands; (M.T.); (H.R.)
| | - Pravin Mahajan
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK;
| | - Jolanta Wiejak
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh Campus, Edinburgh EH14 4AS, UK; (J.W.); (U.L.-S.)
| | - Urszula Luchowska-Stańska
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh Campus, Edinburgh EH14 4AS, UK; (J.W.); (U.L.-S.)
| | - David Morgan
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK; (D.M.); (G.B.)
| | - Graeme Barker
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK; (D.M.); (G.B.)
| | - Holger Rehmann
- Department of Molecular Cancer Research, Centre of Biomedical Genetics and Cancer Genomics Centre, University Medical Centre Utrecht, 3508 TC Utrecht, The Netherlands;
| | - Stephen J. Yarwood
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh Campus, Edinburgh EH14 4AS, UK; (J.W.); (U.L.-S.)
- Correspondence:
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Omolo CA, Kalhapure RS, Agrawal N, Jadhav M, Rambharose S, Mocktar C, Govender T. A hybrid of mPEG-b-PCL and G1-PEA dendrimer for enhancing delivery of antibiotics. J Control Release 2018; 290:112-128. [DOI: 10.1016/j.jconrel.2018.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/17/2018] [Accepted: 10/06/2018] [Indexed: 01/02/2023]
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Ronzetti M, Baljinnyam B, Yasgar A, Simeonov A. Testing for drug-human serum albumin binding using fluorescent probes and other methods. Expert Opin Drug Discov 2018; 13:1005-1014. [DOI: 10.1080/17460441.2018.1534824] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Michael Ronzetti
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Bolormaa Baljinnyam
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
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