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S A, Das A, Kalita PJ, Patil RI, Pandey N, Bhattacharjee M, Sharma BK, Das D, Acharjee S. Improved methods for total and chloroplast protein extraction from Cajanus species for two-dimensional gel electrophoresis and mass spectrometry. PLoS One 2024; 19:e0308909. [PMID: 39146296 PMCID: PMC11326652 DOI: 10.1371/journal.pone.0308909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/22/2024] [Indexed: 08/17/2024] Open
Abstract
The recent advances in pigeon pea genomics, including high-quality whole genome and chloroplast genome sequence information helped develop improved varieties. However, a comprehensive Cajanus proteome, including the organelle proteome, is yet to be fully mapped. The spatial delineation of pigeon pea proteins at sub-cellular levels and inter-organelle communication could offer valuable insights into its defense mechanism against various stresses. However, the major bottleneck in the proteomic study is the lack of a suitable method of protein extraction and sample preparation compatible with two-dimensional gel electrophoresis (2D-PAGE), liquid chromatography-mass spectrometry (LCMS), or matrix-assisted laser desorption ionization-time of flight (MALDi-ToF). Our study introduces two efficient methods, one for isolating total proteins and another for organelle (chloroplast) proteins from various Cajanus spp. For total protein extraction, we have optimized a protocol using phenol in combination with a reducing agent (DTT) and protease inhibitor cocktail, also washing (6-7 times) with ice-cold acetone after overnight protein precipitation of total proteins. Our modified extraction method using phenol for total leaf protein yielded approximately 2-fold more proteins than the previously reported protocols from C. cajan (3.18 ± 0.11 mg/gm) and C. scarabaeoides (2.06 ± 0.08 mg/gm). We have also optimized a protocol for plastid protein extraction, which yielded 1.33 ± 0.25 mg/10 gm plastid proteins from C. cajan and 0.88 ± 0.19 mg/10 gm plastid proteins from C. scarabaeoides. The 2D-PAGE analysis revealed 678 ± 08 reproducible total protein spots from C. cajan and 597 ± 22 protein spots from C. scarabaeoides. Similarly, we found 566 ± 10 and 486 ± 14 reproducible chloroplast protein spots in C. cajan and C. scarabaeoides, respectively. We confirmed the plastid protein fractions through immunoblot analysis using antibodies against LHCb1/LHCⅡ type Ⅰ protein. We found both methods suitable for 2D-PAGE and mass spectrometry (MS). This is the first report on developing protocols for total and chloroplastic protein extraction of Cajanus spp. suitable for advanced proteomics research.
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Affiliation(s)
- Arunima S
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Alakesh Das
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- DBT-North-East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Prakash Jyoti Kalita
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- DBT-North-East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Rahul Ishwar Patil
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Neha Pandey
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Mamta Bhattacharjee
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- DBT-North-East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Bidyut Kumar Sharma
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- DBT-North-East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Debajit Das
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- DBT-North-East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Sumita Acharjee
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- DBT-North-East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
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2
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Golla K, Yasgar A, Manjuprasanna VN, Naik MU, Baljinnyam B, Zakharov AV, Jain S, Rai G, Jadhav A, Simeonov A, Naik UP. Small-Molecule Disruptors of the Interaction between Calcium- and Integrin-Binding Protein 1 and Integrin α IIbβ 3 as Novel Antiplatelet Agents. ACS Pharmacol Transl Sci 2024; 7:1971-1982. [PMID: 39022362 PMCID: PMC11249646 DOI: 10.1021/acsptsci.4c00026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 07/20/2024]
Abstract
Thrombosis, a key factor in most cardiovascular diseases, is a major contributor to human mortality. Existing antithrombotic agents carry a risk of bleeding. Consequently, there is a keen interest in discovering innovative antithrombotic agents that can prevent thrombosis without negatively impacting hemostasis. Platelets play crucial roles in both hemostasis and thrombosis. We have previously characterized calcium- and integrin-binding protein 1 (CIB1) as a key regulatory molecule that regulates platelet function. CIB1 interacts with several platelet proteins including integrin αIIbβ3, the major glycoprotein receptor for fibrinogen on platelets. Given that CIB1 regulates platelet function through its interaction with αIIbβ3, we developed a fluorescence polarization (FP) assay to screen for potential inhibitors. The assay was miniaturized to 1536-well and screened in quantitative high-throughput screening (qHTS) format against a diverse compound library of 14,782 compounds. After validation and selectivity testing using the FP assay, we identified 19 candidate inhibitors and validated them using an in-gel binding assay that monitors the interaction of CIB1 with αIIb cytoplasmic tail peptide, followed by testing of top hits by intrinsic tryptophan fluorescence (ITF) and microscale thermophoresis (MST) to ascertain their interaction with CIB1. Two of the validated hits shared similar chemical structures, suggesting a common mechanism of action. Docking studies further revealed promising interactions within the hydrophobic binding pocket of the target protein, particularly forming key hydrogen bonds with Ser180. The compounds exhibited a potent antiplatelet activity based on their inhibition of thrombin-induced human platelet aggregation, thus indicating that disruptors of the CIB1- αIIbβ3 interaction could carry a translational potential as antithrombotic agents.
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Affiliation(s)
- Kalyan Golla
- Cardeza
Center for Hemostasis, Thrombosis, and Vascular Biology, Cardeza Foundation
for Hematologic Research, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Adam Yasgar
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Voddarahally N. Manjuprasanna
- Cardeza
Center for Hemostasis, Thrombosis, and Vascular Biology, Cardeza Foundation
for Hematologic Research, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Meghna U. Naik
- Cardeza
Center for Hemostasis, Thrombosis, and Vascular Biology, Cardeza Foundation
for Hematologic Research, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Bolormaa Baljinnyam
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Alexey V. Zakharov
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Sankalp Jain
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Ganesha Rai
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Ulhas P. Naik
- Cardeza
Center for Hemostasis, Thrombosis, and Vascular Biology, Cardeza Foundation
for Hematologic Research, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
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3
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Ruiz-Moreno AJ, Cedillo-González R, Cordova-Bahena L, An Z, Medina-Franco JL, Velasco-Velázquez MA. Consensus Pharmacophore Strategy For Identifying Novel SARS-Cov-2 M pro Inhibitors from Large Chemical Libraries. J Chem Inf Model 2024; 64:1984-1995. [PMID: 38472094 PMCID: PMC10966741 DOI: 10.1021/acs.jcim.3c01439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main Protease (Mpro) is an enzyme that cleaves viral polyproteins translated from the viral genome and is critical for viral replication. Mpro is a target for anti-SARS-CoV-2 drug development, and multiple Mpro crystals complexed with competitive inhibitors have been reported. In this study, we aimed to develop an Mpro consensus pharmacophore as a tool to expand the search for inhibitors. We generated a consensus model by aligning and summarizing pharmacophoric points from 152 bioactive conformers of SARS-CoV-2 Mpro inhibitors. Validation against a library of conformers from a subset of ligands showed that our model retrieved poses that reproduced the crystal-binding mode in 77% of the cases. Using models derived from a consensus pharmacophore, we screened >340 million compounds. Pharmacophore-matching and chemoinformatics analyses identified new potential Mpro inhibitors. The candidate compounds were chemically dissimilar to the reference set, and among them, demonstrating the relevance of our model. We evaluated the effect of 16 candidates on Mpro enzymatic activity finding that seven have inhibitory activity. Three compounds (1, 4, and 5) had IC50 values in the midmicromolar range. The Mpro consensus pharmacophore reported herein can be used to identify compounds with improved activity and novel chemical scaffolds against Mpro. The method developed for its generation is provided as an open-access code (https://github.com/AngelRuizMoreno/ConcensusPharmacophore) and can be applied to other pharmacological targets.
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Affiliation(s)
- Angel J. Ruiz-Moreno
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
| | - Raziel Cedillo-González
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
- Graduate
Program in Biochemical Sciences, Universidad
Nacional Autónoma de México, Mexico City 04510, Mexico
- DIFACQUIM
Research Group, School of Chemistry, Universidad
Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Luis Cordova-Bahena
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
- Consejo
Nacional de Humanidades, Ciencias y Tecnología, Mexico City 03940, Mexico
| | - Zhiqiang An
- Texas
Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - José L. Medina-Franco
- DIFACQUIM
Research Group, School of Chemistry, Universidad
Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Marco A. Velasco-Velázquez
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
- Texas
Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, United States
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Brier L, Hassan H, Hanoulle X, Landry V, Moschidi D, Desmarets L, Rouillé Y, Dumont J, Herledan A, Warenghem S, Piveteau C, Carré P, Ikherbane S, Cantrelle FX, Dupré E, Dubuisson J, Belouzard S, Leroux F, Deprez B, Charton J. Novel dithiocarbamates selectively inhibit 3CL protease of SARS-CoV-2 and other coronaviruses. Eur J Med Chem 2023; 250:115186. [PMID: 36796300 PMCID: PMC9901219 DOI: 10.1016/j.ejmech.2023.115186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023]
Abstract
Since end of 2019, the global and unprecedented outbreak caused by the coronavirus SARS-CoV-2 led to dramatic numbers of infections and deaths worldwide. SARS-CoV-2 produces two large viral polyproteins which are cleaved by two cysteine proteases encoded by the virus, the 3CL protease (3CLpro) and the papain-like protease, to generate non-structural proteins essential for the virus life cycle. Both proteases are recognized as promising drug targets for the development of anti-coronavirus chemotherapy. Aiming at identifying broad spectrum agents for the treatment of COVID-19 but also to fight emergent coronaviruses, we focused on 3CLpro that is well conserved within this viral family. Here we present a high-throughput screening of more than 89,000 small molecules that led to the identification of a new chemotype, potent inhibitor of the SARS-CoV-2 3CLpro. The mechanism of inhibition, the interaction with the protease using NMR and X-Ray, the specificity against host cysteine proteases and promising antiviral properties in cells are reported.
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Affiliation(s)
- Lucile Brier
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Haitham Hassan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Xavier Hanoulle
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Valerie Landry
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Danai Moschidi
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Lowiese Desmarets
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Yves Rouillé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Julie Dumont
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Sandrine Warenghem
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Paul Carré
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Sarah Ikherbane
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - François-Xavier Cantrelle
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Elian Dupré
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Jean Dubuisson
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Sandrine Belouzard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France.
| | - Julie Charton
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France
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5
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Pickens CA, Courtney E, Isenberg SL, Cuthbert C, Petritis K. Multiplexing Homocysteine into First-Tier Newborn Screening Mass Spectrometry Assays Using Selective Thiol Derivatization. Clin Chem 2023; 69:470-481. [PMID: 36920064 DOI: 10.1093/clinchem/hvad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/09/2023] [Indexed: 03/16/2023]
Abstract
BACKGROUND Classical homocystinuria (HCU) results from deficient cystathionine β-synthase activity, causing elevated levels of Met and homocysteine (Hcy). Newborn screening (NBS) aims to identify HCU in pre-symptomatic newborns by assessing Met concentrations in first-tier screening. However, unlike Hcy, Met testing leads to a high number of false-positive and -negative results. Therefore, screening for Hcy directly in first-tier screening would be a better biomarker for use in NBS. METHODS Dried blood spot (DBS) quality control and residual clinical specimens were used in analyses. Several reducing and maleimide reagents were investigated to aid in quantification of total Hcy (tHcy). The assay which was developed and validated was performed by flow injection analysis-tandem mass spectrometry (FIA-MS/MS). RESULTS Interferents of tHcy measurement were identified, so selective derivatization of Hcy was employed. Using N-ethylmaleimide (NEM) to selectively derivatize Hcy allowed interferent-free quantification of tHcy by FIA-MS/MS in first-tier NBS. The combination of tris(2-carboxyethyl)phosphine (TCEP) and NEM yielded significantly less matrix effects compared to dithiothreitol (DTT) and NEM. Analysis of clinical specimens demonstrated that the method could distinguish between HCU-positive, presumptive normal newborns, and newborns receiving total parenteral nutrition. CONCLUSIONS Here we present the first known validated method capable of screening tHcy in DBS during FIA-MS/S first-tier NBS.
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Affiliation(s)
- C Austin Pickens
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Elya Courtney
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Samantha L Isenberg
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Carla Cuthbert
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Konstantinos Petritis
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, United States
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6
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Ren J, Vaid TM, Lee H, Ojeda I, Johnson ME. Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations. J Comput Aided Mol Des 2023; 37:53-65. [PMID: 36427108 PMCID: PMC9839505 DOI: 10.1007/s10822-022-00490-1] [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: 08/20/2022] [Accepted: 11/17/2022] [Indexed: 11/26/2022]
Abstract
The Hepatitis C Virus (HCV) NS3/4A is an attractive target for the treatment of Hepatitis C infection. Herein, we present an investigation of HCV NS3/4A inhibitors based on a sulfonamidobenzamide scaffold. Inhibitor interactions with HCV NS3/4A were explored by molecular docking, molecular dynamics simulations, and MM/PBSA binding free energy calculations. All of the inhibitors adopt similar molecular docking poses in the catalytic site of the protease that are stabilized by hydrogen bond interactions with G137 and the catalytic S139, which are known to be important for potency and binding stability. The quantitative assessments of binding free energies from MM/PBSA correlate well with the experimental results, with a high coefficient of determination, R2 of 0.92. Binding free energy decomposition analyses elucidate the different contributions of Q41, F43, H57, R109, K136, G137, S138, S139, A156, M485, and Q526 in binding different inhibitors. The importance of these sidechain contributions was further confirmed by computational alanine scanning mutagenesis. In addition, the sidechains of K136 and S139 show crucial but distinct contributions to inhibitor binding with HCV NS3/4A. The structural basis of the potency has been elucidated, demonstrating the importance of the R155 sidechain conformation. This extensive exploration of binding energies and interactions between these compounds and HCV NS3/4A at the atomic level should benefit future antiviral drug design.
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Affiliation(s)
- Jinhong Ren
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
- BeiGene (Beijing) Co., Ltd, No. 30 Science Park Road, Zhong-Guan-Cun Life Sciences Park, Changping District, Beijing, 102206, People's Republic of China
| | - Tasneem M Vaid
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Hyun Lee
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
- Biophysics Core at Research Resource Center, University of Illinois at Chicago, 1100 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Isabel Ojeda
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Michael E Johnson
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA.
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7
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Röhrig UF, Majjigapu SR, Vogel P, Reynaud A, Pojer F, Dilek N, Reichenbach P, Ascenção K, Irving M, Coukos G, Michielin O, Zoete V. Structure-based optimization of type III indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors. J Enzyme Inhib Med Chem 2022; 37:1773-1811. [PMID: 35758198 PMCID: PMC9246256 DOI: 10.1080/14756366.2022.2089665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The haem enzyme indoleamine 2,3-dioxygenase 1 (IDO1) catalyses the rate-limiting step in the kynurenine pathway of tryptophan metabolism and plays an essential role in immunity, neuronal function, and ageing. Expression of IDO1 in cancer cells results in the suppression of an immune response, and therefore IDO1 inhibitors have been developed for use in anti-cancer immunotherapy. Here, we report an extension of our previously described highly efficient haem-binding 1,2,3-triazole and 1,2,4-triazole inhibitor series, the best compound having both enzymatic and cellular IC50 values of 34 nM. We provide enzymatic inhibition data for almost 100 new compounds and X-ray diffraction data for one compound in complex with IDO1. Structural and computational studies explain the dramatic drop in activity upon extension to pocket B, which has been observed in diverse haem-binding inhibitor scaffolds. Our data provides important insights for future IDO1 inhibitor design.
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Affiliation(s)
- Ute F Röhrig
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland
| | - Somi Reddy Majjigapu
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland.,Laboratory of Glycochemistry and Asymmetric Synthesis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pierre Vogel
- Laboratory of Glycochemistry and Asymmetric Synthesis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Aline Reynaud
- Protein Production and Structure Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nahzli Dilek
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland
| | - Patrick Reichenbach
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, Epalinges, Switzerland
| | - Kelly Ascenção
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland
| | - Melita Irving
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, Epalinges, Switzerland
| | - George Coukos
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, Epalinges, Switzerland
| | - Olivier Michielin
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Ludwig Cancer Research-Lausanne Branch, Lausanne, CH-1011, Switzerland
| | - Vincent Zoete
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland.,Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, Epalinges, Switzerland
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8
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Grimm TM, Herbinger M, Krüger L, Müller S, Mayer TU, Hauck CR. Lockdown, a selective small-molecule inhibitor of the integrin phosphatase PPM1F, blocks cancer cell invasion. Cell Chem Biol 2022; 29:930-946.e9. [PMID: 35443151 DOI: 10.1016/j.chembiol.2022.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 03/04/2022] [Accepted: 03/23/2022] [Indexed: 12/18/2022]
Abstract
Phosphatase PPM1F is a regulator of cell adhesion by fine-tuning integrin activity and actin cytoskeleton structures. Elevated expression of this enzyme in human tumors is associated with high invasiveness, enhanced metastasis, and poor prognosis. Thus, PPM1F is a target for pharmacological intervention, yet inhibitors of this enzyme are lacking. Here, we use high-throughput screening to identify Lockdown, a reversible and non-competitive PPM1F inhibitor. Lockdown is selective for PPM1F, because this compound does not inhibit other protein phosphatases in vitro and does not induce additional phenotypes in PPM1F knockout cells. Importantly, Lockdown-treated glioblastoma cells fully re-capitulate the phenotype of PPM1F-deficient cells as assessed by increased phosphorylation of PPM1F substrates and corruption of integrin-dependent cellular processes. Ester modification yields LockdownPro with increased membrane permeability and prodrug-like properties. LockdownPro suppresses tissue invasion by PPM1F-overexpressing human cancer cells, validating PPM1F as a therapeutic target and providing an access point to control tumor cell dissemination.
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Affiliation(s)
- Tanja M Grimm
- Lehrstuhl Zellbiologie, Department of Biology, University of Konstanz, Maildrop 621, Universitätsstrasse 10, 78467 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany
| | - Marleen Herbinger
- Lehrstuhl Zellbiologie, Department of Biology, University of Konstanz, Maildrop 621, Universitätsstrasse 10, 78467 Konstanz, Germany
| | - Lena Krüger
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany
| | - Silke Müller
- Lehrstuhl Molekulare Genetik, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany; Screening Center, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany
| | - Thomas U Mayer
- Lehrstuhl Molekulare Genetik, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany; Screening Center, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany
| | - Christof R Hauck
- Lehrstuhl Zellbiologie, Department of Biology, University of Konstanz, Maildrop 621, Universitätsstrasse 10, 78467 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany.
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9
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Ihssen J, Faccio G, Yao C, Sirec T, Spitz U. Fluorogenic in vitro activity assay for the main protease M pro from SARS-CoV-2 and its adaptation to the identification of inhibitors. STAR Protoc 2021; 2:100793. [PMID: 34423318 PMCID: PMC8367757 DOI: 10.1016/j.xpro.2021.100793] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
This protocol describes an in vitro fluorogenic assay to measure the proteolytic activity and identify inhibitors of Mpro, the main protease produced by SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2). Studies to identify potential inhibitors of Mpro mainly rely on in silico molecular dynamics simulations or on FRET (Fluorescence Resonance Energy Transfer) substrates. The protocol is based on an aminomethyl coumarin substrate. High sensitivity, specificity, and an easily detectable fluorescent read-out are the advantages offered by this rapid assay, which allows high throughput screening of new Mpro inhibitors. Mpro is the main protease produced by SARS-CoV-2 An in vitro fluorogenic assay for the measurement of the proteolytic activity of Mpro An in vitro fluorogenic assay for the inhibitor screening of Mpro High sensitivity, specificity, and an easily detectable fluorescent read-out
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Affiliation(s)
- Julien Ihssen
- Biosynth Carbosynth, Rietlistrasse 4, 9422 Staad, Switzerland
| | - Greta Faccio
- Biosynth Carbosynth, Rietlistrasse 4, 9422 Staad, Switzerland
| | - Chunyan Yao
- Biosynth Carbosynth, Rietlistrasse 4, 9422 Staad, Switzerland
| | - Teja Sirec
- Biosynth Carbosynth, Rietlistrasse 4, 9422 Staad, Switzerland
| | - Urs Spitz
- Biosynth Carbosynth, Rietlistrasse 4, 9422 Staad, Switzerland
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10
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A novel GSK-3 inhibitor binds to GSK-3β via a reversible, time and Cys-199-dependent mechanism. Bioorg Med Chem 2021; 40:116179. [PMID: 33991821 DOI: 10.1016/j.bmc.2021.116179] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 11/21/2022]
Abstract
Glycogen synthase kinase-3 (GSK-3) has been implicated in numerous pathologies making GSK-3 an attractive therapeutic target. Our group has identified a compound termed COB-187 that is a potent and selective inhibitor of GSK-3. In this study, we probed the mechanism by which COB-187 inhibits GSK-3β. Progress curves, generated via real-time monitoring of kinase activity, indicated that COB-187 inhibition of GSK-3β is time-dependent and subsequent jump dilution assays revealed that COB-187 binding to GSK-3β is reversible. Further, a plot of the kinetic constant (kobs) versus COB-187 concentration suggested that, within the range of concentrations studied, COB-187 binds to GSK-3β via an induced-fit mechanism. There is a critical cysteine residue at the entry to the active site of GSK-3β (Cys-199). We generated a mutant version of GSK-3β wherein Cys-199 was substituted with an alanine. This mutation caused a dramatic decrease in the activity of COB-187; specifically, an IC50 in the nM range for wild type versus >100 µM for the mutant. A screen of COB-187 against 34 kinases that contain a conserved cysteine in their active site revealed that COB-187 is highly selective for GSK-3 indicating that COB-187's inhibition of GSK-3β via Cys-199 is specific. Combined, these findings suggest that COB-187 inhibits GSK-3β via a specific, reversible, time and Cys-199-dependent mechanism.
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11
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Gurard-Levin ZA, Liu C, Jekle A, Jaisinghani R, Ren S, Vandyck K, Jochmans D, Leyssen P, Neyts J, Blatt LM, Beigelman L, Symons JA, Raboisson P, Scholle MD, Deval J. Evaluation of SARS-CoV-2 3C-like protease inhibitors using self-assembled monolayer desorption ionization mass spectrometry. Antiviral Res 2020; 182:104924. [PMID: 32896566 PMCID: PMC7834858 DOI: 10.1016/j.antiviral.2020.104924] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/21/2020] [Accepted: 08/22/2020] [Indexed: 01/25/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the COVID-19 pandemic that began in 2019. The coronavirus 3-chymotrypsin-like cysteine protease (3CLpro) controls replication and is therefore considered a major target for antiviral discovery. This study describes the evaluation of SARS-CoV-2 3CLpro inhibitors in a novel self-assembled monolayer desorption ionization mass spectrometry (SAMDI-MS) enzymatic assay. Compared with a traditional FRET readout, the label-free SAMDI-MS assay offers greater sensitivity and eliminates false positive inhibition from compound interference with the optical signal. The SAMDI-MS assay was optimized and validated with known inhibitors of coronavirus 3CLpro such as GC376 (IC50 = 0.060 μM), calpain inhibitors II and XII (IC50 ~20-25 μM). The FDA-approved drugs shikonin, disulfiram, and ebselen did not inhibit SARS-CoV-2 3CLpro activity in the SAMDI-MS assay under physiologically relevant reducing conditions. The three drugs did not directly inhibit human β-coronavirus OC-43 or SARS-CoV-2 in vitro, but instead induced cell death. In conclusion, the SAMDI-MS 3CLpro assay, combined with antiviral and cytotoxic assessment, provides a robust platform to evaluate antiviral agents directed against SARS-CoV-2.
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Affiliation(s)
| | - Cheng Liu
- Aligos Therapeutics, Inc, South San Francisco, USA
| | | | | | - Suping Ren
- Aligos Therapeutics, Inc, South San Francisco, USA
| | | | | | | | | | | | | | | | | | | | - Jerome Deval
- Aligos Therapeutics, Inc, South San Francisco, USA.
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12
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Seaberg J, Flynn N, Cai A, Ramsey JD. Effect of redox‐responsive DTSSP crosslinking on poly(
l
‐lysine)‐grafted‐poly(ethylene glycol) nanoparticles for delivery of proteins. Biotechnol Bioeng 2020; 117:2504-2515. [DOI: 10.1002/bit.27369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/20/2020] [Accepted: 05/01/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Joshua Seaberg
- School of Chemical Engineering Oklahoma State University Stillwater Oklahoma
| | - Nicholas Flynn
- School of Chemical Engineering Oklahoma State University Stillwater Oklahoma
| | - Amanda Cai
- School of Chemical Engineering Oklahoma State University Stillwater Oklahoma
| | - Joshua D. Ramsey
- School of Chemical Engineering Oklahoma State University Stillwater Oklahoma
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13
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Protein Stability and Functional Characterization of Intra-Melanosomal Domain of Human Recombinant Tyrosinase-Related Protein 1. Int J Mol Sci 2020; 21:ijms21010331. [PMID: 31947795 PMCID: PMC6981619 DOI: 10.3390/ijms21010331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/28/2019] [Accepted: 12/31/2019] [Indexed: 12/19/2022] Open
Abstract
Pigmentation is the result of a complex process by which the biopolymer melanin is synthesized and packed into melanosomes of melanocytes. Various types of oculocutaneous albinism (OCA), a series of autosomal recessive disorders, are associated with reduced pigmentation in the skin, eyes, and hair due to genetic mutations of proteins involved in melanogenesis. Human tyrosinase (Tyr) and tyrosinase-related protein 1 (Tyrp1) drives the enzymatic process of pigment bio-polymerization. However, within the melanogenic pathway, Tyrp1 has catalytic functions not clearly defined and distinct from Tyr. Here, we characterize the biochemical and biophysical properties of recombinant human Tyrp1. For this purpose, we purified and analyzed the intra-melanosomal domain (Tyrp1tr) for protein stability and enzymatic function in conditions mimicking the environment within melanosomes and the endoplasmic reticulum. The study suggests that Tyrp1tr is a monomeric molecule at ambient temperatures and below (<25 °C). At higher temperatures, >31 °C, higher protein aggregates form with a concurrent decrease of monomers in solution. Also, Tyrp1tr diphenol oxidase activity at pH 5.5 rises as both the pre-incubation temperature and the higher molecular weight protein aggregates formation increases. The enhanced protein activity is consistent with the volume exclusion change caused by protein aggregates.
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14
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Henschke L, Frese M, Hellmuth S, Marx A, Stemmann O, Mayer TU. Identification of Bioactive Small Molecule Inhibitors of Separase. ACS Chem Biol 2019; 14:2155-2159. [PMID: 31553567 DOI: 10.1021/acschembio.9b00661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Separase, a cysteine protease of the CD clan, triggers chromosome segregation during mitosis by cleaving the cohesin ring entrapping the two sister chromatids. Deregulated separase activity is associated with aneuploidy, a hallmark of most human cancers. In fact, separase is highly overexpressed in many solid cancers, making it an attractive chemotherapeutic target. To identify small molecules capable of inhibiting separase in its complex cellular environment, we established a highly sensitive assay to quantify separase activity in cells and screened a 51 009-member library for separase inhibitors. In vitro assays confirmed that the identified compounds efficiently inhibited separase, while not affecting caspase-1, another CD-clan protease structurally related to separase. Importantly, HeLa cells with compromised separase activity displayed severe chromosome segregation defects upon compound treatment, confirming that the identified inhibitors are bioactive in tumor tissue culture cells. Structure-activity relationship studies succeeded in the optimization of the most promising inhibitor. Overall, this study demonstrates the feasibility of identifying separase-specific inhibitors, which serve as promising lead compounds for the development of clinically relevant separase inhibiting drugs.
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Affiliation(s)
- Lars Henschke
- Department of Biology and Konstanz Research School Chemical-Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78467 Konstanz, Germany
| | - Matthias Frese
- Department of Chemistry and Konstanz Research School Chemical-Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78467 Konstanz, Germany
| | - Susanne Hellmuth
- Chair of Genetics, University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical-Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78467 Konstanz, Germany
| | - Olaf Stemmann
- Chair of Genetics, University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Thomas U. Mayer
- Department of Biology and Konstanz Research School Chemical-Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78467 Konstanz, Germany
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15
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Meewan I, Zhang X, Roy S, Ballatore C, O’Donoghue AJ, Schooley RT, Abagyan R. Discovery of New Inhibitors of Hepatitis C Virus NS3/4A Protease and Its D168A Mutant. ACS OMEGA 2019; 4:16999-17008. [PMID: 31646247 PMCID: PMC6796237 DOI: 10.1021/acsomega.9b02491] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/02/2019] [Indexed: 06/01/2023]
Abstract
Hepatitis C virus (HCV) is a human pathogen with high morbidity. The HCV NS3/4A protease is essential for viral replication and is one of the top three drug targets. Several drugs targeting the protease have been developed, but drug-resistant mutant strains emerged. Here, we screened a library and synthesized a novel class of small molecules based on a tryptophan derivative scaffold identified as HCV NS3/4A protease inhibitors that are active against both wild type and mutant form of the protease. Only the compounds with predicted binding poses not affected by the most frequent mutations in the active site were selected for experimental validation. The antiviral activities were evaluated by replicon and enzymatic assays. Twenty-two compounds were found to inhibit HCV with EC50 values ranging between 0.64 and 63 μM with compound 22 being the most active. In protease assays, 22 had a comparable inhibition profile for the common mutant HCV GT1b D168A and the wild-type enzyme. However, in the same assay, the potency of the approved drug, simeprevir, decreased 5.7-fold for the mutant enzyme relative to the wild type. The top three inhibitors were also tested against four human serine proteases and were shown to be specific to the viral protease. The fluorescence-based cell viability assay demonstrated a sufficient therapeutic range for the top three candidates.
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Affiliation(s)
- Ittipat Meewan
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Xingquan Zhang
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Suchismita Roy
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Carlo Ballatore
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Anthony J. O’Donoghue
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Robert T. Schooley
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Ruben Abagyan
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
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16
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Novel adenosine-derived inhibitors of Cryptosporidium parvum inosine 5'-monophosphate dehydrogenase. J Antibiot (Tokyo) 2019; 72:934-942. [PMID: 31296916 DOI: 10.1038/s41429-019-0199-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 11/08/2022]
Abstract
We have found cyclophane-type adenosine derivatives having p-quinone amide moieties (1 and 2) as weak inhibitors of Cryptosporidium parvum inosine 5'-monophosphate dehydrogenase (CpIMPDH) from the Hokkaido University Chemical Library via the luciferase-based high-throughput screening. To obtain more potent inhibitors, we synthesized four new derivatives free from cyclophane rings (3-6). The N-H derivatives 3 and 5 showed more potent activities (24.4 and 11.1 μM, respectively) in the presence of dithiothreitol (DTT), whereas the N-methyl derivative 4 indicated more potent activity (2.1 μM) without DTT. Conformational analysis of compounds 3 and 4 suggested that N-H amide 3 binds to IMP-binding site in the DTT mediated manner.
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17
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Fraga H, Rodriguez B, Bardera A, Cid C, Akopian T, Kandror O, Park A, Colmenarejo G, Lelievre J, Goldberg A. Development of high throughput screening methods for inhibitors of ClpC1P1P2 from Mycobacteria tuberculosis. Anal Biochem 2018; 567:30-37. [PMID: 30543804 DOI: 10.1016/j.ab.2018.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 12/03/2018] [Indexed: 01/10/2023]
Abstract
Tuberculosis affects about 100 million people worldwide and causes nearly 2 million deaths annually. It has been estimated that one third of all humans is infected with latent Mycobacterium tuberculosis (Mtb). Moreover, Mtb has become increasingly resistant to available antibiotics. Consequently, it is important to identify and characterize new therapeutic targets in Mtb and to synthesize selective inhibitors. ClpP1, ClpP2 and their associated regulatory ATPases, ClpX and ClpC1 are required for the growth of Mtb and for its virulence during murine infection and are highly attractive drug targets, especially since they are not present in the cytosol of mammalian cells, and they differ markedly from the mitochondrial ClpP complex. The importance of these proteins in Mtb is emphasized by the existence of several natural antibiotics targeting this system. In order to find new inhibitors of ClpC1P1P2 system, we developed an assay based on the ATP-dependent degradation of a fluorescent protein substrate. The hits obtained were further characterized with a set of secondary assays to identify precise targets within a complex. A large library of compounds was screened and led to the identification of a ClpC1 ATPase inhibitor demonstrating that this approach can be used in future searches for anti-TB agents.
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Affiliation(s)
- Hugo Fraga
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain; Department Cell Biology, Harvard Medical School, USA; Institut de Biologie Structurale, Grenoble, France; Departamento de Bioquímica, Faculdade de Medicina da Universidade do Porto, Portugal.
| | - Beatriz Rodriguez
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain
| | - Ana Bardera
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain
| | - Concha Cid
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain
| | - Tatos Akopian
- School of Public Health, Harvard Medical School, USA
| | - Olga Kandror
- School of Public Health, Harvard Medical School, USA
| | - Annie Park
- School of Public Health, Harvard Medical School, USA
| | - Gonzalo Colmenarejo
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain; Biostatisics and Bioinformatics Unit, IMDEA Food Institute, Madrid, Spain
| | - Joel Lelievre
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain
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18
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Hansson P, Boyd H, Dale IL, Dahl G, Nicolaus F, Bowen W, Doering K, Dunsmore C, Cotton G, Lindmark H. A Comparative Study of Fluorescence Assays in Screening for BRD4. Assay Drug Dev Technol 2018; 16:372-383. [PMID: 30307314 DOI: 10.1089/adt.2018.850] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Fluorescence assay technologies are commonly used in high-throughput screening because of their sensitivity and ease of use. Different technologies have their characteristics and the rationale for choosing one over the other can differ between projects because of factors such as availability of reagents, assay performance, and cost. Another important factor to consider is the assay susceptibility to artifacts, which is almost as important as the ability of the assay to pick up active compounds. Spending time and money on false positives or missing the opportunity to build chemistry around false negatives is something that every drug project tries to avoid. We used a BET family Bromodomain, BRD4(1), to explore the outcome of a screening campaign using three fluorescent assay technologies as primary assays. A diverse 7,038 compound set was screened in fluorescence lifetime, fluorescence polarization, and homogeneous time-resolved fluorescence to look at primary hit rates, compound overlap, and hit confirmation rates. The results show a difference between the fluorescence assay technologies with three separate hit lists and some overlap. The confirmed hits from each assay were further evaluated for translation into cells (NanoBRET™). Most of the actives confirmed in cells originated from compounds that overlapped between the assays. In addition, a well-annotated set of compounds with undesirable mechanism of inhibition was screened against BRD4(1) to compare the ability to discriminate true hits from artifact compounds. The results indicate a difference between the assays in their ability to generate false positives and negatives.
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Affiliation(s)
- Pia Hansson
- 1 AstraZeneca R&D, Discovery Biology , Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Helen Boyd
- 1 AstraZeneca R&D, Discovery Biology , Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Ian L Dale
- 2 AstraZeneca R&D, Discovery Biology , Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Göran Dahl
- 3 AstraZeneca R&D, Structure and Biophysics , Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Felix Nicolaus
- 4 Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
| | | | | | | | | | - Helena Lindmark
- 1 AstraZeneca R&D, Discovery Biology , Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
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19
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Hayek SS, Koh KH, Grams ME, Wei C, Ko YA, Li J, Samelko B, Lee H, Dande RR, Lee HW, Hahm E, Peev V, Tracy M, Tardi NJ, Gupta V, Altintas MM, Garborcauskas G, Stojanovic N, Winkler CA, Lipkowitz MS, Tin A, Inker LA, Levey AS, Zeier M, Freedman BI, Kopp JB, Skorecki K, Coresh J, Quyyumi AA, Sever S, Reiser J. A tripartite complex of suPAR, APOL1 risk variants and α vβ 3 integrin on podocytes mediates chronic kidney disease. Nat Med 2017; 23:945-953. [PMID: 28650456 PMCID: PMC6019326 DOI: 10.1038/nm.4362] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 06/01/2017] [Indexed: 12/17/2022]
Abstract
Soluble urokinase plasminogen activator receptor (suPAR) independently predicts chronic kidney disease (CKD) incidence and progression. Apolipoprotein L1 (APOL1) gene variants G1 and G2, but not the reference allele (G0), are associated with an increased risk of CKD in individuals of recent African ancestry. Here we show in two large, unrelated cohorts that decline in kidney function associated with APOL1 risk variants was dependent on plasma suPAR levels: APOL1-related risk was attenuated in patients with lower suPAR, and strengthened in those with higher suPAR levels. Mechanistically, surface plasmon resonance studies identified high-affinity interactions between suPAR, APOL1 and αvβ3 integrin, whereby APOL1 protein variants G1 and G2 exhibited higher affinity for suPAR-activated avb3 integrin than APOL1 G0. APOL1 G1 or G2 augments αvβ3 integrin activation and causes proteinuria in mice in a suPAR-dependent manner. The synergy of circulating factor suPAR and APOL1 G1 or G2 on αvβ3 integrin activation is a mechanism for CKD.
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Affiliation(s)
- Salim S Hayek
- Emory Clinical Cardiovascular Research Institute, Division of Cardiology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kwi Hye Koh
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Morgan E Grams
- Welch Center for Prevention and Johns Hopkins Bloomberg School of Public Health, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Changli Wei
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Yi-An Ko
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Jing Li
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Beata Samelko
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Hyun Lee
- Center for Biomolecular Science and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ranadheer R Dande
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Ha Won Lee
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Eunsil Hahm
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Vasil Peev
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Melissa Tracy
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Nicholas J Tardi
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Vineet Gupta
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Mehmet M Altintas
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Garrett Garborcauskas
- Harvard Medical School and Division of Nephrology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Nikolina Stojanovic
- Harvard Medical School and Division of Nephrology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Cheryl A Winkler
- Molecular Genetic Epidemiology Section, Basic Research Laboratory, Basic Science Program, NCI, Leidos Biomedical Research, Frederick National Laboratory, Frederick, Maryland, USA
| | - Michael S Lipkowitz
- Division of Nephrology and Hypertension, Georgetown University Medical Center, Washington, DC, USA
| | - Adrienne Tin
- Welch Center for Prevention and Johns Hopkins Bloomberg School of Public Health, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lesley A Inker
- Division of Nephrology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Andrew S Levey
- Division of Nephrology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Martin Zeier
- Division of Nephrology, Ruprecht Karls University, Heidelberg, Germany
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Karl Skorecki
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Rambam Health Care Campus, Haifa, Israel
| | - Josef Coresh
- Welch Center for Prevention and Johns Hopkins Bloomberg School of Public Health, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Arshed A Quyyumi
- Emory Clinical Cardiovascular Research Institute, Division of Cardiology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sanja Sever
- Harvard Medical School and Division of Nephrology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Jochen Reiser
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
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20
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Gopinath P, Mahammed A, Eilon-Shaffer T, Nawatha M, Ohayon S, Shabat D, Gross Z, Brik A. Switching Futilepara-Quinone to Efficient Reactive Oxygen Species Generator: Ubiquitin-Specific Protease-2 Inhibition, Electrocatalysis, and Quantification. Chembiochem 2017. [DOI: 10.1002/cbic.201700330] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Pushparathinam Gopinath
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Atif Mahammed
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Tal Eilon-Shaffer
- School of Chemistry; Raymond and Beverly Sackler; Faculty of Exact Sciences; Tel Aviv University; Tel Aviv 69978 Israel
| | - Mickal Nawatha
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Shimrit Ohayon
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Doron Shabat
- School of Chemistry; Raymond and Beverly Sackler; Faculty of Exact Sciences; Tel Aviv University; Tel Aviv 69978 Israel
| | - Zeev Gross
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
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21
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Yoon HY, Hong JI. Sulfatase activity assay using an activity-based probe by generation of N -methyl isoindole under reducing conditions. Anal Biochem 2017; 526:33-38. [DOI: 10.1016/j.ab.2017.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/15/2017] [Accepted: 03/13/2017] [Indexed: 01/01/2023]
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22
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The effect of the antioxidant on the properties of thiolated poly(aspartic acid) polymers in aqueous ocular formulations. Eur J Pharm Biopharm 2017; 113:178-187. [DOI: 10.1016/j.ejpb.2016.12.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/29/2016] [Accepted: 12/06/2016] [Indexed: 11/20/2022]
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23
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Gooyit MD, Janda KD. Modulation of the Surface-Layer Protein of Clostridium difficile through Cwp84 Inhibition. ACS Infect Dis 2016; 2:465-70. [PMID: 27626098 DOI: 10.1021/acsinfecdis.6b00061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cysteine protease Cwp84 is responsible for surface-layer processing in Clostridium difficile and was also shown to cleave several human extracellular matrix components in vitro. To enable the facile identification and characterization of Cwp84 inhibitors, we developed a fluorogenic 10-mer peptide based on the enzyme's natural substrate SlpA that is amenable for use in FRET-based high-throughput screening. The design of substrate-mimetic inhibitors led to epoxysuccinate 8c, which displayed an inactivation efficiency (kinact/KI) of (4.7 ± 0.3) × 10(4) M(-1) min(-1). Further evaluation of 8c demonstrated its ability to inhibit fibronectin cleavage and, more importantly, subvert surface-layer biogenesis in C. difficile.
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Affiliation(s)
- Major D. Gooyit
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, and The Worm Institute
of Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kim D. Janda
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, and The Worm Institute
of Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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24
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Hu X, Compton JR, Leary DH, Olson MA, Lee MS, Cheung J, Ye W, Ferrer M, Southall N, Jadhav A, Morazzani EM, Glass PJ, Marugan J, Legler PM. Kinetic, Mutational, and Structural Studies of the Venezuelan Equine Encephalitis Virus Nonstructural Protein 2 Cysteine Protease. Biochemistry 2016; 55:3007-19. [PMID: 27030368 DOI: 10.1021/acs.biochem.5b00992] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Venezuelan equine encephalitis virus (VEEV) nonstructural protein 2 (nsP2) cysteine protease (EC 3.4.22.-) is essential for viral replication and is involved in the cytopathic effects (CPE) of the virus. The VEEV nsP2 protease is a member of MEROPS Clan CN and characteristically contains a papain-like protease linked to an S-adenosyl-l-methionine-dependent RNA methyltransferase (SAM MTase) domain. The protease contains an alternative active site motif, (475)NVCWAK(480), which differs from papain's (CGS(25)CWAFS), and the enzyme lacks a transition state-stabilizing residue homologous to Gln-19 in papain. To understand the roles of conserved residues in catalysis, we determined the structure of the free enzyme and the first structure of an inhibitor-bound alphaviral protease. The peptide-like E64d inhibitor was found to bind beneath a β-hairpin at the interface of the SAM MTase and protease domains. His-546 adopted a conformation that differed from that found in the free enzyme; one or both of the conformers may assist in leaving group departure of either the amine or Cys thiolate during the catalytic cycle. Interestingly, E64c (200 μM), the carboxylic acid form of the E64d ester, did not inhibit the nsP2 protease. To identify key residues involved in substrate binding, a number of mutants were analyzed. Mutation of the motif residue, N475A, led to a 24-fold reduction in kcat/Km, and the conformation of this residue did not change after inhibition. N475 forms a hydrogen bond with R662 in the SAM MTase domain, and the R662A and R662K mutations both led to 16-fold decreases in kcat/Km. N475 forms the base of the P1 binding site and likely orients the substrate for nucleophilic attack or plays a role in product release. An Asn homologous to N475 is similarly found in coronaviral papain-like proteases (PLpro) of the Severe Acute Respiratory Syndrome (SARS) virus and Middle East Respiratory Syndrome (MERS) virus. Mutation of another motif residue, K480A, led to a 9-fold decrease in kcat and kcat/Km. K480 likely enhances the nucleophilicity of the Cys. Consistent with our substrate-bound models, the SAM MTase domain K706A mutation increased Km 4.5-fold to 500 μM. Within the β-hairpin, the N545A mutation slightly but not significantly increased kcat and Km. The structures and identified active site residues may facilitate the discovery of protease inhibitors with antiviral activity.
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Affiliation(s)
- Xin Hu
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences , Rockville, Maryland 20850, United States
| | | | - Dagmar H Leary
- Center for Bio/molecular Science and Engineering, U.S. Naval Research Laboratory , Washington, D.C. 20375, United States
| | - Mark A Olson
- United States Army Medical Research Institute of Infectious Diseases , Frederick, Maryland 21702, United States
| | - Michael S Lee
- United States Army Medical Research Institute of Infectious Diseases , Frederick, Maryland 21702, United States
| | - Jonah Cheung
- New York Structural Biology Center , New York, New York 10027, United States
| | - Wenjuan Ye
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences , Rockville, Maryland 20850, United States
| | - Mark Ferrer
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences , Rockville, Maryland 20850, United States
| | - Noel Southall
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences , Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences , Rockville, Maryland 20850, United States
| | - Elaine M Morazzani
- United States Army Medical Research Institute of Infectious Diseases , Frederick, Maryland 21702, United States
| | - Pamela J Glass
- United States Army Medical Research Institute of Infectious Diseases , Frederick, Maryland 21702, United States
| | - Juan Marugan
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences , Rockville, Maryland 20850, United States
| | - Patricia M Legler
- Center for Bio/molecular Science and Engineering, U.S. Naval Research Laboratory , Washington, D.C. 20375, United States
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25
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Chen T, Su D, Gruenhagen J, Gu C, Li Y, Yehl P, Chetwyn NP, Medley CD. Chemical de-conjugation for investigating the stability of small molecule drugs in antibody-drug conjugates. J Pharm Biomed Anal 2016; 117:304-10. [DOI: 10.1016/j.jpba.2015.09.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/08/2015] [Accepted: 09/13/2015] [Indexed: 01/06/2023]
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26
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Phillips DJ, Gibson MI. Redox-sensitive materials for drug delivery: targeting the correct intracellular environment, tuning release rates, and appropriate predictive systems. Antioxid Redox Signal 2014; 21:786-803. [PMID: 24219144 DOI: 10.1089/ars.2013.5728] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
SIGNIFICANCE The development of responsive drug delivery systems (DDS) holds great promise as a tool for improving the pharmacokinetic properties of drug compounds. Redox-sensitive systems are particularly attractive given the rich variety of redox gradients present in vivo. These gradients, where the circulation is generally considered oxidizing and the cellular environment is substantially more reducing, provide attractive options for targeted, specific cargo delivery. RECENT ADVANCES Experimental evidence suggests that a "one size fits all" redox gradient does not exist. Rather, there are subtle differences in redox potential within a cell, while the chemical nature of reducing agents in these microenvironments varies. Recent works have demonstrated an ability to modulate the degradation rate of redox-susceptible groups and, hence, provide new tools to engineer precision-targeted DDS. CRITICAL ISSUES Modern synthetic and macromolecular chemistry provides access to a wide range of redox-susceptible architectures. However, in order to utilize these in real applications, the actual chemical nature of the redox-susceptible group, the sub-cellular location being targeted, and the redox microenvironment being encountered should be considered in detail. This is critical to avoid the over-simplification possible when using non-biological reducing agents, which may provide inaccurate kinetic information, and to ensure these materials can be advanced beyond simple "on/off" systems. Furthermore, a strong case can be made for the use of biorelevant reducing agents such as glutathione when demonstrating a materials redox response. FUTURE DIRECTIONS A further understanding of the complexities of the extra- and intracellular microenvironments would greatly assist with the design and application of DDS.
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Affiliation(s)
- Daniel J Phillips
- Department of Chemistry, University of Warwick , Coventry, United Kingdom
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27
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Weir C, Hudson AL, Moon E, Ross A, Alexander M, Peters L, Langova V, Clarke SJ, Pavlakis N, Davey R, Howell VM. Streptavidin: A Novel Immunostimulant for the Selection and Delivery of Autologous and Syngeneic Tumor Vaccines. Cancer Immunol Res 2014; 2:469-79. [DOI: 10.1158/2326-6066.cir-13-0157] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Lee H, Mittal A, Patel K, Gatuz JL, Truong L, Torres J, Mulhearn DC, Johnson ME. Identification of novel drug scaffolds for inhibition of SARS-CoV 3-Chymotrypsin-like protease using virtual and high-throughput screenings. Bioorg Med Chem 2014; 22:167-77. [PMID: 24332657 PMCID: PMC3971864 DOI: 10.1016/j.bmc.2013.11.041] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/12/2013] [Accepted: 11/20/2013] [Indexed: 12/11/2022]
Abstract
We have used a combination of virtual screening (VS) and high-throughput screening (HTS) techniques to identify novel, non-peptidic small molecule inhibitors against human SARS-CoV 3CLpro. A structure-based VS approach integrating docking and pharmacophore based methods was employed to computationally screen 621,000 compounds from the ZINC library. The screening protocol was validated using known 3CLpro inhibitors and was optimized for speed, improved selectivity, and for accommodating receptor flexibility. Subsequently, a fluorescence-based enzymatic HTS assay was developed and optimized to experimentally screen approximately 41,000 compounds from four structurally diverse libraries chosen mainly based on the VS results. False positives from initial HTS hits were eliminated by a secondary orthogonal binding analysis using surface plasmon resonance (SPR). The campaign identified a reversible small molecule inhibitor exhibiting mixed-type inhibition with a K(i) value of 11.1 μM. Together, these results validate our protocols as suitable approaches to screen virtual and chemical libraries, and the newly identified compound reported in our study represents a promising structural scaffold to pursue for further SARS-CoV 3CLpro inhibitor development.
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Affiliation(s)
- Hyun Lee
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Anuradha Mittal
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Kavankumar Patel
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Joseph L Gatuz
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Lena Truong
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Jaime Torres
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Debbie C Mulhearn
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Michael E Johnson
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA.
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29
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Lee H, Zhu T, Patel K, Zhang YY, Truong L, Hevener KE, Gatuz JL, Subramanya G, Jeong HY, Uprichard SL, Johnson ME. High-throughput screening (HTS) and hit validation to identify small molecule inhibitors with activity against NS3/4A proteases from multiple hepatitis C virus genotypes. PLoS One 2013; 8:e75144. [PMID: 24130685 PMCID: PMC3793977 DOI: 10.1371/journal.pone.0075144] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/09/2013] [Indexed: 01/08/2023] Open
Abstract
Development of drug-resistant mutations has been a major problem with all currently developed Hepatitis C Virus (HCV) NS3/4A inhibitors, including the two FDA approved drugs, significantly reducing the efficacy of these inhibitors. The high incidence of drug-resistance mutations and the limited utility of these inhibitors against only genotype 1 highlight the need for novel, broad-spectrum HCV therapies. Here we used high-throughput screening (HTS) to identify low molecular weight inhibitors against NS3/4A from multiple genotypes. A total of 40,967 compounds from four structurally diverse molecular libraries were screened by HTS using fluorescence-based enzymatic assays, followed by an orthogonal binding analysis using surface plasmon resonance (SPR) to eliminate false positives. A novel small molecule compound was identified with an IC50 value of 2.2 µM against the NS3/4A from genotype 1b. Mode of inhibition analysis subsequently confirmed this compound to be a competitive inhibitor with respect to the substrate, indicating direct binding to the protease active site, rather than to the allosteric binding pocket that was discovered to be the binding site of a few recently discovered small molecule inhibitors. This newly discovered inhibitor also showed promising inhibitory activity against the NS3/4As from three other HCV genotypes, as well as five common drug-resistant mutants of genotype 1b NS3/4A. The inhibitor was selective for NS3 from multiple HCV genotypes over two human serine proteases, and a whole cell lysate assay confirmed inhibitory activity in the cellular environment. This compound provides a lead for further development of potentially broader spectrum inhibitors.
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Affiliation(s)
- Hyun Lee
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Tian Zhu
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Kavankumar Patel
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Yan-Yan Zhang
- Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Lena Truong
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Kirk E. Hevener
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Joseph L. Gatuz
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Gitanjali Subramanya
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Hyun-Young Jeong
- Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Susan L. Uprichard
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Michael E. Johnson
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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30
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Rice AJ, Truong L, Johnson ME, Lee H. A colorimetric assay optimization for high-throughput screening of dihydroorotase by detecting ureido groups. Anal Biochem 2013; 441:87-94. [PMID: 23769705 DOI: 10.1016/j.ab.2013.05.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/24/2013] [Accepted: 05/28/2013] [Indexed: 12/15/2022]
Abstract
Dihydroorotase (DHOase) is the third enzyme in the de novo pyrimidine biosynthesis pathway and is a potential new antibacterial drug target. No target-based high-throughput screening (HTS) assay for this enzyme has been reported to date. Here, we optimized two colorimetric-based enzymatic assays that detect the ureido moiety of the DHOase substrate, carbamyl-aspartate (Ca-asp). Each assay was developed in a 40-μl assay volume using 384-well plates with a different color mix, diacetylmonoxime (DAMO)-thiosemicarbazide (TSC) or DAMO-antipyrine. The sensitivity and color interference of both color mixes were compared in the presence of common HTS buffer additives, including dimethyl sulfoxide, reducing agents, detergents, and bovine serum albumin. DAMO-TSC (Z'-factors 0.7-0.8) was determined to be superior to DAMO-antipyrine (Z'-factors 0.5-0.6) with significantly less variability within replicates. An HTS pilot screening with 29,552 compounds from four structurally diverse libraries confirmed the quality of our newly optimized colorimetric assay with DAMO-TSC. This robust method has no heating requirement, which was the main obstacle to applying previous assays to HTS. More important, this well-optimized HTS assay for DHOase, the first of its kind, should make it possible to screen large-scale compound libraries to develop new inhibitors against any enzymes that produce ureido functional groups.
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Affiliation(s)
- Amy J Rice
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA
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31
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Chaudhuri R, Lee H, Truong L, Torres J, Patel K, Johnson ME. Identification of non-macrocyclic small molecule inhibitors against the NS3/4A serine protease of hepatitis C virus through in silico screening. J Chem Inf Model 2012; 52:2245-56. [PMID: 22697413 DOI: 10.1021/ci300177p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Drug discovery and design for inhibition of the Hepatitis C Virus (HCV) NS3/4A serine protease is a major challenge. The broad, shallow, and generally featureless nature of the active site makes it a difficult target for "hit" selection especially using standard docking programs. There are several macrocyclic NS3/4A protease inhibitors that have been approved or are in clinical trials to treat chronic HCV (alone or as combination therapy), but most of the current therapies for HCV infection have untoward side effects, indicating a continuing medical need for the discovery of novel therapeutics with improved efficacy. In this study, we designed and implemented a two-tiered and progressive docking regime that successfully identified five non-macrocyclic small molecules that show inhibitory activity in the low micromolar range. Of these, four compounds show varying inhibition against HCV subgenotypes 1b, 1a, 2a, and 4d. The top inhibitor (3) has an IC(50) value of 15 μM against both subgenotypes 1b and 2a of the NS3/4A protease enzyme. Another inhibitor, 1, inhibits all four subgenotypes with moderate activity, showing highest activity for genotype 2a (24 μM). The five inhibitors presented in this study could be valuable candidates for future hit to lead optimization. Additionally, enzyme-inhibitor interaction models presented herein provide key information regarding structural differences between the active sites of the NS3/4A protease of the HCV subgenotype 1a and 1b that might explain the variable inhibitory activity between subgenotypes of the small molecule inhibitors identified here.
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Affiliation(s)
- Rima Chaudhuri
- Center for Pharmaceutical Biotechnology, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Ave., M/C 870, Chicago, Illinois 60607, USA
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