1
|
Yanagita RC, Otani M, Hatanaka S, Nishi H, Miyake S, Hanaki Y, Sato M, Kawanami Y, Irie K. Analysis of binding mode of vibsanin A with protein kinase C C1 domains: An experimental and molecular dynamics simulation study. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
2
|
Ha JH, Yu X, Carpizo DR, Loh SN. Urea Denaturation, Zinc Binding, and DNA Binding Assays of Mutant p53 DNA-binding Domains and Full-length Proteins. Bio Protoc 2021; 11:e4188. [PMID: 34786438 DOI: 10.21769/bioprotoc.4188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 11/02/2022] Open
Abstract
In the cell, the thermodynamic stability of a protein - and hence its biological activity - can change dramatically as a result of perturbations in its amino acid sequence and the concentration of stabilizing ligands. This interplay is particularly evident in zinc-binding transcription factors such as the p53 tumor suppressor, whose DNA-binding activity can critically depend on levels of intracellular zinc as well as point mutations that alter either metal binding or folding stability. Separate protocols exist for determining a protein's metal affinity and its folding free energy. These properties, however, are intimately connected, and a technique is needed to integrate these measurements. Our protocols employ common non-fluorescent and fluorescent zinc chelators to control and report on free Zn2+ concentration, respectively, combined with biophysical assays of full-length human p53 and its DNA-binding domain. Fitting the data to equations that contain stability and metal-binding terms results in a more complete picture of how metal-dependent proteins can lose and gain DNA-binding function in a range of physiological conditions. Graphic abstract: Figure 1.Raising intracellular zinc can restore tumor-suppressing function to p53 that has been unfolded by missense mutation or cellular conditions.
Collapse
Affiliation(s)
- Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, United States
| | - Xin Yu
- Department of Surgery, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, United States
| | - Darren R Carpizo
- Department of Surgery, University of Rochester School of Medicine and Dentistry and Wilmot Cancer Center, Rochester, United States
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, United States
| |
Collapse
|
3
|
Ligand Discovery: High-Throughput Binding: Fluorescence Polarization (Anisotropy). Methods Mol Biol 2021. [PMID: 33877601 DOI: 10.1007/978-1-0716-1197-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
High-throughput assays based on fluorescence polarization (or fluorescence anisotropy) technology have often been employed for primary hit-finding in drug discovery. These binding assays provide a homogeneous format and consistent performance and offer advantages over some other optical methods. Developments in assay design and improvements in fluorescent probes have enabled the application of the technique to even complex biological systems. Here we describe the practical considerations for development of FP assays applied in high-throughput screening, including fluorophore selection, assay design, data analysis, and approaches for detecting compound interference.
Collapse
|
4
|
Blanden AR, Yu X, Blayney AJ, Demas C, Ha JH, Liu Y, Withers T, Carpizo DR, Loh SN. Zinc shapes the folding landscape of p53 and establishes a pathway for reactivating structurally diverse cancer mutants. eLife 2020; 9:61487. [PMID: 33263541 PMCID: PMC7728444 DOI: 10.7554/elife.61487] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/19/2020] [Indexed: 12/19/2022] Open
Abstract
Missense mutations in the p53 DNA-binding domain (DBD) contribute to half of new cancer cases annually. Here we present a thermodynamic model that quantifies and links the major pathways by which mutations inactivate p53. We find that DBD possesses two unusual properties—one of the highest zinc affinities of any eukaryotic protein and extreme instability in the absence of zinc—which are predicted to poise p53 on the cusp of folding/unfolding in the cell, with a major determinant being available zinc concentration. We analyze the 20 most common tumorigenic p53 mutations and find that 80% impair zinc affinity, thermodynamic stability, or both. Biophysical, cell-based, and murine xenograft experiments demonstrate that a synthetic zinc metallochaperone rescues not only mutations that decrease zinc affinity, but also mutations that destabilize DBD without impairing zinc binding. The results suggest that zinc metallochaperones have the capability to treat 120,500 patients annually in the U.S.
Collapse
Affiliation(s)
- Adam R Blanden
- Department of Neurology, SUNY Upstate Medical University, Syracuse, Syracuse, United States
| | - Xin Yu
- Rutgers Cancer Institute of New Jersey, Department of Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, United States
| | - Alan J Blayney
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, United States
| | - Christopher Demas
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, United States
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, United States
| | - Yue Liu
- Rutgers Cancer Institute of New Jersey, Department of Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, United States
| | - Tracy Withers
- Rutgers Cancer Institute of New Jersey, Department of Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, United States
| | - Darren R Carpizo
- Department of Surgery, University of Rochester School of Medicine and Dentistry and Wilmot Cancer Center, Rochester, United States
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, United States
| |
Collapse
|
5
|
Jurewicz MM, Willis RA, Ramachandiran V, Altman JD, Stern LJ. MHC-I peptide binding activity assessed by exchange after cleavage of peptide covalently linked to β2-microglobulin. Anal Biochem 2019; 584:113328. [PMID: 31201791 DOI: 10.1016/j.ab.2019.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/14/2019] [Accepted: 05/31/2019] [Indexed: 10/26/2022]
Abstract
A common approach to measuring binding constants involves combining receptor and ligand and measuring the distribution of bound and free states after equilibration. For class I major histocompatibility (MHC-I) proteins, which bind short peptides for presentation to T cells, this approach is precluded by instability of peptide-free protein. Here we develop a method wherein a weakly-binding peptide covalently attached to the N-terminus of the MHC-I β2m subunit is released from the peptide binding site after proteolytic cleavage of the linker. The resultant protein is able to bind added peptide. A direct binding assay and method for estimation of peptide binding constant (Kd) are described, in which fluorescence polarization is used to follow peptide binding. A competition binding assay and method for estimation of inhibitor binding constant (Ki) using the same principle also are also described. The method uses a cubic equation to relate observed binding to probe concentration, probe Kd, inhibitor concentration, and inhibitor Ki under general reaction conditions without assumptions relating to relative binding affinities or concentrations. We also delineate advantages of this approach compared to the Cheng-Prusoff and Munson-Rodbard approaches for estimation of Ki using competition binding data.
Collapse
Affiliation(s)
- Mollie M Jurewicz
- Program in Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA, 01605, United States; Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01605, United States
| | - Richard A Willis
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, 30329, United States
| | - Vasanthi Ramachandiran
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, 30329, United States
| | - John D Altman
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, 30329, United States; Department of Microbiology and Immunology, Emory Vaccine Center at Yerkes, Emory University School of Medicine, Atlanta, GA, 30329, United States
| | - Lawrence J Stern
- Program in Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA, 01605, United States; Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01605, United States; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, United States.
| |
Collapse
|
6
|
Reiner D, Stark H. Ligand binding kinetics at histamine H3 receptors by fluorescence-polarization with real-time monitoring. Eur J Pharmacol 2019; 848:112-120. [DOI: 10.1016/j.ejphar.2019.01.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/24/2019] [Accepted: 01/24/2019] [Indexed: 01/07/2023]
|
7
|
Carr BJ, Mihara K, Ramachandran R, Saifeddine M, Nathanson NM, Stell WK, Hollenberg MD. Myopia-Inhibiting Concentrations of Muscarinic Receptor Antagonists Block Activation of Alpha2A-Adrenoceptors In Vitro. Invest Ophthalmol Vis Sci 2019; 59:2778-2791. [PMID: 29860464 DOI: 10.1167/iovs.17-22562] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Myopia is a refractive disorder that degrades vision. It can be treated with atropine, a muscarinic acetylcholine receptor (mAChR) antagonist, but the mechanism is unknown. Atropine may block α-adrenoceptors at concentrations ≥0.1 mM, and another potent myopia-inhibiting ligand, mamba toxin-3 (MT3), binds equally well to human mAChR M4 and α1A- and α2A-adrenoceptors. We hypothesized that mAChR antagonists could inhibit myopia via α2A-adrenoceptors, rather than mAChR M4. Methods Human mAChR M4 (M4), chicken mAChR M4 (cM4), or human α2A-adrenergic receptor (hADRA2A) clones were cotransfected with CRE/promoter-luciferase (CRE-Luc; agonist-induced luminescence) and Renilla luciferase (RLuc; normalizing control) into human cells. Inhibition of normalized agonist-induced luminescence by antagonists (ATR: atropine; MT3; HIM: himbacine; PRZ: pirenzepine; TRP: tropicamide; OXY: oxyphenonium; QNB: 3-quinuclidinyl benzilate; DIC: dicyclomine; MEP: mepenzolate) was measured using the Dual-Glo Luciferase Assay System. Results Relative inhibitory potencies of mAChR antagonists at mAChR M4/cM4, from most to least potent, were QNB > OXY ≥ ATR > MEP > HIM > DIC > PRZ > TRP. MT3 was 56× less potent at cM4 than at M4. Relative potencies of mAChR antagonists at hADRA2A, from most to least potent, were MT3 > HIM > ATR > OXY > PRZ > TRP > QNB > MEP; DIC did not antagonize. Conclusions Muscarinic antagonists block hADRA2A signaling at concentrations comparable to those used to inhibit chick myopia (≥0.1 mM) in vivo. Relative potencies at hADRA2A, but not M4/cM4, correlate with reported abilities to inhibit chick form-deprivation myopia. mAChR antagonists might inhibit myopia via α2-adrenoceptors, instead of through the mAChR M4/cM4 receptor subtype.
Collapse
Affiliation(s)
- Brittany J Carr
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Inflammation Research Network-Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Neuroscience, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Koichiro Mihara
- Inflammation Research Network-Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Rithwik Ramachandran
- Inflammation Research Network-Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Physiology and Pharmacology, Western University, London, Ontario, Canada
| | - Mahmoud Saifeddine
- Inflammation Research Network-Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Neil M Nathanson
- Department of Pharmacology, University of Washington, Seattle, Washington, United States
| | - William K Stell
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Morley D Hollenberg
- Inflammation Research Network-Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
8
|
McGrath AE, Martyn AP, Whittell LR, Dawes FE, Beck JL, Dixon NE, Kelso MJ, Oakley AJ. Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens. J Struct Biol 2018; 204:396-405. [DOI: 10.1016/j.jsb.2018.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/19/2022]
|
9
|
Substrate-assisted enzymatic formation of lysinoalanine in duramycin. Nat Chem Biol 2018; 14:928-933. [PMID: 30177849 PMCID: PMC6372306 DOI: 10.1038/s41589-018-0122-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 07/17/2018] [Indexed: 02/07/2023]
Abstract
Duramycin is a heavily post-translationally modified peptide that binds phosphatidylethanolamine. It has been investigated as an antibiotic, inhibitor of viral entry, therapeutic for cystic fibrosis, and tumor and vasculature imaging agent. Duramycin contains a β-hydroxylated Asp (Hya) and four macrocycles, including an essential lysinoalanine (Lal) crosslink. The mechanism of Lal formation is not known. We here show that Lal is installed stereospecifically by DurN via addition of Lys19 to a dehydroalanine. The structure of DurN reveals an unusual dimer with a new fold. Surprisingly, in the structure of duramycin bound to DurN, no residues of the enzyme are near the Lal crosslink. Instead, Hya15 of the substrate makes interactions with Lal, suggesting it acts as a base to deprotonate Lys19 during catalysis. Biochemical data suggest that DurN preorganizes the reactive conformation of the substrate, such that the Hya15 of the substrate can serve as the catalytic base for Lal formation.
Collapse
|
10
|
Puyang X, Furman C, Zheng GZ, Wu ZJ, Banka D, Aithal K, Agoulnik S, Bolduc DM, Buonamici S, Caleb B, Das S, Eckley S, Fekkes P, Hao MH, Hart A, Houtman R, Irwin S, Joshi JJ, Karr C, Kim A, Kumar N, Kumar P, Kuznetsov G, Lai WG, Larsen N, Mackenzie C, Martin LA, Melchers D, Moriarty A, Nguyen TV, Norris J, O'Shea M, Pancholi S, Prajapati S, Rajagopalan S, Reynolds DJ, Rimkunas V, Rioux N, Ribas R, Siu A, Sivakumar S, Subramanian V, Thomas M, Vaillancourt FH, Wang J, Wardell S, Wick MJ, Yao S, Yu L, Warmuth M, Smith PG, Zhu P, Korpal M. Discovery of Selective Estrogen Receptor Covalent Antagonists for the Treatment of ERα WT and ERα MUT Breast Cancer. Cancer Discov 2018; 8:1176-1193. [PMID: 29991605 DOI: 10.1158/2159-8290.cd-17-1229] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/11/2018] [Accepted: 06/19/2018] [Indexed: 11/16/2022]
Abstract
Mutations in estrogen receptor alpha (ERα) that confer resistance to existing classes of endocrine therapies are detected in up to 30% of patients who have relapsed during endocrine treatments. Because a significant proportion of therapy-resistant breast cancer metastases continue to be dependent on ERα signaling, there remains a critical need to develop the next generation of ERα antagonists that can overcome aberrant ERα activity. Through our drug-discovery efforts, we identified H3B-5942, which covalently inactivates both wild-type and mutant ERα by targeting Cys530 and enforcing a unique antagonist conformation. H3B-5942 belongs to a class of ERα antagonists referred to as selective estrogen receptor covalent antagonists (SERCA). In vitro comparisons of H3B-5942 with standard-of-care (SoC) and experimental agents confirmed increased antagonist activity across a panel of ERαWT and ERαMUT cell lines. In vivo, H3B-5942 demonstrated significant single-agent antitumor activity in xenograft models representing ERαWT and ERαY537S breast cancer that was superior to fulvestrant. Lastly, H3B-5942 potency can be further improved in combination with CDK4/6 or mTOR inhibitors in both ERαWT and ERαMUT cell lines and/or tumor models. In summary, H3B-5942 belongs to a class of orally available ERα covalent antagonists with an improved profile over SoCs.Significance: Nearly 30% of endocrine therapy-resistant breast cancer metastases harbor constitutively activating mutations in ERα. SERCA H3B-5942 engages C530 of both ERαWT and ERαMUT, promotes a unique antagonist conformation, and demonstrates improved in vitro and in vivo activity over SoC agents. Importantly, single-agent efficacy can be further enhanced by combining with CDK4/6 or mTOR inhibitors. Cancer Discov; 8(9); 1176-93. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 1047.
Collapse
Affiliation(s)
| | | | | | | | | | - Kiran Aithal
- Aurigene Discovery Technologies Ltd., Bangalore, Karnataka, India
| | | | | | | | | | | | | | | | | | | | - René Houtman
- PamGene International, Den Bosch, the Netherlands
| | - Sean Irwin
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | | | - Craig Karr
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | - Amy Kim
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | | | - Pavan Kumar
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | | | | | | | | | - Lesley-Ann Martin
- Breast Cancer Now, Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | | | | | | | | | - Sunil Pancholi
- Breast Cancer Now, Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | | | | | | | | | - Ricardo Ribas
- Breast Cancer Now, Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Amy Siu
- Eisai Inc., Andover, Massachusetts
| | | | | | | | | | - John Wang
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | | | | | - Shihua Yao
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | - Lihua Yu
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | | | | | - Ping Zhu
- H3 Biomedicine, Inc., Cambridge, Massachusetts.
| | | |
Collapse
|
11
|
Chessum NEA, Sharp SY, Caldwell JJ, Pasqua AE, Wilding B, Colombano G, Collins I, Ozer B, Richards M, Rowlands M, Stubbs M, Burke R, McAndrew PC, Clarke PA, Workman P, Cheeseman MD, Jones K. Demonstrating In-Cell Target Engagement Using a Pirin Protein Degradation Probe (CCT367766). J Med Chem 2018; 61:918-933. [PMID: 29240418 PMCID: PMC5815658 DOI: 10.1021/acs.jmedchem.7b01406] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Indexed: 01/03/2023]
Abstract
Demonstrating intracellular protein target engagement is an essential step in the development and progression of new chemical probes and potential small molecule therapeutics. However, this can be particularly challenging for poorly studied and noncatalytic proteins, as robust proximal biomarkers are rarely known. To confirm that our recently discovered chemical probe 1 (CCT251236) binds the putative transcription factor regulator pirin in living cells, we developed a heterobifunctional protein degradation probe. Focusing on linker design and physicochemical properties, we generated a highly active probe 16 (CCT367766) in only three iterations, validating our efficient strategy for degradation probe design against nonvalidated protein targets.
Collapse
Affiliation(s)
- Nicola E. A. Chessum
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Swee Y. Sharp
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - John J. Caldwell
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - A. Elisa Pasqua
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Birgit Wilding
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Giampiero Colombano
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Ian Collins
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Bugra Ozer
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Meirion Richards
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Martin Rowlands
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Mark Stubbs
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Rosemary Burke
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - P. Craig McAndrew
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul A. Clarke
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul Workman
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Matthew D. Cheeseman
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| | - Keith Jones
- Cancer Research
UK Cancer Therapeutics Unit at The Institute
of Cancer Research, London SW7 3RP, United Kingdom
| |
Collapse
|
12
|
Ku AF, Cuny GD. Discovery of 7-hydroxyaporphines as conformationally restricted ligands for beta-1 and beta-2 adrenergic receptors. MEDCHEMCOMM 2018; 9:353-356. [PMID: 30108929 PMCID: PMC6083790 DOI: 10.1039/c7md00656j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 01/05/2018] [Indexed: 11/21/2022]
Abstract
A series of (-)-nornuciferidine derivatives was synthesized and the non-natural enantiomer of the aporphine alkaloid was discovered to be a potent β1- and β2-adrenergic receptor ligand that antagonized isoproterenol and procaterol induced cyclic AMP increases from adenylyl cyclase, respectively. Progressive deconstruction of the tetracyclic scaffold to less complex cyclic and acyclic analogues revealed that the conformationally restricted (6a-R,7-R)-7-hydroxyaporphine 2 (AK-2-202) was necessary for efficient receptor binding and antagonism.
Collapse
Affiliation(s)
- Angela F Ku
- Department of Pharmacological and Pharmaceutical Sciences , University of Houston , Science and Research Building 2 , Houston , Texas 77204 , USA .
| | - Gregory D Cuny
- Department of Pharmacological and Pharmaceutical Sciences , University of Houston , Science and Research Building 2 , Houston , Texas 77204 , USA .
| |
Collapse
|
13
|
Holdgate GA, Meek TD, Grimley RL. Mechanistic enzymology in drug discovery: a fresh perspective. Nat Rev Drug Discov 2017; 17:115-132. [PMID: 29192286 DOI: 10.1038/nrd.2017.219] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Given the therapeutic and commercial success of small-molecule enzyme inhibitors, as exemplified by kinase inhibitors in oncology, a major focus of current drug-discovery and development efforts is on enzyme targets. Understanding the course of an enzyme-catalysed reaction can help to conceptualize different types of inhibitor and to inform the design of screens to identify desired mechanisms. Exploiting this information allows the thorough evaluation of diverse compounds, providing the knowledge required to efficiently optimize leads towards differentiated candidate drugs. This review highlights the rationale for conducting high-quality mechanistic enzymology studies and considers the added value in combining such studies with orthogonal biophysical methods.
Collapse
Affiliation(s)
- Geoffrey A Holdgate
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
| | - Thomas D Meek
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Rachel L Grimley
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
| |
Collapse
|
14
|
Hedglin M, Aitha M, Benkovic SJ. Monitoring the Retention of Human Proliferating Cell Nuclear Antigen at Primer/Template Junctions by Proteins That Bind Single-Stranded DNA. Biochemistry 2017; 56:3415-3421. [PMID: 28590137 DOI: 10.1021/acs.biochem.7b00386] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In humans, proliferating cell nuclear antigen (PCNA) sliding clamps encircling DNA coordinate various aspects of DNA metabolism throughout the cell cycle. A critical aspect of this is restricting PCNA to the vicinity of its DNA target site. For example, PCNA must be maintained at or near primer/template (P/T) junctions during DNA synthesis. With a diverse array of cellular factors implicated, many of which interact with PCNA, DNA, or both, it is unknown how this critical feat is achieved. Furthermore, current biochemical assays that examine the retention of PCNA near P/T junctions are inefficient, discontinuous, and qualitative and significantly deviate from physiologically relevant conditions. To overcome these challenges and limitations, we recently developed a novel and convenient Förster resonance energy transfer (FRET) assay that directly and continuously monitors the retention of human PCNA at a P/T junction. Here we describe in detail the design, methodology, interpretation, and limitations of this quantitative FRET assay using the single-stranded DNA-binding protein, SSB, from Escherichia coli as an example. This powerful tool is broadly applicable to any single-stranded DNA-binding protein and may be utilized and/or expanded upon to dissect DNA metabolic pathways that are dependent upon PCNA.
Collapse
Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Mahesh Aitha
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| |
Collapse
|
15
|
Hedglin M, Pandey B, Benkovic SJ. Characterization of human translesion DNA synthesis across a UV-induced DNA lesion. eLife 2016; 5. [PMID: 27770570 PMCID: PMC5123862 DOI: 10.7554/elife.19788] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/21/2016] [Indexed: 12/11/2022] Open
Abstract
Translesion DNA synthesis (TLS) during S-phase uses specialized TLS DNA polymerases to replicate a DNA lesion, allowing stringent DNA synthesis to resume beyond the offending damage. Human TLS involves the conjugation of ubiquitin to PCNA clamps encircling damaged DNA and the role of this post-translational modification is under scrutiny. A widely-accepted model purports that ubiquitinated PCNA recruits TLS polymerases such as pol η to sites of DNA damage where they may also displace a blocked replicative polymerase. We provide extensive quantitative evidence that the binding of pol η to PCNA and the ensuing TLS are both independent of PCNA ubiquitination. Rather, the unique properties of pols η and δ are attuned to promote an efficient and passive exchange of polymerases during TLS on the lagging strand. DOI:http://dx.doi.org/10.7554/eLife.19788.001
Collapse
Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, United States
| | - Binod Pandey
- Department of Chemistry, The Pennsylvania State University, University Park, United States
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, United States
| |
Collapse
|
16
|
Bollini S, Herbst JJ, Gaughan GT, Verdoorn TA, Ditta J, Dubowchik GM, Vinitsky A. High-Throughput Fluorescence Polarization Method for Identification of FKBP12 Ligands. ACTA ACUST UNITED AC 2016; 7:526-30. [PMID: 14599350 DOI: 10.1177/1087057102238626] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
FKBP12 is best known as the target of the widely used immunosuppressive drug FK506 but may also play a role in neuronal survival. Nonimmunosuppressive ligands of FKBP12 have been shown to have neuroprotective and neuroregenerative activity both in vitro and in vivo, stimulating interest in the development of high-throughput screens to rapidly identify novel ligands. FKBP12 was expressed as a His6-fusion in bacteria and purified by metal ion affinity and gel filtration chromatography. A high-throughput fluorescence polarization assay was developed to identify novel ligands of FKBP12. Dissociation constant values of known FKBP12 ligands measured by the new method agreed closely with Kivalues obtained by assaying inhibition of the rotamase activity of the enzyme. The fluorescence polarization assay is rapid, robust, and inexpensive and does not generate radioactive waste. It is very well suited for high-throughput screening efforts.
Collapse
Affiliation(s)
- S Bollini
- Department of Neuroscience, Pharmaceutical Research Institute, Bristol-Myers Squibb, Inc., Wallingford, CT, USA
| | | | | | | | | | | | | |
Collapse
|
17
|
Young SM, Bologa C, Prossnitz ER, Oprea TI, Sklar LA, Edwards BS. High-Throughput Screening with HyperCyt® Flow Cytometry to Detect Small Molecule Formylpeptide Receptor Ligands. ACTA ACUST UNITED AC 2016; 10:374-82. [PMID: 15964939 DOI: 10.1177/1087057105274532] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-throughput flow cytometry (HTFC), enabled by faster automated sample processing, represents a promising high- content approach for compound library screening. HyperCyt® is a recently developed automated HTFC analysis system by which cell samples are rapidly aspirated from microplate wells and delivered to the flow cytometer. The formylpeptide receptor (FPR) family of G protein–coupled receptors contributes to the localization and activation of tissue-damaging leukocytes at sites of chronic inflammation. Here, the authors describe development and application of an HTFC screening approach to detect potential anti-inflammatory compounds that block ligand binding to FPR. Using a homogeneous no-wash assay, samples were routinely processed at 1.5 s/well (~2500 cells analyzed/sample), allowing a 96-well plate to be processed in less than 2.5 min. Assay sensitivity and accuracy were validated by detection of a previously documented active compound with relatively low FPR affinity (sulfinpyrazone, inhibition constant [Ki]=14 μM) from among a collection of 880 compounds in the Prestwick Chemical Library. The HyperCyt® system was therefore demonstrated to be a robust, sensitive, and highly quantitative method with which to screen lead compound libraries in a 96-well format.
Collapse
Affiliation(s)
- Susan M Young
- Cytometry and Department of Pathology, Cancer Research and Treatment Center, University of New Mexico, Health Sciences Center, Albuquerque, NM 87131, USA
| | | | | | | | | | | |
Collapse
|
18
|
Du X, Li Y, Xia YL, Ai SM, Liang J, Sang P, Ji XL, Liu SQ. Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods. Int J Mol Sci 2016; 17:ijms17020144. [PMID: 26821017 PMCID: PMC4783878 DOI: 10.3390/ijms17020144] [Citation(s) in RCA: 724] [Impact Index Per Article: 90.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/13/2016] [Accepted: 01/18/2016] [Indexed: 01/16/2023] Open
Abstract
Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein–ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models—the “lock-and-key”, “induced fit”, and “conformational selection”—are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein–ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed.
Collapse
Affiliation(s)
- Xing Du
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Yi Li
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Yuan-Ling Xia
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Shi-Meng Ai
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Department of Applied Mathematics, Yunnan Agricultural University, Kunming 650201, China.
| | - Jing Liang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Peng Sang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Laboratory of Molecular Cardiology, Department of Cardiology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, China.
| | - Xing-Lai Ji
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Key Laboratory for Tumor molecular biology of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming 650091, China.
| | - Shu-Qun Liu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Key Laboratory for Tumor molecular biology of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming 650091, China.
| |
Collapse
|
19
|
Zhen J, Antonio T, Jacob JC, Grandy DK, Reith MEA, Dutta AK, Selley DE. Efficacy of Hybrid Tetrahydrobenzo[d]thiazole Based Aryl Piperazines D-264 and D-301 at D₂ and D₃ Receptors. Neurochem Res 2015; 41:328-339. [PMID: 26718829 DOI: 10.1007/s11064-015-1808-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/08/2015] [Accepted: 12/14/2015] [Indexed: 01/15/2023]
Abstract
In elucidating the role of pharmacodynamic efficacy at D3 receptors in therapeutic effectiveness of dopamine receptor agonists, the influence of study system must be understood. Here two compounds with D3 over D2 selectivity developed in our earlier work, D-264 and D-301, are compared in dopamine receptor-mediated G-protein activation in striatal regions of wild-type and D2 receptor knockout mice and in CHO cells expressing D2 or D3 receptors. In caudate-putamen of D2 knockout mice, D-301 was ~3-fold more efficacious than D-264 in activating G-proteins as assessed by [(35)S]GTPγS binding; in nucleus accumbens, D-301 stimulated G-protein activation whereas D-264 did not. In contrast, the two ligands exerted similar efficacy in both regions of wild-type mice, suggesting both ligands activate D2 receptors with similar efficacy. In D2 and D3 receptor-expressing CHO cells, D-264 and D-301 appeared to act in the [(35)S]GTPγS assay as full agonists because they produced maximal stimulation equal to dopamine. Competition for [(3)H]spiperone binding was then performed to determine Ki/EC50 ratios as an index of receptor reserve for each ligand. Action of D-301, but not D-264, showed receptor reserve in D3 but not in D2 receptor-expressing cells, whereas dopamine showed receptor reserve in both cell lines. Gαo1 is highly expressed in brain and is important in D2-like receptor-G protein coupling. Transfection of Gαo1 in D3- but not D2-expressing CHO cells led to receptor reserve for D-264 without altering receptor expression levels. D-301 and dopamine exhibited receptor reserve in D3-expressing cells both with and without transfection of Gαo1. Altogether, these results indicate that D-301 has greater intrinsic efficacy to activate D3 receptors than D-264, whereas the two compounds act on D2 receptors with similar intrinsic efficacy. These findings also suggest caution in interpreting Emax values from functional assays in receptor-transfected cell models without accounting for receptor reserve.
Collapse
Affiliation(s)
- Juan Zhen
- Department of Psychiatry, New York University School of Medicine, New York, NY, USA
| | - Tamara Antonio
- Department of Psychiatry, New York University School of Medicine, New York, NY, USA
| | - Joanna C Jacob
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - David K Grandy
- DKG Department of Physiology & Pharmacology, School of Medicine and the Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
| | - Maarten E A Reith
- Department of Psychiatry, New York University School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Aloke K Dutta
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, USA
| | - Dana E Selley
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| |
Collapse
|
20
|
Nasiri HR, Linge S, Ullmann D. Thermodynamic profiling of inhibitors of Nrf2:Keap1 interactions. Bioorg Med Chem Lett 2015; 26:526-529. [PMID: 26653613 DOI: 10.1016/j.bmcl.2015.11.082] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/20/2015] [Accepted: 11/21/2015] [Indexed: 12/31/2022]
Abstract
Keap1 binds to the transcription factor Nrf2 and negatively modulates the expression of genes involved in cellular protection against oxidative stress. Small molecules have been discovered to inhibit the Nrf2:Keap1 interactions and act as antagonists of Keap1. The affinities of these small molecules are not very high and need further improvement in follow up hit-to-lead programs. In addition to the affinity parameters Ki, Kd, and IC50 thermodynamic parameters provide useful information for the selection and optimization of these hit molecules at the early stage of the lead discovery process. In this letter a tracer displacement assay was used to determine the thermodynamic signature of some of the known inhibitors of the Nrf2:Keap1 interaction. An optimized assay protocol is presented, which can be applied to other small molecules in hit-to-lead programs in a medium throughput manner.
Collapse
Affiliation(s)
- Hamid R Nasiri
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, D-22419 Hamburg, Germany.
| | - Sandra Linge
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, D-22419 Hamburg, Germany
| | - Dirk Ullmann
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, D-22419 Hamburg, Germany.
| |
Collapse
|
21
|
Prossnitz ER, Arterburn JB. International Union of Basic and Clinical Pharmacology. XCVII. G Protein-Coupled Estrogen Receptor and Its Pharmacologic Modulators. Pharmacol Rev 2015; 67:505-40. [PMID: 26023144 PMCID: PMC4485017 DOI: 10.1124/pr.114.009712] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Estrogens are critical mediators of multiple and diverse physiologic effects throughout the body in both sexes, including the reproductive, cardiovascular, endocrine, nervous, and immune systems. As such, alterations in estrogen function play important roles in many diseases and pathophysiological conditions (including cancer), exemplified by the lower prevalence of many diseases in premenopausal women. Estrogens mediate their effects through multiple cellular receptors, including the nuclear receptor family (ERα and ERβ) and the G protein-coupled receptor (GPCR) family (GPR30/G protein-coupled estrogen receptor [GPER]). Although both receptor families can initiate rapid cell signaling and transcriptional regulation, the nuclear receptors are traditionally associated with regulating gene expression, whereas GPCRs are recognized as mediating rapid cellular signaling. Estrogen-activated pathways are not only the target of multiple therapeutic agents (e.g., tamoxifen, fulvestrant, raloxifene, and aromatase inhibitors) but are also affected by a plethora of phyto- and xeno-estrogens (e.g., genistein, coumestrol, bisphenol A, dichlorodiphenyltrichloroethane). Because of the existence of multiple estrogen receptors with overlapping ligand specificities, expression patterns, and signaling pathways, the roles of the individual receptors with respect to the diverse array of endogenous and exogenous ligands have been challenging to ascertain. The identification of GPER-selective ligands however has led to a much greater understanding of the roles of this receptor in normal physiology and disease as well as its interactions with the classic estrogen receptors ERα and ERβ and their signaling pathways. In this review, we describe the history and characterization of GPER over the past 15 years focusing on the pharmacology of steroidal and nonsteroidal compounds that have been employed to unravel the biology of this most recently recognized estrogen receptor.
Collapse
Affiliation(s)
- Eric R Prossnitz
- Department of Internal Medicine (E.R.P.) and University of New Mexico Cancer Center (E.R.P., J.B.A.), The University of New Mexico Health Sciences Center, Albuquerque, New Mexico; and Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico (J.B.A.)
| | - Jeffrey B Arterburn
- Department of Internal Medicine (E.R.P.) and University of New Mexico Cancer Center (E.R.P., J.B.A.), The University of New Mexico Health Sciences Center, Albuquerque, New Mexico; and Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico (J.B.A.)
| |
Collapse
|
22
|
Zhen J, Antonio T, Ali S, Neve KA, Dutta AK, Reith MEA. Use of radiolabeled antagonist assays for assessing agonism at D2 and D3 dopamine receptors: comparison with functional GTPγS assays. J Neurosci Methods 2015; 248:7-15. [PMID: 25840364 DOI: 10.1016/j.jneumeth.2015.03.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 01/13/2023]
Abstract
BACKGROUND Cell-based drug screening assays are essential tools for drug discovery and development targeting G protein-coupled receptors, which include dopamine D3 receptors. D3 is notorious for its poor coupling to G protein in most heterologous cell lines, and therefore D3 agonist-stimulated binding of [(35)S]GTPγS to G protein cannot be observed in many "non-functional" D3 expressing cell lines. NEW METHOD The present work explores the use of an alternate method for assessing agonist activity, consisting of measuring the difference in agonist competition between [(3)H]spiperone bound to low-affinity states of the receptor and that with radioligand bound to high-affinity states (GTP shift assay). COMPARISON WITH EXISTING METHOD The current study describes the determination of GTP shifts in [(3)H]spiperone binding assays for the assessment of agonists' potencies (at D2 and D3) and efficacies (at D3). Compared with GTPγ(35)S binding assays, the new method removes the cumbersome need of functional D3 cell lines and limited project duration due to short half-life of isotope (35)S. CONCLUSION The new method allows the estimation of potency (D2 and D3) and efficacy (D3) at the level of receptor and G protein activation in a simple fashion from shifts in monophasic-inhibition curves. Moreover, it does not require [(35)S]GTPγS binding assays with functional D3 cells. This method will have wide applicability for D3-selective agonist screening. It may also be useful for other GPCRs circumventing the need for functional assays and offering the ability to detect agonist activity regardless of the particular signaling pathway.
Collapse
Affiliation(s)
- Juan Zhen
- Department of Psychiatry, New York University School of Medicine, New York, NY, USA.
| | - Tamara Antonio
- Department of Psychiatry, New York University School of Medicine, New York, NY, USA
| | - Solav Ali
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY, USA
| | - Kim A Neve
- Research Service, Department of Veterans Affairs Medical Center, Portland, OR, USA
| | - Aloke K Dutta
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, USA
| | - Maarten E A Reith
- Department of Psychiatry, New York University School of Medicine, New York, NY, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| |
Collapse
|
23
|
Liu L, Bernard D, Wang S. Case Study: discovery of inhibitors of the MDM2-p53 protein-protein interaction. Methods Mol Biol 2015; 1278:567-585. [PMID: 25859977 DOI: 10.1007/978-1-4939-2425-7_38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The p53 protein, a tumor suppressor, is inactivated in many human cancers through mutations or by its interaction with an oncoprotein, MDM2. Blocking the MDM2-p53 protein-protein interaction has the effect of activating wild-type p53 and has been pursued as a novel anticancer strategy. Small-molecule inhibitors of the MDM2-p53 interaction have been discovered through various approaches, and a number of them have progressed into clinical trials for cancer treatment. Here, we describe the methods and techniques used in the discovery of small-molecule inhibitors of the MDM2-p53 interaction.
Collapse
Affiliation(s)
- Liu Liu
- Comprehensive Cancer Center and Departments of Internal Medicine, University of Michigan, 1500 E. Medical Center Drive, Ann Arbor, MI, 48109, USA
| | | | | |
Collapse
|
24
|
Kong X, Chen L, Jiao L, Jiang X, Lian F, Lu J, Zhu K, Du D, Liu J, Ding H, Zhang N, Shen J, Zheng M, Chen K, Liu X, Jiang H, Luo C. Astemizole arrests the proliferation of cancer cells by disrupting the EZH2-EED interaction of polycomb repressive complex 2. J Med Chem 2014; 57:9512-21. [PMID: 25369470 DOI: 10.1021/jm501230c] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Polycomb Repressive Complex 2 (PRC2) modulates the chromatin structure and transcriptional repression by trimethylation lysine 27 of histone H3 (H3K27me3), a process that necessitates the protein-protein interaction (PPI) between the catalytic subunit EZH2 and EED. Deregulated PRC2 is intimately involved in tumorigenesis and progression, making it an invaluable target for epigenetic cancer therapy. However, until now, there have been no reported small molecule compounds targeting the EZH2-EED interactions. In the present study, we identified astemizole, an FDA-approved drug, as a small molecule inhibitor of the EZH2-EED interaction of PRC2. The disruption of the EZH2-EED interaction by astemizole destabilizes the PRC2 complex and inhibits its methyltransferase activity in cancer cells. Multiple lines of evidence have demonstrated that astemizole arrests the proliferation of PRC2-driven lymphomas primarily by disabling the PRC2 complex. Our findings demonstrate the chemical tractability of the difficult PPI target by a small molecule compound, highlighting the therapeutic promise for PRC2-driven human cancers via targeted destruction of the EZH2-EED complex.
Collapse
Affiliation(s)
- Xiangqian Kong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 P. R. China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Yin L, Stern LJ. A novel method to measure HLA-DM-susceptibility of peptides bound to MHC class II molecules based on peptide binding competition assay and differential IC(50) determination. J Immunol Methods 2014; 406:21-33. [PMID: 24583195 DOI: 10.1016/j.jim.2014.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/07/2014] [Accepted: 02/18/2014] [Indexed: 01/17/2023]
Abstract
HLA-DM (DM) functions as a peptide editor that mediates the exchange of peptides loaded onto MHCII molecules by accelerating peptide dissociation and association kinetics. The relative DM-susceptibility of peptides bound to MHCII molecules correlates with antigen presentation and immunodominance hierarchy, and measurement of DM-susceptibility has been a key effort in this field. Current assays of DM-susceptibility, based on differential peptide dissociation rates measured for individually labeled peptides over a long time base, are difficult and cumbersome. Here, we present a novel method to measure DM-susceptibility based on peptide binding competition assays performed in the presence and absence of DM, reported as a delta-IC(50) (change in 50% inhibition concentration) value. We simulated binding competition reactions of peptides with various intrinsic and DM-catalyzed kinetic parameters and found that under a wide range of conditions the delta-IC(50) value is highly correlated with DM-susceptibility as measured in off-rate assay. We confirmed experimentally that DM-susceptibility measured by delta-IC(50) is comparable to that measured by traditional off-rate assay for peptides with known DM-susceptibility hierarchy. The major advantage of this method is that it allows simple, fast and high throughput measurement of DM-susceptibility for a large set of unlabeled peptides in studies of the mechanism of DM action and for identification of CD4+ T cell epitopes.
Collapse
Affiliation(s)
- Liusong Yin
- Program in Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA 01605, United States
| | - Lawrence J Stern
- Program in Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA 01605, United States; Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, United States; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, United States.
| |
Collapse
|
26
|
Kral AM, Ozerova N, Close J, Jung J, Chenard M, Fleming J, Haines BB, Harrington P, Maclean J, Miller TA, Secrist P, Wang H, Heidebrecht RW. Divergent Kinetics Differentiate the Mechanism of Action of Two HDAC Inhibitors. Biochemistry 2014; 53:725-34. [DOI: 10.1021/bi400936h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Astrid M. Kral
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Nicole Ozerova
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Joshua Close
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Joon Jung
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Melissa Chenard
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Judith Fleming
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Brian B. Haines
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Paul Harrington
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - John Maclean
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Thomas A. Miller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Paul Secrist
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Hongmei Wang
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | | |
Collapse
|
27
|
Michino M, Donthamsetti P, Beuming T, Banala A, Duan L, Roux T, Han Y, Trinquet E, Newman AH, Javitch JA, Shi L. A single glycine in extracellular loop 1 is the critical determinant for pharmacological specificity of dopamine D2 and D3 receptors. Mol Pharmacol 2013; 84:854-64. [PMID: 24061855 DOI: 10.1124/mol.113.087833] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Subtype-selective agents for the dopamine D3 receptor (D3R) have been considered as potential medications for drug addiction and other neuropsychiatric disorders. Medicinal chemistry efforts have led to the discovery of 4-phenylpiperazine derivatives that are >100-fold selective for the dopamine D3 receptor over dopamine D2 receptor (D2R), despite high sequence identity (78% in the transmembrane domain). Based on the recent crystal structure of D3R, we demonstrated that the 4-phenylpiperazine moiety in this class of D3R-selective compounds binds to the conserved orthosteric binding site, whereas the extended aryl amide moiety is oriented toward a divergent secondary binding pocket (SBP). In an effort to further characterize molecular determinants of the selectivity of these compounds, we modeled their binding modes in D3R and D2R by comparative ligand docking and molecular dynamics simulations. We found that the aryl amide moiety in the SBP differentially induces conformational changes in transmembrane segment 2 and extracellular loop 1 (EL1), which amplify the divergence of the SBP in D3R and D2R. Receptor chimera and site-directed mutagenesis studies were used to validate these binding modes and to identify a divergent glycine in EL1 as critical to D3R over D2R subtype selectivity. A better understanding of drug-dependent receptor conformations such as these is key to the rational design of compounds targeting a specific receptor among closely related homologs, and may also lead to discovery of novel chemotypes that exploit subtle differences in protein conformations.
Collapse
Affiliation(s)
- Mayako Michino
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, New York, New York (P.D., L.D., Y.H., J.A.J.); Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., L.D., Y.H., J.A.J.); Schrödinger, Inc., New York, New York (T.B.); Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program of the National Institutes of Health National Institute on Drug Abuse, Baltimore, Maryland (A.B., A.H.N.); and Cisbio Bioassays, Codolet, France (T.R., E.T.)
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Pinilla C, Edwards BS, Appel JR, Yates-Gibbins T, Giulianotti MA, Medina-Franco JL, Young SM, Santos RG, Sklar LA, Houghten RA. Selective agonists and antagonists of formylpeptide receptors: duplex flow cytometry and mixture-based positional scanning libraries. Mol Pharmacol 2013; 84:314-24. [PMID: 23788657 DOI: 10.1124/mol.113.086595] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The formylpeptide receptor (FPR1) and formylpeptide-like 1 receptor (FPR2) are G protein-coupled receptors that are linked to acute inflammatory responses, malignant glioma stem cell metastasis, and chronic inflammation. Although several N-formyl peptides are known to bind to these receptors, more selective small-molecule, high-affinity ligands are needed for a better understanding of the physiologic roles played by these receptors. High-throughput assays using mixture-based combinatorial libraries represent a unique, highly efficient approach for rapid data acquisition and ligand identification. We report the superiority of this approach in the context of the simultaneous screening of a diverse set of mixture-based small-molecule libraries. We used a single cross-reactive peptide ligand for a duplex flow cytometric screen of FPR1 and FPR2 in color-coded cell lines. Screening 37 different mixture-based combinatorial libraries totaling more than five million small molecules (contained in 5,261 mixture samples) resulted in seven libraries that significantly inhibited activity at the receptors. Using positional scanning deconvolution, selective high-affinity (low nM K(i)) individual compounds were identified from two separate libraries, namely, pyrrolidine bis-diketopiperazine and polyphenyl urea. The most active individual compounds were characterized for their functional activities as agonists or antagonists with the most potent FPR1 agonist and FPR2 antagonist identified to date with an EC₅₀ of 131 nM (4 nM K(i)) and an IC₅₀ of 81 nM (1 nM K(i)), respectively, in intracellular Ca²⁺ response determinations. Comparative analyses of other previous screening approaches clearly illustrate the efficiency of identifying receptor selective, individual compounds from mixture-based combinatorial libraries.
Collapse
Affiliation(s)
- Clemencia Pinilla
- Torrey Pines Institute for Molecular Studies, San Diego, California, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
McLoughlin D, Bertelli F, Williams C. The A, B, Cs of G-protein-coupled receptor pharmacology in assay development for HTS. Expert Opin Drug Discov 2013; 2:603-19. [PMID: 23488953 DOI: 10.1517/17460441.2.5.603] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
G-protein-coupled receptors represent one of the most important areas of research in the pharmaceutical industry, being one of the largest druggable gene families. Recognising this fact, manufacturers have developed a huge variety of homogeneous assay technologies that facilitate the quantification of receptor ligand binding events and their downstream signalling cascades. However, while early emphasis was placed on the most sensitive, high-throughput and cost-effective screening technologies to enable identification of the most lead matter for further development, in recent years emphasis has shifted to a focus on maximising the identification of compounds that are new and developing assays that are more biologically/pharmacologically relevant. Therefore, this review provides an overview of the binding and functional techniques available for high-throughput screening, with particular attention on how assay application and configuration can be maximised to ensure their successful identification of relevant chemical matter and thereby optimising project success.
Collapse
Affiliation(s)
- Dj McLoughlin
- HTS CoE, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent, CT13 9NJ, UK +44(0)1304644616 ; +44(0)1304655592 ;
| | | | | |
Collapse
|
30
|
Lévy-Bimbot M, Major G, Courilleau D, Blondeau JP, Lévi Y. Tetrabromobisphenol-A disrupts thyroid hormone receptor alpha function in vitro: use of fluorescence polarization to assay corepressor and coactivator peptide binding. CHEMOSPHERE 2012; 87:782-788. [PMID: 22277881 DOI: 10.1016/j.chemosphere.2011.12.080] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 12/16/2011] [Accepted: 12/30/2011] [Indexed: 05/27/2023]
Abstract
Thyroid hormone receptors (TRs) recruit corepressor or coactivator factors to the promoters of target genes to regulate their transcription. Corepressors such as nuclear hormone receptor corepressor (NCoR) are recruited by unliganded TRs, whereas coactivators such as steroid receptor coactivator-2 (SRC2) are recruited when triiodothyronine (T3) is bound to TRs. These coregulator proteins interact with the ligand binding domain (LBD) of TRs via short, conserved peptide sequences that can be used to probe the conformational changes induced in TR LBD by TR ligands. Recombinant LBD of the human TRα1 isoform (hTRα1 LBD) was produced as a fusion with glutathione S-transferase, and used to develop assays based on fluorescence polarization to quantify the binding of either NCoR- or SRC2-derived fluorescent peptides to the hTRα1 LBD. The optimum concentrations of recombinant hTRα1 LBD, and of peptide probes were adjusted in order to produce the greatest possible T3-dependent signal variations in fluorescence polarization. Under these conditions, T3 induced a dose-dependent decrease in NCoR peptide binding, and a reciprocal dose-dependent increase in SRC2 peptide binding, in both cases at similar 50%-effective doses. The TR agonists triiodothyroacetic acid and thyroxine were also effective in preventing NCoR peptide binding and increasing SRC2 peptide binding, whereas reverse-triiodothyronine was less efficient and the biologically inactive thyronine had no effect on either process. These experiments validate cell-free assays based on the use of binding of corepressor or coactivator peptide probes, as measured by fluorescence polarization, for investigating the conformational changes of TRα1 LBD induced by potentially TR-interfering compounds. Both these methods were used to elucidate the mechanism of the disrupting effects of tetrabromobisphenol-A (TBBPA) on the hTRα1 LBD conformation related to the transcriptional activity of the receptor. TBBPA is a flame retardant that is released into the environment, and is a suspected disrupter of thyroid homeostasis. The present results indicate that TBBPA did indeed interfere with the ability of the hTRα1 LBD to bind both NCoR and SRC2. TBBPA behaved similarly to T3 in promoting the release of NCoR from LBD, whereas it failed to promote LBD interactions with SRC2. However, it did reduce the T3-induced interactions between LBD and the coactivator peptide. This study therefore suggests that TBBPA in the micromolar range can affect the regulation of transcription by both the apo- and the holo-TRα1, with potential disruption of the expression of genes that are either up- or down-regulated by T3.
Collapse
|
31
|
Bilen Ç, Beyaztaş S, Arslan O, Güler ÖÖ. Investigation of heavy metal effects on immobilized paraoxanase by glutaraldehyde. J Enzyme Inhib Med Chem 2012; 28:440-6. [PMID: 22233542 DOI: 10.3109/14756366.2011.647007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Serum paraoxonase 1 (PON1) was purified from bovine serum using hydrophobic interaction chromotography on Sepharose 4B-coupled l-tyrosine 1-naphthylamine gel, and monitored by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Paraoxonase enzyme was immobilized using different ratios of glutaraldehyde and the maximum activity was observed with 7% glutaraldehyde. The effects of inhibition by Mn(+2), Co(+2) and Cu(+2) heavy metals on the immobilized and free enzyme activities were studied. At the optimum pH and temperature, the K(m) and V(max) kinetic values for bovine serum paraoxonase and immobilized paraoxonase towards paraoxon substrate were determined as 0.296 × 10(-3) M & 37.04 EU vs. 0.727-10(-3) M & 36.36 EU, respectively.
Collapse
Affiliation(s)
- Çiğdem Bilen
- Department of Chemistry/Biochemistry div., Balikesir University Science and Art Faculty , Balikesir , Turkey
| | | | | | | |
Collapse
|
32
|
Cho EJ, Xia S, Ma LC, Robertus J, Krug RM, Anslyn EV, Montelione GT, Ellington AD. Identification of influenza virus inhibitors targeting NS1A utilizing fluorescence polarization-based high-throughput assay. ACTA ACUST UNITED AC 2012; 17:448-59. [PMID: 22223052 DOI: 10.1177/1087057111431488] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This article describes the development of a simple and robust fluorescence polarization (FP)-based binding assay and adaptation to high-throughput identification of small molecules blocking dsRNA binding to NS1A protein (nonstructural protein 1 from type A influenza strains). This homogeneous assay employs fluorescein-labeled 16-mer dsRNA and full-length NS1A protein tagged with glutathione S-transferase to monitor the changes in FP and fluorescence intensity simultaneously. The assay was optimized for high-throughput screening in a 384-well format and achieved a z' score greater than 0.7. Its feasibility for high-throughput screening was demonstrated using the National Institutes of Health clinical collection. Six of 446 small molecules were identified as possible ligands in an initial screening. A series of validation tests confirmed epigallocatechine gallate (EGCG) to be active in the submicromolar range. A mechanism of EGCG inhibition involving interaction with the dsRNA-binding motif of NS1A, including Arg38, was proposed. This structural information is anticipated to provide a useful basis for the modeling of antiflu therapeutic reagents. Overall, the FP-based binding assay demonstrated its superior capability for simple, rapid, inexpensive, and robust identification of NS1A inhibitors and validation of their activity targeting NS1A.
Collapse
Affiliation(s)
- Eun Jeong Cho
- Texas Institute for Drug and Diagnostic Development, University of Texas at Austin, Austin, TX 78712, USA.
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Yuan Z, Kumar EA, Campbell SJ, Palermo NY, Kizhake S, Glover JNM, Natarajan A. Exploiting the P-1 pocket of BRCT domains toward a structure guided inhibitor design. ACS Med Chem Lett 2011; 2:764-767. [PMID: 22046493 DOI: 10.1021/ml200147a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Breast cancer gene 1 carboxy terminus (BRCT) domains are found in a number of proteins that are important for DNA damage response (DDR). The BRCT domains bind phosphorylated proteins and these protein-protein interactions are essential for DDR and DNA repair. High affinity domain specific inhibitors are needed to facilitate the dissection of the protein-protein interactions in the DDR signaling. The BRCT domains of BRCA1 bind phosphorylated protein through a pSXXF consensus recognition motif. We identified a hydrophobic pocket at the P-1 position of the pSXXF binding site. Here we conducted a structure-guided synthesis of peptide analogs with hydrophobic functional groups at the P-1 position. Evaluation of these led to the identification of a peptide mimic 15 with a inhibitory constant (K(i)) of 40 nM for BRCT(BRCA1). Analysis of the TopBP1 and MDC1 BRCT domains suggests a similar approach is viable to design high affinity inhibitors.
Collapse
Affiliation(s)
| | | | - Stephen J. Campbell
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | | | | | - J. N. Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | | |
Collapse
|
34
|
Abstract
IMPORTANCE OF THE FIELD Fluorescence polarization (FP) is a homogeneous method that allows rapid and quantitative analysis of diverse molecular interactions and enzyme activities. This technique has been widely utilized in clinical and biomedical settings, including the diagnosis of certain diseases and monitoring therapeutic drug levels in body fluids. Recent developments in the field have been symbolized by the facile adoption of FP in high-throughput screening and small molecule drug discovery of an increasing range of target classes. AREAS COVERED IN THIS REVIEW The article provides a brief overview of the theoretical foundation of FP, followed by updates on recent advancements in its application for various drug target classes, including GPCRs, enzymes and protein-protein interactions. The strengths and weaknesses of this method, practical considerations in assay design, novel applications and future directions are also discussed. WHAT THE READER WILL GAIN The reader is informed of the most recent advancements and future directions of FP application to small molecule screening. TAKE HOME MESSAGE In addition to its continued utilization in high-throughput screening, FP has expanded into new disease and target areas and has been marked by increased use of labeled small molecule ligands for receptor-binding studies.
Collapse
Affiliation(s)
- Wendy A. Lea
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-3370, U.S.A
| | - Anton Simeonov
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-3370, U.S.A
| |
Collapse
|
35
|
Multivalent cyclic RGD ligands: influence of linker lengths on receptor binding. Nucl Med Biol 2010; 37:885-91. [PMID: 21055618 DOI: 10.1016/j.nucmedbio.2010.06.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 05/25/2010] [Accepted: 06/01/2010] [Indexed: 11/20/2022]
Abstract
UNLABELLED Peptides involving the RGD motive (arginine-glycine-aspartic acid) recognize members of the integrin receptor family. Since the receptors are located mainly on the surface of endothelial cells, structural modifications including multimers of c(RGDfE) were recently found to improve the binding avidity for α(v)β(3) integrin significantly. The multivalent RGD peptides exhibited rather loose linkages partly including oligo(ethylene glycol) spacers (EG(n)) with different chain lengths. Therefore, the dependence of multivalent RGD systems with and without EG(n) linkers were investigated on their binding properties to cultured α(v)β(3) integrin-expressing U87MG cells. METHODS We synthesized a series of di-, tri- and tetravalent rigid scaffolds (terephthalic acid, trimesic acid and adamantane-1,3,5,7-tetracarboxylic acid) conjugated to c(RGDyK) ligands, which were linked contiguously or separated by the oligo(ethylene glycol) spacers. The inhibition constants of these c(RGDyK) derivatives were determined by competition assays with (125)I-labeled echistatin. RESULTS While c(RGDyK) function is a relative weak competitor against [(125)I]echistatin (K(i), 329 ± 18 nM) for α(v)β(3) integrin-expressing U87MG cells, RGD dimers improved the competition potency considerably (K(i), 64 ± 23 nM). This effect was even more pronounced with the RGD trimers (K(i), 40 ± 7 nM) and tetramers (K(i), 26±9 nM). The introduction of EG(n) spacers and the increase of linker lengths proved to be detrimental since more competitors were needed to compete with [(125)I]echistatin. The EG(6) group, for example, reduced the inhibition constants by 29% (dimer), 57% (trimer) and 97% (tetramer). CONCLUSION The binding experiments performed with the three forms of multivalent RGD ligands indicate the weakening of competitive potency against [(125)I]echistatin with the introduction of EG(n) spacers. This effect may be related to the decrease of the effective RGD molarity, which becomes most prominent within the tetravalent series.
Collapse
|
36
|
Arai T, Yatabe M, Furui M, Akatsuka H, Uehata M, Kamiyama T. A fluorescence polarization-based assay for the identification and evaluation of calmodulin antagonists. Anal Biochem 2010; 405:147-52. [PMID: 20599654 DOI: 10.1016/j.ab.2010.06.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2009] [Revised: 04/20/2010] [Accepted: 06/14/2010] [Indexed: 11/16/2022]
Abstract
A fluorescence polarization (FP) assay was developed to identify calmodulin (CaM) antagonists. A fluorescent tracer was newly designed by covalently labeling N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide (W-7), which is a well-known CaM antagonist, with the Cy5 dye. In the FP assay, the tracer (Cy5-W-7) was bound to CaM with a dissociation constant (K(d)) of 6.5 microM and demonstrated efficient competitive activity with other CaM antagonists, including W-7, chlorpromazine, trifluoperazine, W-5, and clozapine, indicating that Cy5-W-7 binds to the ligand-binding site of CaM in a specific manner. The inhibitory activities of Cy5-W-7 and CaM antagonists were subsequently measured by the CaM-dependent calcineurin phosphatase assay, and the results were confirmed with those of the FP assays. In addition, assay optimization for high-throughput screening was performed, and a Z' factor of 0.7 was achieved in a 1536-well format. The FP assay was found to be a simple and reliable alternative to conventional assays for evaluating CaM antagonists.
Collapse
Affiliation(s)
- Tomonori Arai
- Medicinal Chemistry Laboratory, Mitsubishi Tanabe Pharma, 2-2-50 Kawagishi, Toda-shi, Saitama 335-8505, Japan.
| | | | | | | | | | | |
Collapse
|
37
|
Concentration of receptor and ligand revisited in a modified receptor binding protocol for high-affinity radioligands: [3H]Spiperone binding to D2 and D3 dopamine receptors. J Neurosci Methods 2010; 188:32-8. [PMID: 20122961 DOI: 10.1016/j.jneumeth.2010.01.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 01/08/2010] [Accepted: 01/25/2010] [Indexed: 11/21/2022]
Abstract
In receptor binding assays with ultra-high-affinity radioligands, it is difficult, in practice, to adhere the golden rule that the receptor concentration in the assay should be substantially (at least 10-fold) lower than the dissociation constant (K(d)) of the radioligand and inhibition constant (K(i)) of compound. Especially for low specific activity radioligands (usually tritiated ligands of a couple of TBq/mmol), routinely applied in concentrations at around or below the K(d), the use of extremely small amounts of receptor protein per assay will result in low levels of bound radioactivity; the alternative use of larger assay volumes will make it difficult to apply 96-well filtration devices. For assessing the inhibition constant (K(i)) of competitive inhibitors under conditions violating the above golden rule, equations are available incorporating both [receptor] and [ligand] versus K(d); however, their application requires precise knowledge of [receptor] or initial bound/free [radioligand] ratio. In this study, we present the theoretical basis for determining the K(i) for a competitive inhibitor in a new protocol at high [protein] and high [radioligand] with the simple Cheng-Prusoff correction without the need to correct for [receptor] or initial bound/free [radioligand] ratio. In addition, we present results on the binding of the ultra-high-affinity ligand [(3)H]spiperone to dopamine D(2) and D(3) receptors validating the K(i) values calculated with the new protocol for competitive inhibitors as compared with those calculated with the most comprehensive equation available to date, that of Munson and Rodbard (1988). Binding was measured at varying [radioligand] and [receptor], test compounds (including (-)5-OH-DPAT, (+/-)7-OH-DPAT, and ropinirole) were run with varying [receptor], and simulations were done at vastly varying [radioligand] for inhibitors with vastly different K(i)s. The modified high [radioligand] protocol presented here removes a major hindrance in the proper execution of binding assays with ultra-high-affinity tritiated ligands with K(d) values in the sub-nanomolar range, allowing the use of 96-well plates with small volumes of 100-200 microl per binding assay.
Collapse
|
38
|
Dodatko T, Akoachere M, Jimenez N, Alvarez Z, Abel-Santos E. Dissecting interactions between nucleosides and germination receptors in Bacillus cereus 569 spores. MICROBIOLOGY-SGM 2009; 156:1244-1255. [PMID: 20035009 DOI: 10.1099/mic.0.030270-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacillus cereus 569 spores germinate either with inosine as a sole germinant or with a combination of nucleosides and L-alanine. Whereas the inosine-only germination pathway requires the presence of two different germination receptors (GerI and GerQ) to be activated, the nucleoside/alanine germination pathway only needs one of the two receptors. To differentiate how nucleoside recognition varies between the inosine-only germination pathway and the nucleoside/alanine germination pathway, we tested 61 purine analogues as agonists and antagonists of the two pathways in wild-type, DeltagerI and DeltagerQ spores. The structure-activity relationships of germination agonists and antagonists suggest that the inosine-only germination pathway is restricted to recognize a single germinant (inosine), but can be inhibited in predictable patterns by structurally distinct purine nucleosides. B. cereus spores encoding GerI as the only nucleoside receptor (DeltagerQ mutant) showed a germination inhibition profile similar to wild-type spores treated with inosine only. Thus, GerI seems to have a well-organized binding site that recognizes inosine and inhibitors through specific substrate-protein interactions. Structure-activity analysis also showed that the nucleoside/alanine germination pathway is more promiscuous toward purine nucleoside agonists, and is only inhibited by hydrophobic analogues. B. cereus spores encoding GerQ as the only nucleoside receptor (DeltagerI mutant) behaved like wild-type spores treated with inosine and L-alanine. Thus, the GerQ receptor seems to recognize substrates in a more flexible binding site through non-specific interactions. We propose that the GerI receptor is responsible for germinant detection in the inosine-only germination pathway. On the other hand, supplementing inosine with l-alanine allows bypassing of the GerI receptor to activate the more flexible GerQ receptor.
Collapse
Affiliation(s)
- Tetyana Dodatko
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Monique Akoachere
- Department of Chemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Nadia Jimenez
- Department of Chemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Zadkiel Alvarez
- Department of Chemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Ernesto Abel-Santos
- Department of Chemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| |
Collapse
|
39
|
Young SM, Bologa CM, Fara D, Bryant BK, Strouse JJ, Arterburn JB, Ye RD, Oprea TI, Prossnitz ER, Sklar LA, Edwards BS. Duplex high-throughput flow cytometry screen identifies two novel formylpeptide receptor family probes. Cytometry A 2009; 75:253-63. [PMID: 18785269 DOI: 10.1002/cyto.a.20645] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Of recent, clinical interest have been two related human G-protein coupled receptors: formylpeptide receptor (FPR), linked to antibacterial inflammation and malignant glioma cell metastasis; and FPR like-1 (FPRL1), linked to chronic inflammation in systemic amyloidosis, Alzheimer's disease, and prion diseases. In association with the National Institutes of Health (NIH) Molecular Library Screening Network, we implemented a flow-cytometry-based high-throughput screening (HTS) approach for identifying selective small molecule FPR and FPRL1 ligands. The screening assay measured the ability of test compounds to competitively displace a high-affinity, fluorescein- labeled peptide ligand from FPR, FPRL1, or both. U937 cells expressing FPR and rat basophil leukemia (RBL) cells expressing FPRL1 were tested together in a "duplex" format. The U937 cells were color coded with red-fluorescent dye allowing their distinction during analysis. Compounds, cells, and fluorescent ligand were sequentially combined (no wash) in 15 microl assay volumes in 384-well plates. Throughput averaged approximately 11 min per plate to analyze approximately 4,000 cells ( approximately 2,000/receptor) in a 2 microl aspirate from each well. In primary single concentration HTS of 24,304 NIH Small Molecule Repository compounds, 253 resulted in inhibition >30% (181 for FPR, 72 for FPRL1) of which 40 had selective binding inhibition constants (K(i)) < or = 4 microM (34 for FPR and 6 for FPRL1). An additional 1,446 candidate compounds were selected by structure-activity-relationship analysis of the hits and screened to identify novel ligands for FPR (3570-0208, K(i) = 95 +/- 10 nM) and FPRL1 (BB-V-115, K(i) = 270 +/- 51 nM). Each was a selective antagonist in calcium response assays and the most potent small molecule antagonist reported for its respective receptor to date. The duplex assay format reduced assay time, minimized reagent requirements, and provided selectivity information at every screening stage, thus proving to be an efficient means to screen for selective receptor ligand probes.
Collapse
|
40
|
Design, Synthesis, and Pharmacology of Fluorescently Labeled Analogs of Serotonin: Application to Screening of the 5-HT2C Receptor. ACTA ACUST UNITED AC 2009; 14:360-70. [DOI: 10.1177/1087057109331804] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Novel fluorescent derivatives of serotonin have been synthesized and used as tracers for the development of a 5-HT2C fluorescence polarization assay. Serotonin analogs that feature a fluorescent probe attached through an ether linkage at the tryptamine 5-position have high affinity for the 5-HT2C receptor, and affinity is dependent on both linker length and pendent dye. These variables have been optimized to generate Cy3B derivative 5a, which has 10-fold higher 5-HT2C affinity relative to serotonin (Kd = 0.23 nM). In receptor activation experiments, 5a acts as a full agonist of 5-HT2C. Upon binding to 5-HT2C cell membranes, 5a shows a robust increase in fluorescence polarization (FP) signal. In an FP binding assay using 5a as a tracer ligand, Ki values for known 5-HT2C agonists and antagonists showed excellent agreement with Ki values from radioligand binding ( r2 = 0.93). The FP ligand assay is suitable for high-throughput drug screening applications with respect to speed of analysis, displaceable signal, precision, and sensitivity to various reagents. A 384-well-based high-throughput assay that is rapid, economical, and predictive of test compounds' ability to bind to the 5-HT2C receptor has been compiled and validated. ( Journal of Biomolecular Screening 2009:360-370)
Collapse
|
41
|
Cer RZ, Mudunuri U, Stephens R, Lebeda FJ. IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding. Nucleic Acids Res 2009; 37:W441-5. [PMID: 19395593 PMCID: PMC2703898 DOI: 10.1093/nar/gkp253] [Citation(s) in RCA: 287] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new web-server tool estimates Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules (e.g. proteins, polynucleic acids) and ligands. This converter was developed to enable end users to help gauge the quality of the underlying assumptions used in these calculations which depend on the type of mechanism of inhibitor action and the concentrations of the interacting molecular species. Additional calculations are performed for nonclassical, tightly bound inhibitors of enzyme-substrate or of macromolecule-ligand systems in which free, rather than total concentrations of the reacting species are required. Required user-defined input values include the total enzyme (or another target molecule) and substrate (or ligand) concentrations, the Km of the enzyme-substrate (or the Kd of the target-ligand) reaction, and the IC50 value. Assumptions and caveats for these calculations are discussed along with examples taken from the literature. The host database for this converter contains kinetic constants and other data for inhibitors of the proteolytic clostridial neurotoxins (http://botdb.abcc.ncifcrf.gov/toxin/kiConverter.jsp).
Collapse
Affiliation(s)
- R Z Cer
- Advanced Biomedical Computing Center, Advanced Technology Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD 21702, USA
| | | | | | | |
Collapse
|
42
|
Hassan AQ, Wang Y, Plate L, Stubbe J. Methodology to probe subunit interactions in ribonucleotide reductases. Biochemistry 2009; 47:13046-55. [PMID: 19012414 DOI: 10.1021/bi8012559] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides, providing the monomeric precursors required for DNA replication and repair. Escherichia coli RNR is a 1:1 complex of two homodimeric subunits, alpha2 and beta2. The interactions between alpha2 and beta2 are thought to be largely associated with the C-terminal 20 amino acids (residues 356-375) of beta2. To study subunit interactions, a single reactive cysteine has been introduced into each of 15 positions along the C-terminal tail of beta2. Each cysteine has been modified with the photo-cross-linker benzophenone (BP) and the environmentally sensitive fluorophore dimethylaminonaphthalene (DAN). Each construct has been purified to homogeneity and characterized by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and electrospray ionization mass spectrometry (ESI-MS). Each BP-beta2 has been incubated with 1 equiv of alpha2 and photolyzed, and the results have been analyzed quantitatively by SDS-PAGE. Each DAN-beta2 was incubated with a 50-fold excess of alpha2, and the emission maximum and intensity were measured. A comparison of the results from the two sets of probes reveals that sites with the most extensive cross-linking are also associated with the greatest changes in fluorescence. Titration of four different DAN-beta2 variants (351, 356, 365, and 367) with alpha2 gave a K(d) approximately 0.4 microM for subunit interaction. Disruption of the interaction of the alpha2-DAN-beta2 complex is accompanied by a decrease in fluorescence intensity and can serve as a high-throughput screen for inhibitors of subunit interactions.
Collapse
Affiliation(s)
- A Quamrul Hassan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | |
Collapse
|
43
|
Mazitschek R, Patel V, Wirth DF, Clardy J. Development of a fluorescence polarization based assay for histone deacetylase ligand discovery. Bioorg Med Chem Lett 2008; 18:2809-12. [PMID: 18430569 DOI: 10.1016/j.bmcl.2008.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 04/01/2008] [Accepted: 04/01/2008] [Indexed: 10/22/2022]
Abstract
Histone deacetylases (HDACs) regulate many important physiological processes and the discovery of small molecules that modulate HDAC activity has both academic and clinical relevance. HDAC inhibitors, most notably SAHA, have been pursued as cancer chemotherapeutics but may be useful in treating psychiatric disorders, malaria, and other diseases. Herein, we describe an inexpensive and robust assay, based on fluorescence polarization, for HDAC ligand discovery. The assay is well suited for high-throughput screening and enzyme kinetic studies.
Collapse
Affiliation(s)
- Ralph Mazitschek
- The Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | | | | | | |
Collapse
|
44
|
Translational control by a small RNA: dendritic BC1 RNA targets the eukaryotic initiation factor 4A helicase mechanism. Mol Cell Biol 2008; 28:3008-19. [PMID: 18316401 DOI: 10.1128/mcb.01800-07] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Translational repressors, increasing evidence suggests, participate in the regulation of protein synthesis at the synapse, thus providing a basis for the long-term plastic modulation of synaptic strength. Dendritic BC1 RNA is a non-protein-coding RNA that represses translation at the level of initiation. However, the molecular mechanism of BC1 repression has remained unknown. Here we identify the catalytic activity of eukaryotic initiation factor 4A (eIF4A), an ATP-dependent RNA helicase, as a target of BC1-mediated translational control. BC1 RNA specifically blocks the RNA duplex unwinding activity of eIF4A but, at the same time, stimulates its ATPase activity. BC200 RNA, the primate-specific BC1 counterpart, targets eIF4A activity in identical fashion, as a result decoupling ATP hydrolysis from RNA duplex unwinding. In vivo, BC1 RNA represses translation of a reporter mRNA with 5' secondary structure. The eIF4A mechanism places BC RNAs in a central position to modulate protein synthesis in neurons.
Collapse
|
45
|
Whiteson KL, Rice PA. Binding and catalytic contributions to site recognition by flp recombinase. J Biol Chem 2008; 283:11414-23. [PMID: 18276592 DOI: 10.1074/jbc.m800106200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Flp catalyzes site-specific recombination in a highly sequence-specific manner despite making few direct contacts to the bases within its binding site. Sequence discrimination could take place in the binding and/or the catalytic steps. In this study, we independently measure the binding affinity and initial cleavage rate of Flp recombinase with approximately 20 designed alternate target DNA sequences. Our results show that Flp specificity is largely, although not entirely, imparted at the binding step and is the result of a combination of direct and indirect readout. The Flp binding site includes an A/T-rich region that displays a characteristically narrow minor groove. We find that many A --> T changes are tolerated at the binding step, whereas C or G substitutions tend to decrease binding affinity. The effects of the latter can be alleviated by replacing guanine with inosine, which removes the N2 amino group that protrudes into the minor groove. Some A --> T changes reduce binding affinity, due to clashing with nearby residues, reinforcing that specificity requires avoiding negative contacts as well as creating positive ones. A tracts, which can lead to unusually rigid DNA structure, are tolerated during the binding step when placed within the region where the minor groove is already narrow. However, most A tracts slow catalysis more than C or G substitutions. Understanding what kind of sequence variation is tolerated in the binding and catalytic steps helps us understand how the target DNA is recognized by Flp and will be useful in guiding the design of Flp variants with altered specificities.
Collapse
Affiliation(s)
- Katrine L Whiteson
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | | |
Collapse
|
46
|
Mathias U, Jung M. Determination of drug–serum protein interactions via fluorescence polarization measurements. Anal Bioanal Chem 2007; 388:1147-56. [PMID: 17554529 DOI: 10.1007/s00216-007-1351-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 05/04/2007] [Accepted: 05/08/2007] [Indexed: 10/23/2022]
Abstract
New fast methods for the determination of pharmacokinetic behaviour of potential drug candidates are receiving increasing interest. We present a new homogeneous method for the determination of drug binding and drug competition for human serum albumin and alpha(1)-acid glycoprotein that is amenable to high-throughput-screening. It is based on selective fluorescent probes and the measurement of fluorescence polarization. This leads to decreased interference with fluorescent drugs as compared with previously published methods based on similar probes and the measurement of fluorescence intensity. The binding of highly fluorescent drugs that still interfere with the probes can be measured by simply titrating the drugs in a two-component system with the serum protein. The assay may also be used to discover strongly binding protein ligands that are interesting for drug-targeting strategies. Additionally, binding data could be obtained from larger libraries of compounds for in silico predictive pharmacokinetics. Figure Fluorescence polarization displacement titration of dansylsarcosine (3D-structure as insert) bound to human serum albumin (HSA) by naproxene.
Collapse
Affiliation(s)
- Ulf Mathias
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr 25, Freiburg, Germany
| | | |
Collapse
|
47
|
Abel-Santos E, Dodatko T. Differential nucleoside recognition during Bacillus cereus 569 (ATCC 10876) spore germination. NEW J CHEM 2007. [DOI: 10.1039/b616695d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
48
|
Chou TC. Theoretical basis, experimental design, and computerized simulation of synergism and antagonism in drug combination studies. Pharmacol Rev 2006; 58:621-81. [PMID: 16968952 DOI: 10.1124/pr.58.3.10] [Citation(s) in RCA: 3744] [Impact Index Per Article: 208.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The median-effect equation derived from the mass-action law principle at equilibrium-steady state via mathematical induction and deduction for different reaction sequences and mechanisms and different types of inhibition has been shown to be the unified theory for the Michaelis-Menten equation, Hill equation, Henderson-Hasselbalch equation, and Scatchard equation. It is shown that dose and effect are interchangeable via defined parameters. This general equation for the single drug effect has been extended to the multiple drug effect equation for n drugs. These equations provide the theoretical basis for the combination index (CI)-isobologram equation that allows quantitative determination of drug interactions, where CI < 1, = 1, and > 1 indicate synergism, additive effect, and antagonism, respectively. Based on these algorithms, computer software has been developed to allow automated simulation of synergism and antagonism at all dose or effect levels. It displays the dose-effect curve, median-effect plot, combination index plot, isobologram, dose-reduction index plot, and polygonogram for in vitro or in vivo studies. This theoretical development, experimental design, and computerized data analysis have facilitated dose-effect analysis for single drug evaluation or carcinogen and radiation risk assessment, as well as for drug or other entity combinations in a vast field of disciplines of biomedical sciences. In this review, selected examples of applications are given, and step-by-step examples of experimental designs and real data analysis are also illustrated. The merging of the mass-action law principle with mathematical induction-deduction has been proven to be a unique and effective scientific method for general theory development. The median-effect principle and its mass-action law based computer software are gaining increased applications in biomedical sciences, from how to effectively evaluate a single compound or entity to how to beneficially use multiple drugs or modalities in combination therapies.
Collapse
Affiliation(s)
- Ting-Chao Chou
- Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA.
| |
Collapse
|
49
|
Edwards BS, Bologa C, Young SM, Balakin KV, Prossnitz ER, Savchuck NP, Sklar LA, Oprea TI. Integration of virtual screening with high-throughput flow cytometry to identify novel small molecule formylpeptide receptor antagonists. Mol Pharmacol 2005; 68:1301-10. [PMID: 16118363 DOI: 10.1124/mol.105.014068] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The formylpeptide receptor (FPR) family of G-protein-coupled receptors contributes to the localization and activation of tissue-damaging leukocytes at sites of chronic inflammation. We developed a FPR homology model and pharmacophore (based on the bovine rhodopsin crystal structure and known FPR ligands, respectively) for in silico screening of approximately 480,000 drug-like small molecules. A subset of 4324 compounds that matched the pharmacophore was then physically screened with the HyperCyt flow cytometry platform in high-throughput, no-wash assays that directly measure human FPR binding, with samples (each approximately 2500 cells in 2 microl) analyzed at 40/min. From 52 confirmed hits (1.2% hit rate), we identified 30 potential lead compounds (inhibition constant, Ki= 1-32 microM) representing nine distinct chemical families. Four compounds in one family were weak partial agonists. All others were antagonists. This virtual screening approach improved the physical screening hit rate by 12-fold (versus 0.1% hit-rate in a random compound collection), providing an efficient process for identifying small molecule antagonists.
Collapse
Affiliation(s)
- Bruce S Edwards
- Department of Cytometry, University of New Mexico, Albuquerque, NM 87131-0001, USA
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Zhen J, Maiti S, Chen N, Dutta AK, Reith MEA. Interaction between a hydroxypiperidine analogue of 4-(2-benzhydryloxy-ethyl)-1-(4-fluorobenzyl)piperidine and Aspartate 68 in the human dopamine transporter. Eur J Pharmacol 2005; 506:17-26. [PMID: 15588620 DOI: 10.1016/j.ejphar.2004.10.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Revised: 10/07/2004] [Accepted: 10/12/2004] [Indexed: 10/26/2022]
Abstract
Compound (+)-R,R-D-84 is an optically active trans-hydroxy-substituted derivative of 4-(2-benzhydryloxy-ethyl)-1-(4-fluorobenzyl)piperidine (D-164). As a hydroxypiperidine analog of GBR 12935, (+)-R,R-D-84 is a candidate dopamine transporter compound for the treatment of cocaine dependence. The present work addresses the functional activity of (+)-R,R-D-84 at monoamine transporters and its potential molecular mechanism involving acidic amino acids (D and E). The selectivity for the dopamine vs. serotonin transporter of (+)-R,R-D-84 was greater than that of (-)-S,S-D-83, its enantiomer, and the selectivity of both compounds was greater than that of GBR 12909 (diphenyl-fluorinated GBR 12935). Only (+)-R,R-D-84 displayed improved selectivity vs. the norepinephrine transporter. D313N or E215Q mutation did not alter the pattern of affinities (measured by membrane binding of the cocaine analog [3H]CFT) for the dopamine transporter of (+)-R,R-D-84, (-)-S,S-D-83, D-164 (non-hydroxylated analog), or GBR 12909. In contrast, D68N mutation specifically lowered the affinity of (+)-R,R-D-84, pointing to a role for D68 in the interaction with (+)-R,R-D-84, possibly through hydrogen bonding between the hydroxyl and the carboxyl group of D68 which is lacking in N68. The present results, combined with behavioral data, implicate D68 in the dopamine transporter in cocaine antagonist activity of (+)-R,R-D-84.
Collapse
Affiliation(s)
- Juan Zhen
- Department of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | | | | | | | | |
Collapse
|