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Erbacher C, Athmer M, Kröger E, Dahrendorf L, Imberg L, Kalinin DV, Karst U. An automated analysis method enabling the screening of covalent thrombin and factor XIIa inhibitors via liquid chromatography-mass spectrometry. Drug Test Anal 2024; 16:314-322. [PMID: 37482900 DOI: 10.1002/dta.3549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023]
Abstract
An automated sample preparation and separation method for the analysis of various enzyme-inhibitor combinations using liquid chromatography (LC) coupled to mass spectrometry (MS) is presented. As conventional anticoagulants have several drawbacks, the most severe being the elevated risk of internal bleedings, it is necessary to develop new-generation anticoagulants with reduced side effects. Therefore, the screening of potential inhibitors against anticoagulation targets like thrombin and FXIIa is important to design a potent and selective inhibitor. To facilitate the analysis of numerous enzyme-inhibitor covalent complexes, automation of the analysis using an LC system with a user-defined injection sequence is helpful. The developed method ensures comparable reaction conditions like reaction time and temperature for all enzyme-inhibitor complexes. Furthermore, it prevents time-consuming manual sample preparation and potential manual errors. To achieve good reproducibility with relative standard deviation of approximately 3% for three-fold determination, multiple cleaning steps were added to the automated sample preparation. Subsequently, this method was applied to screen a variety of 15 aminopyrazole- and aminotriazole-based inhibitors with a covalent mechanism of action against thrombin and to test two covalent inhibitors for FXIIa. Successful complex formation and acylation of the catalytic center of the enzymes was monitored using deconvoluted mass spectra and the matching mass shifts of the acyl moiety of the analyzed inhibitors. The inhibitors' structure directly influenced reaction yields. Sterically demanding aminotriazoles and acyl moieties both affected the product formation negatively. However, the screening yielded several promising candidates for new covalent thrombin inhibitors, which might find their application as prospective anticoagulants.
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Affiliation(s)
- Catharina Erbacher
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Mathis Athmer
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Erik Kröger
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Laureen Dahrendorf
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Lukas Imberg
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
| | - Dmitrii V Kalinin
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
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2
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Kato Y, Sakanishi A, Matsuda K, Hattori M, Kaneko I, Nishikawa M, Ikushiro S. Covalent adduction of serotonin-derived quinones to the SARS-CoV-2 main protease expressed in a cultured cell. Free Radic Biol Med 2023; 206:74-82. [PMID: 37391098 PMCID: PMC10300202 DOI: 10.1016/j.freeradbiomed.2023.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023]
Abstract
The SARS-CoV-2 main protease is an essential molecule for viral replication and is often targeted by medications to treat the infection. In this study, we investigated the possible inhibitory action of endogenous quinones on the enzyme. Recombinant SARS-CoV-2 main protease was exposed to tryptamine-4,5-dione (TD) or quinone from 5-hydroxyindoleacetic acid (Q5HIAA). As a result, the protease activity was considerably decreased in a dose-dependent manner. The IC50 values of the quinones toward the enzyme were approximately 0.28 μM (TD) and 0.49 μM (Q5HIAA). Blot analyses using specific antibodies to quinone-modified proteins revealed that quinones were adducted to the enzyme at concentrations as low as 0.12 μM. Intact mass analyses showed that one or two quinone molecules were covalently adducted onto the main protease. Chymotrypsin-digested main protease analyses revealed that the quinones bind to thiol residues at the enzyme's active site. When TD or Q5HIAA were exposed to cultured cells expressing the viral enzyme, quinone-modified enzyme was identified in the cell lysate, suggesting that even extracellularly generated quinones could react with the viral enzyme expressed in an infected cell. Thus, these endogenous quinones could act as inhibitors of the viral enzyme.
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Affiliation(s)
- Yoji Kato
- School of Human Science and Environment, University of Hyogo, Himeji, Hyogo, 670-0092, Japan; Research Institute for Food and Nutritional Sciences, University of Hyogo, Himeji, Hyogo, 670-0092, Japan.
| | - Asahi Sakanishi
- School of Human Science and Environment, University of Hyogo, Himeji, Hyogo, 670-0092, Japan
| | - Kaoru Matsuda
- School of Human Science and Environment, University of Hyogo, Himeji, Hyogo, 670-0092, Japan
| | - Mai Hattori
- School of Human Science and Environment, University of Hyogo, Himeji, Hyogo, 670-0092, Japan
| | - Ichiro Kaneko
- School of Human Science and Environment, University of Hyogo, Himeji, Hyogo, 670-0092, Japan; Research Institute for Food and Nutritional Sciences, University of Hyogo, Himeji, Hyogo, 670-0092, Japan
| | - Miyu Nishikawa
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, 939-0398, Japan
| | - Shinichi Ikushiro
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, 939-0398, Japan
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3
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Nzimande B, Makhwitine JP, Mkhwanazi NP, Ndlovu SI. Developments in Exploring Fungal Secondary Metabolites as Antiviral Compounds and Advances in HIV-1 Inhibitor Screening Assays. Viruses 2023; 15:v15051039. [PMID: 37243125 DOI: 10.3390/v15051039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/16/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
The emergence of drug-resistant Human Immunodeficiency Virus-1 strains against anti-HIV therapies in the clinical pipeline, and the persistence of HIV in cellular reservoirs remains a significant concern. Therefore, there is a continuous need to discover and develop new, safer, and effective drugs targeting novel sites to combat HIV-1. The fungal species are gaining increasing attention as alternative sources of anti-HIV compounds or immunomodulators that can escape the current barriers to cure. Despite the potential of the fungal kingdom as a source for diverse chemistries that can yield novel HIV therapies, there are few comprehensive reports on the progress made thus far in the search for fungal species with the capacity to produce anti-HIV compounds. This review provides insights into the recent research developments on natural products produced by fungal species, particularly fungal endophytes exhibiting immunomodulatory or anti-HIV activities. In this study, we first explore currently existing therapies for various HIV-1 target sites. Then we assess the various activity assays developed for gauging antiviral activity production from microbial sources since they are crucial in the early screening phases for discovering novel anti-HIV compounds. Finally, we explore fungal secondary metabolites compounds that have been characterized at the structural level and demonstrate their potential as inhibitors of various HIV-1 target sites.
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Affiliation(s)
- Bruce Nzimande
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, Medical School, University of KwaZulu-Natal, Durban 4000, South Africa
| | - John P Makhwitine
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, Medical School, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Nompumelelo P Mkhwanazi
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Sizwe I Ndlovu
- Department of Biotechnology and Food Technology, Doornfontein Campus, University of Johannesburg, Johannesburg 2028, South Africa
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4
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The HIV-1 Viral Protease Is Activated during Assembly and Budding Prior to Particle Release. J Virol 2022; 96:e0219821. [PMID: 35438536 DOI: 10.1128/jvi.02198-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 encodes a viral protease that is essential for the maturation of infectious viral particles. While protease inhibitors are effective antiretroviral agents, recent studies have shown that prematurely activating, rather than inhibiting, protease function leads to the pyroptotic death of infected cells, with exciting implications for efforts to eradicate viral reservoirs. Despite 40 years of research into the kinetics of protease activation, it remains unclear exactly when protease becomes activated. Recent reports have estimated that protease activation occurs minutes to hours after viral release, suggesting that premature protease activation is challenging to induce efficiently. Here, monitoring viral protease activity with sensitive techniques, including nanoscale flow cytometry and instant structured illumination microscopy, we demonstrate that the viral protease is activated within cells prior to the release of free virions. Using genetic mutants that lock protease into a precursor conformation, we further show that both the precursor and mature protease have rapid activation kinetics and that the activity of the precursor protease is sufficient for viral fusion with target cells. Our finding that HIV-1 protease is activated within producer cells prior to release of free virions helps resolve a long-standing question of when protease is activated and suggests that only a modest acceleration of protease activation kinetics is required to induce potent and specific elimination of HIV-infected cells. IMPORTANCE HIV-1 protease inhibitors have been a mainstay of antiretroviral therapy for more than 2 decades. Although antiretroviral therapy is effective at controlling HIV-1 replication, persistent reservoirs of latently infected cells quickly reestablish replication if therapy is halted. A promising new strategy to eradicate the latent reservoir involves prematurely activating the viral protease, which leads to the pyroptotic killing of infected cells. Here, we use highly sensitive techniques to examine the kinetics of protease activation during and shortly after particle formation. We found that protease is fully activated before virus is released from the cell membrane, which is hours earlier than recent estimates. Our findings help resolve a long-standing debate as to when the viral protease is initially activated during viral assembly and confirm that prematurely activating HIV-1 protease is a viable strategy to eradicate infected cells following latency reversal.
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5
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Li KS, Quinn JG, Saabye MJ, Guerrero JFS, Nonomiya J, Lian Q, Phung W, Izrayelit Y, Walters BT, Gustafson A, Endres NF, Beresini MH, Mulvihill MM. High-Throughput Kinetic Characterization of Irreversible Covalent Inhibitors of KRASG12C by Intact Protein MS and Targeted MRM. Anal Chem 2022; 94:1230-1239. [DOI: 10.1021/acs.analchem.1c04463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ke Sherry Li
- Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - John G. Quinn
- Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Matthew J. Saabye
- Confluence, 4340 Duncan Avenue, Suite 400, St. Louis, Missouri 63110, United States
| | - Jesus F. Salcido Guerrero
- Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Jim Nonomiya
- Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Qihui Lian
- WuXi AppTec Co. Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wilson Phung
- Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, California 94080, United States
| | - Yevgeniy Izrayelit
- Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Benjamin T. Walters
- Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Amy Gustafson
- Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Nicholas F. Endres
- Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Maureen H. Beresini
- Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Melinda M. Mulvihill
- Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
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6
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Tao D, Xu M, Farkhondeh A, Burns AP, Rodems S, Might M, Zheng W, LeClair CA. High-throughput protein modification quantitation analysis using intact protein MRM and its application on hENGase inhibitor screening. Talanta 2021; 231:122384. [PMID: 33965046 DOI: 10.1016/j.talanta.2021.122384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/27/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022]
Abstract
Proteins are widely used as drug targets, enzyme substrates, and biomarkers for numerous diseases. The emerging demand for proteins quantitation has been increasing in multiple fields. Currently, there is still a big gap for high-throughput protein quantitation at intact protein level using label-free method. Here we choose ribonuclease B (RNB) as a model, which is the substrate for human endo-β-N-acetylglucosaminidase (hENGase), a promising drug target for the treatment of N-Glycanase deficiency. Intact proteinlevel multiple reaction monitoring (MRM) methods were initally developed and optimized to quantify RNB and deglycosylated RNB (RNB-deg), with the S/N ratio improved by nearly 20-fold compared to the traditional full MS scan methods. To further increase the throughput making it possible for hENGase inhibitors screen, the protein MRM methods were introduced to the RapidFire-MS/MS system, achieving at least 12-fold throughput improvement. This assay was further optimized into 384-well plate format for compound screening with S/B ratio >37-fold and Z' factor >0.7 that is suitable for high-throughput screening of compound collections with a speed of 2 h per 384-well plate and an ability to screen over 3000 compounds per day at a single concentration dose. This 384-well plate based automated SPE-MS/MS assay is efficient and robust for compound screening and the assay format has a wide applicability to protein targets for other disease models.
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Affiliation(s)
- Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA.
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Atena Farkhondeh
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Andrew P Burns
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | | | - Matthew Might
- University of Alabama at Birmingham, Birmingham, AL, 35210, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA.
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7
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Malla TR, Tumber A, John T, Brewitz L, Strain-Damerell C, Owen CD, Lukacik P, Chan HTH, Maheswaran P, Salah E, Duarte F, Yang H, Rao Z, Walsh MA, Schofield CJ. Mass spectrometry reveals potential of β-lactams as SARS-CoV-2 M pro inhibitors. Chem Commun (Camb) 2021; 57:1430-1433. [PMID: 33462575 PMCID: PMC8006714 DOI: 10.1039/d0cc06870e] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The main viral protease (Mpro) of SARS-CoV-2 is a nucleophilic cysteine hydrolase and a current target for anti-viral chemotherapy. We describe a high-throughput solid phase extraction coupled to mass spectrometry Mpro assay. The results reveal some β-lactams, including penicillin esters, are active site reacting Mpro inhibitors, thus highlighting the potential of acylating agents for Mpro inhibition.
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Affiliation(s)
- Tika R Malla
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Claire Strain-Damerell
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK and Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0FA, UK
| | - C David Owen
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK and Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0FA, UK
| | - Petra Lukacik
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK and Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0FA, UK
| | - H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Pratheesh Maheswaran
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Martin A Walsh
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK and Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0FA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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8
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McLaren DG, Shah V, Wisniewski T, Ghislain L, Liu C, Zhang H, Saldanha SA. High-Throughput Mass Spectrometry for Hit Identification: Current Landscape and Future Perspectives. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:168-191. [PMID: 33482074 DOI: 10.1177/2472555220980696] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
For nearly two decades mass spectrometry has been used as a label-free, direct-detection method for both functional and affinity-based screening of a wide range of therapeutically relevant target classes. Here, we present an overview of several established and emerging mass spectrometry platforms and summarize the unique strengths and performance characteristics of each as they apply to high-throughput screening. Multiple examples from the recent literature are highlighted in order to illustrate the power of each individual technique, with special emphasis given to cases where the use of mass spectrometry was found to be differentiating when compared with other detection formats. Indeed, as many of these examples will demonstrate, the inherent strengths of mass spectrometry-sensitivity, specificity, wide dynamic range, and amenability to complex matrices-can be leveraged to enhance the discriminating power and physiological relevance of assays included in screening cascades. It is our hope that this review will serve as a useful guide to readers of all backgrounds and experience levels on the applicability and benefits of mass spectrometry in the search for hits, leads, and, ultimately, drugs.
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A direct peptide reactivity assay using a high-throughput mass spectrometry screening platform for detection of skin sensitizers. Toxicol Lett 2020; 338:67-77. [PMID: 33290830 DOI: 10.1016/j.toxlet.2020.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 11/23/2022]
Abstract
Chemical-peptide conjugation is the molecular initiating event in skin sensitization. The OECD test guideline uses a high-performance liquid chromatography/ultraviolet (HPLC/UV) detection method to quantify chemical-peptide conjugation in a direct peptide reactivity assay (DPRA), which measures the depletion of two synthetic peptides containing lysine or cysteine residues. To improve assay throughput, sensitivity and accuracy, an automated 384-well plate-based RapidFire solid-phase extraction (SPE) system coupled with tandem mass spectrometry (MS/MS) DPRA was developed and validated in the presence of a newly designed internal standard. Compared to the HPLC/UV-based DPRA, the automated SPE-MS/MS-based DPRA improved throughput from 16 min to 10 s per sample, and substrate peptides usage was reduced from 100 mM to 5 μM. When implementing the SPE-MS/MS-based DPRA into a high-throughput platform, we found 10 compounds that depleted lysine peptide and 24 compounds that depleted cysteine peptide (including 7 unreported chemicals from 55 compounds we tested) in a concentration-response manner. The adduct formation between cysteine and cinnamic aldehyde and ethylene glycol dimethacrylate were further analyzed using high-performance liquid chromatography time-of-flight mass spectrometry (HPLC-TOF-MS) to confirm the conjugation. Overall, the automated SPE-MS/MS-based platform is an efficient, economic, and accurate way to detect skin sensitizers.
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10
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Inhibition of HIV-1 Protease by Carpobrotus edulis (L.). EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:9648056. [PMID: 32595755 PMCID: PMC7298281 DOI: 10.1155/2020/9648056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 12/15/2022]
Abstract
Carpobrotus edulis (L.) is a plant commonly found in the Eastern Cape Province of South Africa and is used for the general treatment of infections relating to the human immunodeficiency virus (HIV). HIV-1 protease plays an important role during HIV replication and maturation to its infectious form, and therefore inhibition of the enzyme is one of the main focus areas in drug development. The inhibitory effect of a water extract of C. edulis leaves against HIV-1 protease activity was determined using the SensoLyte® 520 HIV-1 protease assay fluorimetric kit and employing a HiLyte Fluor™488/QXL™520 fluorescence resonance energy transfer (FRET) peptide. Cytotoxicity of the extract towards HeLa Chang cell lines was determined using an in vitro MTT assay, and the phytochemical profile of the extract was determined with FT-IR and LC-MS. HIV-1 protease activity was inhibited 83.06% (IC50 1.6 mg/ml) (p < 0.0001) by the pepstatin A inhibitor control. Treatment with all C. edulis extract concentrations (16, 1.6, 0.16, and 0.016 mg/ml) inhibited HIV-1 protease activity significantly (p < 0.0001) in a typical dose response manner. With regards to cytotoxicity, the negative controls containing untreated HeLa Chang cells exhibited high formazan formation rates in contrast with the positive controls, containing curcumin, which reduced formazan formation significantly (p < 0.001), exhibiting cytotoxicity towards the cells. There was no significant (p > 0.05) difference in the formazan formation rates between the negative controls and 1, 0.5, 0.125, 0.065, 0.031, and 0.015 mg/ml plant extract, confirming no toxicity of C. edulis extracts towards HeLa Chang cells. Major functional phytochemical compounds identified included alcohols, phenols, alkanes, amines, carboxylic acids, and esters. LC-ESI-TOF/MS analysis revealed the putative identities of main compounds present in the aqueous leaves extract, including some that contribute to its anti-HIV-1 protease action.
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11
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Vasiljevic T, Gómez-Ríos GA, Li F, Liang P, Pawliszyn J. High-throughput quantification of drugs of abuse in biofluids via 96-solid-phase microextraction-transmission mode and direct analysis in real time mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1423-1433. [PMID: 31063263 DOI: 10.1002/rcm.8477] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/05/2019] [Accepted: 04/14/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE The workload of clinical laboratories has been steadily increasing over the last few years. High-throughput (HT) sample processing allows scientists to spend more time undertaking matters of critical thinking rather than laborious sample processing. Herein we introduce a HT 96-solid-phase microextraction (SPME) transmission mode (TM) system coupled to direct analysis in real time (DART) mass spectrometry (MS). METHODS Model compounds (opioids) were extracted from urine and plasma samples using a 96-SPME-TM device. A standard voltage and pressure (SVP) DART source was used for all experiments. Examination of SPME-TM performance was done using high-resolution mass spectrometry (HRMS) in full scan mode (100-500 m/z), whereas quantitation of opioids was performed using triple quadrupole MS in multiple reaction monitoring mode and by using a matrix-matched internal standard correction method. RESULTS Thirteen points (0.5 to 200 ng mL-1 ) were used to establish a calibration curve. Low limits of quantitation (LOQ) were obtained (0.5 to 25 ng mL-1 ) for matrices used. Acceptable accuracy (71.4-129.4%) and repeatability (1.1-24%) were obtained for validation levels tested (0.5, 30 and 90 ng mL-1 ). In less than 1.5 hours, 96 samples were extracted, desorbed and processed using the 96-SPME-TM system coupled to DART-MS. CONCLUSIONS A rapid HT method for detection of opioids in urine and plasma samples was developed. This study demonstrated that ambient ionization mass spectrometry coupled to robust sample preparation methods such as SPME-TM can rapidly and efficiently screen/quantify target analytes in a HT context.
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Affiliation(s)
- Tijana Vasiljevic
- Department of Chemistry, University of Waterloo, Ontario, N2L 3G1, Canada
| | - Germán Augusto Gómez-Ríos
- Department of Chemistry, University of Waterloo, Ontario, N2L 3G1, Canada
- Restek Corporation, Bellefonte, Pennsylvania, 16823, USA
| | - Frederick Li
- Ionsense, Inc., Saugus, Massachusetts, 01906, USA
| | - Paul Liang
- Ionsense, Inc., Saugus, Massachusetts, 01906, USA
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, Ontario, N2L 3G1, Canada
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12
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Clausse V, Tao D, Debnath S, Fang Y, Tagad HD, Wang Y, Sun H, LeClair CA, Mazur SJ, Lane K, Shi ZD, Vasalatiy O, Eells R, Baker LK, Henderson MJ, Webb MR, Shen M, Hall MD, Appella E, Appella DH, Coussens NP. Physiologically relevant orthogonal assays for the discovery of small-molecule modulators of WIP1 phosphatase in high-throughput screens. J Biol Chem 2019; 294:17654-17668. [PMID: 31481464 PMCID: PMC6873202 DOI: 10.1074/jbc.ra119.010201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/30/2019] [Indexed: 01/07/2023] Open
Abstract
WT P53-Induced Phosphatase 1 (WIP1) is a member of the magnesium-dependent serine/threonine protein phosphatase (PPM) family and is induced by P53 in response to DNA damage. In several human cancers, the WIP1 protein is overexpressed, which is generally associated with a worse prognosis. Although WIP1 is an attractive therapeutic target, no potent, selective, and bioactive small-molecule modulator with favorable pharmacokinetics has been reported. Phosphatase enzymes are among the most challenging targets for small molecules because of the difficulty of achieving both modulator selectivity and bioavailability. Another major obstacle has been the availability of robust and physiologically relevant phosphatase assays that are suitable for high-throughput screening. Here, we describe orthogonal biochemical WIP1 activity assays that utilize phosphopeptides from native WIP1 substrates. We optimized an MS assay to quantify the enzymatically dephosphorylated peptide reaction product in a 384-well format. Additionally, a red-shifted fluorescence assay was optimized in a 1,536-well format to enable real-time WIP1 activity measurements through the detection of the orthogonal reaction product, Pi. We validated these two optimized assays by quantitative high-throughput screening against the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection and used secondary assays to confirm and evaluate inhibitors identified in the primary screen. Five inhibitors were further tested with an orthogonal WIP1 activity assay and surface plasmon resonance binding studies. Our results validate the application of miniaturized physiologically relevant and orthogonal WIP1 activity assays to discover small-molecule modulators from high-throughput screens.
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Affiliation(s)
- Victor Clausse
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Subrata Debnath
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Harichandra D Tagad
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Hongmao Sun
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Sharlyn J Mazur
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Kelly Lane
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Zhen-Dan Shi
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Olga Vasalatiy
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Rebecca Eells
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Lynn K Baker
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Martin R Webb
- Francis Crick Institute, 1 Midland Road, London NW1 AT, United Kingdom
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Ettore Appella
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Nathan P Coussens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
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Uchiyama N, Dougan DR, Lawson JD, Kimura H, Matsumoto SI, Tanaka Y, Kawamoto T. Identification of AHCY inhibitors using novel high-throughput mass spectrometry. Biochem Biophys Res Commun 2017; 491:1-7. [DOI: 10.1016/j.bbrc.2017.05.107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 05/19/2017] [Indexed: 10/19/2022]
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Identification of PARP14 inhibitors using novel methods for detecting auto-ribosylation. Biochem Biophys Res Commun 2017; 486:626-631. [DOI: 10.1016/j.bbrc.2017.03.052] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/13/2017] [Indexed: 12/19/2022]
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Klumpp M. Non-stoichiometric inhibition in integrated lead finding - a literature review. Expert Opin Drug Discov 2015; 11:149-62. [PMID: 26653534 DOI: 10.1517/17460441.2016.1128892] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Non-stoichiometric inhibition summarizes different mechanisms by which low-molecular weight compounds can reproducibly inhibit high-throughput screening (HTS) and other lead finding assays without binding to a structurally defined site on their molecular target. This disqualifies such molecules from optimization by medicinal chemistry, and therefore their rapid elimination from screening hit lists is essential for productive and effective drug discovery. AREAS COVERED This review covers recent literature that either investigates the various mechanisms behind non-stoichiometric inhibition or suggests assays and readouts to identify them. In addition, combination of the various methods to distill promising molecules out of raw primary hit lists step-by-step is considered. Emerging technologies to demonstrate target engagement in cells are also discussed. EXPERT OPINION Over the last few years, awareness of non-stoichiometric inhibitors within screening libraries and HTS hit lists has considerably increased, not only in the pharmaceutical industry but also in the academic drug discovery community. This has resulted in a variety of methods to detect and handle such compounds. These range from in silico approaches to flag suspicious compounds, and counterassays to measure non-stoichiometric inhibition, to biophysical methods that positively demonstrate stoichiometric binding. In addition, novel technologies to verify target engagement within cells are becoming available. While still a time- and resource-consuming nuisance, non-stoichiometric inhibitors therefore do not fundamentally jeopardize the discovery of low molecular weight lead and drug candidates. Rather, they should be viewed as a manageable issue that with appropriate expertise can be overcome through integration of the above-mentioned approaches.
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Affiliation(s)
- Martin Klumpp
- a Novartis Institute of Biomedical Research Basel, Novartis Pharma AG , Basel , Switzerland
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