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Godoy AS, Mesquita NCMR, Noske GD, Gawriljuk VO, Lithgo RM, Balcomb BH, Aschenbrenner JC, Tomlinson CWE, Winokan M, Scheen J, Marples PG, Chandran AV, Ni X, Thompson W, Fairhead M, Fearon D, Koekemoer L, Xavier MAE, Walsh M, Oliva G, von Delft F. High-throughput crystallographic fragment screening of Zika virus NS3 Helicase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.27.591279. [PMID: 38746241 PMCID: PMC11092484 DOI: 10.1101/2024.04.27.591279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The Zika virus (ZIKV), discovered in Africa in 1947, swiftly spread across continents, causing significant concern due to its recent association with microcephaly in newborns and Guillain-Barré syndrome in adults. Despite a decrease in prevalence, the potential for a resurgence remains, necessitating urgent therapeutic interventions. Like other flaviviruses, ZIKV presents promising drug targets within its replication machinery, notably the NS3 helicase (NS3Hel) protein, which plays critical roles in viral replication. However, a lack of structural information impedes the development of specific inhibitors targeting NS3Hel. Here we applied high-throughput crystallographic fragment screening on ZIKV NS3Hel, which yielded structures that reveal 3D binding poses of 46 fragments at multiple sites of the protein, including 11 unique fragments in the RNA-cleft site. These fragment structures provide templates for direct design of hit compounds and should thus assist the development of novel direct-acting antivirals against ZIKV and related flaviviruses, thus opening a promising avenue for combating future outbreaks.
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Affiliation(s)
- Andre S Godoy
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
- ASAP Discovery Consortium: asapdiscovery.org
| | - Nathalya C M R Mesquita
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Gabriela Dias Noske
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Victor Oliveira Gawriljuk
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Ryan M Lithgo
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Blake H Balcomb
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Jasmin Cara Aschenbrenner
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Charles W E Tomlinson
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Max Winokan
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Jenke Scheen
- Open Molecular Sciences Foundation, Davis, CA 95618, USA
- ASAP Discovery Consortium: asapdiscovery.org
| | - Peter George Marples
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Anu V Chandran
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Xiaomin Ni
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Warren Thompson
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Michael Fairhead
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Daren Fearon
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Lizbé Koekemoer
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Mary-Ann Elvina Xavier
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Martin Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Glaucius Oliva
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Frank von Delft
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- ASAP Discovery Consortium: asapdiscovery.org
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Adelusi TI, Oyedele AQK, Boyenle ID, Ogunlana AT, Adeyemi RO, Ukachi CD, Idris MO, Olaoba OT, Adedotun IO, Kolawole OE, Xiaoxing Y, Abdul-Hammed M. Molecular modeling in drug discovery. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100880] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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3
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li J, Dong Z, Wang B, İşcan A, Jin H, Chen L, Fan Z, Walsh P, Liang G. Arylations with Nitroarenes for One-Pot Syntheses of Triaryl-methanols and Tetraarylmethanes. Org Chem Front 2022. [DOI: 10.1039/d2qo00576j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triarylmethanols are well-known core structures in natural products and pharmacologically relevant compounds. In general, transition metal-based catalysts or highly reactive organometallics are employed for the synthesis of these compounds. Herein,...
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4
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Abrams R, Jesani MH, Browning A, Clayden J. Triarylmethanes and their Medium-Ring Analogues by Unactivated Truce-Smiles Rearrangement of Benzanilides. Angew Chem Int Ed Engl 2021; 60:11272-11277. [PMID: 33830592 PMCID: PMC8252078 DOI: 10.1002/anie.202102192] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/01/2021] [Indexed: 12/17/2022]
Abstract
Intramolecular nucleophilic aromatic substitution (Truce–Smiles rearrangement) of the anions of 2‐benzyl benzanilides leads to triarylmethanes in an operationally simple manner. The reaction succeeds even without electronic activation of the ring that plays the role of electrophile in the SNAr reaction, being accelerated instead by the preferred conformation imposed by the tertiary amide tether. The amide substituent of the product may be removed or transformed into alternative functional groups. A ring‐expanding variant (n to n+4) of the reaction provided a route to doubly benzo‐fused medium ring lactams of 10 or 11 members. Hammett analysis returned a ρ value consistent with the operation of a partially concerted reaction mechanism.
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Affiliation(s)
- Roman Abrams
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Mehul H Jesani
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Alex Browning
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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5
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Abrams R, Jesani MH, Browning A, Clayden J. Triarylmethanes and their Medium‐Ring Analogues by Unactivated Truce–Smiles Rearrangement of Benzanilides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Roman Abrams
- School of Chemistry University of Bristol, Cantock's Close Bristol BS8 1TS UK
| | - Mehul H. Jesani
- School of Chemistry University of Bristol, Cantock's Close Bristol BS8 1TS UK
| | - Alex Browning
- School of Chemistry University of Bristol, Cantock's Close Bristol BS8 1TS UK
| | - Jonathan Clayden
- School of Chemistry University of Bristol, Cantock's Close Bristol BS8 1TS UK
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Identification of aurintricarboxylic acid as a potent allosteric antagonist of P2X1 and P2X3 receptors. Neuropharmacology 2019; 158:107749. [PMID: 31461640 DOI: 10.1016/j.neuropharm.2019.107749] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/14/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022]
Abstract
The homotrimeric P2X3 receptor, one of the seven members of the ATP-gated P2X receptor family, plays a crucial role in sensory neurotransmission. P2X3 receptor antagonists have been identified as promising drugs to treat chronic cough and are suggested to offer pain relief in chronic pain such as neuropathic pain. Here, we analysed whether compounds affect P2X3 receptor activity by high-throughput screening of the Spectrum Collection of 2000 approved drugs, natural products and bioactive substances. We identified aurintricarboxylic acid (ATA) as a nanomolar-potency antagonist of P2X3 receptor-mediated responses. Two-electrode voltage clamp electrophysiology-based concentration-response analysis and selectivity profiling revealed that ATA strongly inhibits the rP2X1 and rP2X3 receptors (with IC50 values of 8.6 nM and 72.9 nM, respectively) and more weakly inhibits P2X2/3, P2X2, P2X4 or P2X7 receptors (IC50 values of 0.76 μM, 22 μM, 763 μM or 118 μM, respectively). Patch-clamp analysis of mouse DRG neurons revealed that ATA inhibited native P2X3 and P2X2/3 receptors to a similar extent than rat P2X3 and P2X2/3 receptors expressed in Xenopus oocytes. In a radioligand binding assay, up to 30 μM ATA did not compete with [3H]-ATP for rP2X3 receptor binding, indicating a non-competitive mechanism of action. Molecular docking studies, site-directed mutagenesis and concentration-response analysis revealed that ATA binds to the negative allosteric site of the hP2X3 receptor. In summary, ATA as a drug-like pharmacological tool compound is a nanomolar-potency, allosteric antagonist with selectivity towards αβ-methylene-ATP-sensitive P2X1 and P2X3 receptors.
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7
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Ashraf MU, Iman K, Khalid MF, Salman HM, Shafi T, Rafi M, Javaid N, Hussain R, Ahmad F, Shahzad-Ul-Hussan S, Mirza S, Shafiq M, Afzal S, Hamera S, Anwar S, Qazi R, Idrees M, Qureshi SA, Chaudhary SU. Evolution of efficacious pangenotypic hepatitis C virus therapies. Med Res Rev 2018; 39:1091-1136. [PMID: 30506705 DOI: 10.1002/med.21554] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022]
Abstract
Hepatitis C compromises the quality of life of more than 350 million individuals worldwide. Over the last decade, therapeutic regimens for treating hepatitis C virus (HCV) infections have undergone rapid advancements. Initially, structure-based drug design was used to develop molecules that inhibit viral enzymes. Subsequently, establishment of cell-based replicon systems enabled investigations into various stages of HCV life cycle including its entry, replication, translation, and assembly, as well as role of host proteins. Collectively, these approaches have facilitated identification of important molecules that are deemed essential for HCV life cycle. The expanded set of putative virus and host-encoded targets has brought us one step closer to developing robust strategies for efficacious, pangenotypic, and well-tolerated medicines against HCV. Herein, we provide an overview of the development of various classes of virus and host-directed therapies that are currently in use along with others that are undergoing clinical evaluation.
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Affiliation(s)
- Muhammad Usman Ashraf
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Kanzal Iman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Farhan Khalid
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Hafiz Muhammad Salman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Plant Biotechnology Laboratory, Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Talha Shafi
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Momal Rafi
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | - Nida Javaid
- Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Rashid Hussain
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Fayyaz Ahmad
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | | | - Shaper Mirza
- Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Shafiq
- Plant Biotechnology Laboratory, Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sadia Hamera
- Department of Plant Genetics, Institute of Life Sciences, University of Rostock, Germany
| | - Saima Anwar
- Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Romena Qazi
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital & Research Centre, Lahore, Pakistan
| | - Muhammad Idrees
- Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Hazara University, Mansehra, Pakistan
| | - Sohail A Qureshi
- Institute of Integrative Biosciences, CECOS-University of Information Technology and Emerging Sciences, Peshawar, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
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8
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Stensrud KF, Zanotti KJ, Waggoner AS, Armitage BA. Spectral Properties of Fluorogenic Thiophene-derived Triarylmethane Dyes. Photochem Photobiol 2018; 95:406-410. [PMID: 30339278 DOI: 10.1111/php.13037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/28/2018] [Indexed: 12/12/2022]
Abstract
Spectral properties and fluorogenic behaviors of five novel thiophene variants of malachite green (MG), termed MGTs, were determined. Appreciable changes as a function of homologation and substitution pattern, including absorption band positions and intensities and fluorescence quantum yields were observed. In particular, the shorter wavelength y-band absorption was found to shift over a nearly 200 nm range based on aryl group variation, allowing fine-tuning of the excitation wavelength for these dyes. In addition, the fluorescence intensity of some MGTs increased significantly (up to 4600-fold) when the dye was bound to a cognate protein partner, which is potentially useful for cell imaging studies.
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Affiliation(s)
- Kenneth F Stensrud
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA
| | | | - Alan S Waggoner
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA
| | - Bruce A Armitage
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA
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Zhang Z, Wang H, Qiu N, Kong Y, Zeng W, Zhang Y, Zhao J. Synthesis of Triarylmethanes via Palladium-Catalyzed Suzuki Coupling of Trimethylammonium Salts and Arylboronic Acids. J Org Chem 2018; 83:8710-8715. [DOI: 10.1021/acs.joc.8b00965] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Zhenming Zhang
- Key Laboratory of Chemical Biology of Jiangxi Province, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P.R. China
| | - Hui Wang
- Key Laboratory of Chemical Biology of Jiangxi Province, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P.R. China
| | - Nianli Qiu
- Key Laboratory of Chemical Biology of Jiangxi Province, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P.R. China
| | - Yujing Kong
- Key Laboratory of Chemical Biology of Jiangxi Province, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P.R. China
| | - Wenjuan Zeng
- Key Laboratory of Chemical Biology of Jiangxi Province, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P.R. China
| | - Yongquan Zhang
- Key Laboratory of Chemical Biology of Jiangxi Province, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P.R. China
| | - Junfeng Zhao
- Key Laboratory of Chemical Biology of Jiangxi Province, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P.R. China
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Datta A, Brosh RM. New Insights Into DNA Helicases as Druggable Targets for Cancer Therapy. Front Mol Biosci 2018; 5:59. [PMID: 29998112 PMCID: PMC6028597 DOI: 10.3389/fmolb.2018.00059] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/06/2018] [Indexed: 12/28/2022] Open
Abstract
Small molecules that deter the functions of DNA damage response machinery are postulated to be useful for enhancing the DNA damaging effects of chemotherapy or ionizing radiation treatments to combat cancer by impairing the proliferative capacity of rapidly dividing cells that accumulate replicative lesions. Chemically induced or genetic synthetic lethality is a promising area in personalized medicine, but it remains to be optimized. A new target in cancer therapy is DNA unwinding enzymes known as helicases. Helicases play critical roles in all aspects of nucleic acid metabolism. We and others have investigated small molecule targeted inhibition of helicase function by compound screens using biochemical and cell-based approaches. Small molecule-induced trapping of DNA helicases may represent a generalized mechanism exemplified by certain topoisomerase and PARP inhibitors that exert poisonous consequences, especially in rapidly dividing cancer cells. Taking the lead from the broader field of DNA repair inhibitors and new information gleaned from structural and biochemical studies of DNA helicases, we predict that an emerging strategy to identify useful helicase-interacting compounds will be structure-based molecular docking interfaced with a computational approach. Potency, specificity, drug resistance, and bioavailability of helicase inhibitor drugs and targeting such compounds to subcellular compartments where the respective helicases operate must be addressed. Beyond cancer therapy, continued and new developments in this area may lead to the discovery of helicase-interacting compounds that chemically rescue clinically relevant helicase missense mutant proteins or activate the catalytic function of wild-type DNA helicases, which may have novel therapeutic application.
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Affiliation(s)
- Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD, United States
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD, United States
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Venkatesan A, Febin Prabhu Dass J. Deciphering molecular properties and docking studies of hepatitis C and non-hepatitis C antiviral inhibitors - A computational approach. Life Sci 2017; 174:8-14. [PMID: 28259653 DOI: 10.1016/j.lfs.2017.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/24/2017] [Accepted: 02/28/2017] [Indexed: 11/19/2022]
Abstract
BACKGROUND Hepatitis C is an infectious liver disease with high mortality rate which is caused by Hepatitis C virus. Several treatment methods have been applied to combat this deadly virus including interferons, vaccine and direct acting antivirals (DAAs). However, the later shows promising effects in HCV treatment with lower adverse effect. Specifically, the DAAs target the non-structural proteins (NS3 and NS5B). PURPOSE The objective of the present study is to hypothesize an alternative antiviral inhibitor for HCV from the available other antivirals. METHODS Computation of 2D molecular descriptors for the selected antiviral inhibitors followed by clustering the descriptor features. The closely clustered compounds were subjected to the interaction studies against the HCV target protein to validate the cluster result. RESULTS AND DISCUSSION The clustering result showed that indinavir (HIV inhibitor) and AT130 (HBV inhibitor) molecule are close to the HCV inhibitor. The indinavir complexed with NS3 protein shows -5.33kcal/mol and AT-130 complexed with NS5B protein possess the binding energy of -8.87kcal/mol. The docking interaction study indicated a better binding affinity than other viral inhibitors. CONCLUSION From the descriptor based feature similarity analysis and the interaction study, it can be concluded that indinavir and AT-130 could be a potential alternative agent for HCV treatment.
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Affiliation(s)
- Arthi Venkatesan
- Department of Integrative Biology, School of Bio Sciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - J Febin Prabhu Dass
- Department of Integrative Biology, School of Bio Sciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India.
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12
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Shape-based virtual screening, synthesis and evaluation of novel pyrrolone derivatives as antiviral agents against HCV. Bioorg Med Chem Lett 2017; 27:936-940. [DOI: 10.1016/j.bmcl.2016.12.087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 12/30/2016] [Accepted: 12/31/2016] [Indexed: 12/18/2022]
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13
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Ablenas CJ, Liu HW, Shkriabai N, Kvaratskhelia M, Cosa G, Götte M. Dynamic Interconversions of HCV Helicase Binding Modes on the Nucleic Acid Substrate. ACS Infect Dis 2017; 3:99-109. [PMID: 28081608 DOI: 10.1021/acsinfecdis.6b00177] [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: 01/27/2023]
Abstract
The dynamics involved in the interaction between hepatitis C virus nonstructural protein 3 (NS3) C-terminal helicase and its nucleic acid substrate have been the subject of interest for some time given the key role of this enzyme in viral replication. Here, we employed fluorescence-based techniques and focused on events that precede the unwinding process. Both ensemble Förster resonance energy transfer (FRET) and ensemble protein induced fluorescence enhancement (PIFE) assays show binding on the 3' single-stranded overhang of model DNA substrates (>5 nucleotides) with no preference for the single-stranded/double-stranded (ss/ds) junction. Single-molecule PIFE experiments revealed three enhancement levels that correspond to three discrete binding sites at adjacent bases. The enzyme is able to transition between binding sites in both directions without dissociating from the nucleic acid. In contrast, the NS3 mutant W501A, which is unable to engage in stacking interactions with the DNA, is severely compromised in this switching activity. Altogether our data are consistent with a model for NS3 dynamics that favors ATP-independent random binding and sliding by one and two nucleotides along the overhang of the loading strand.
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Affiliation(s)
| | - Hsiao-Wei Liu
- Department
of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Nikoloz Shkriabai
- Center for Retrovirus Research and Comprehensive Cancer Center, College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and Comprehensive Cancer Center, College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Gonzalo Cosa
- Department of Chemistry and the Centre for Self-Assembled Chemical
Structures (CSACS/CRMAA), McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Matthias Götte
- Department
of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
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14
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Schumann S, Jackson BR, Yule I, Whitehead SK, Revill C, Foster R, Whitehouse A. Targeting the ATP-dependent formation of herpesvirus ribonucleoprotein particle assembly as an antiviral approach. Nat Microbiol 2016; 2:16201. [PMID: 27798559 DOI: 10.1038/nmicrobiol.2016.201] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/01/2016] [Indexed: 12/16/2022]
Abstract
Human herpesviruses are responsible for a range of debilitating acute and recurrent diseases, including a number of malignancies. Current treatments are limited to targeting the herpesvirus DNA polymerases, but with emerging viral resistance and little efficacy against the oncogenic herpesviruses, there is an urgent need for new antiviral strategies. Here, we describe a mechanism to inhibit the replication of the oncogenic herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV), by targeting the ATP-dependent formation of viral ribonucleoprotein particles (vRNPs). We demonstrate that small-molecule inhibitors which selectively inhibit the ATPase activity of the cellular human transcription/export complex (hTREX) protein UAP56 result in effective inhibition of vRNP formation, viral lytic replication and infectious virion production. Strikingly, as all human herpesviruses use conserved mRNA processing pathways involving hTREX components, we demonstrate the feasibility of this approach for pan-herpesvirus inhibition.
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Affiliation(s)
- Sophie Schumann
- School of Molecular and Cellular Biology, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, Leeds LS2 9JT, UK
| | - Brian R Jackson
- School of Molecular and Cellular Biology, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, Leeds LS2 9JT, UK
| | - Ian Yule
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | | | | | - Richard Foster
- Astbury Centre for Structural Molecular Biology, Leeds LS2 9JT, UK
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, Leeds LS2 9JT, UK
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15
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Nutho B, Meeprasert A, Chulapa M, Kungwan N, Rungrotmongkol T. Screening of hepatitis C NS5B polymerase inhibitors containing benzothiadiazine core: a steered molecular dynamics. J Biomol Struct Dyn 2016; 35:1743-1757. [PMID: 27236925 DOI: 10.1080/07391102.2016.1193444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hepatic C virus (HCV) is a global health problem, resulting in liver cirrhosis and inflammation that can develop to hepatocellular carcinoma and fatality. The NS5B polymerase of HCV plays an important role in viral RNA replication process, making it an attractive therapeutic target for design and development of anti-HCV drugs. To search new potent compounds against the HCV NS5B polymerase, the molecular docking and the steered molecular dynamics (SMD) simulation techniques were performed. The potential potent inhibitors of the NS5B polymerase were screened out from the ZINC database using structural similarity search and molecular docking technique. Five top-hit compounds (the ZINC compounds 49888724, 49054741, 49777239, 49793673, and 49780355) were then studied by the SMD simulations based on the hypothesis that a high rupture force relates to a high binding efficiency. The results demonstrated that the ZINC compound 49888724 had a greater maximum rupture force, reflecting a good binding strength and inhibitory potency than known inhibitors and the rest four ZINC compounds. Therefore, our finding indicated that the ZINC compound 49888724 is a potential candidate to be a novel NS5B inhibitor for further design. Besides, the van der Waals interaction could be considered as the main contribution for stabilizing the NS5B-ligand complex.
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Affiliation(s)
- Bodee Nutho
- a Program in Biotechnology, Faculty of Science , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Arthitaya Meeprasert
- b Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Methat Chulapa
- b Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Nawee Kungwan
- c Department of Chemistry, Faculty of Science , Chiang Mai University , Chiang Mai 50200 , Thailand
| | - Thanyada Rungrotmongkol
- b Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science , Chulalongkorn University , Bangkok 10330 , Thailand.,d PhD Program in Bioinformatics and Computational Biology, Faculty of Science , Chulalongkorn University , Bangkok 10330 , Thailand
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16
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Zhang JK, Ma XF, Wang XW, Cai JQ, Wu XL, Niu YP, Zhou N, Hua RM. X-ray structure and conformational study of tris(2-(dimethylamino)phenyl)methanol salt derivatives: Roles of anions and hydrogen bond. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.07.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Mao J, Eberle K, Zhang J, Rodriguez C, Xi Z, Pericàs MA, Walsh PJ. Synthesis of triarylmethanols via tandem arylation/oxidation of diarylmethanes. Tetrahedron Lett 2015; 56:3604-3607. [PMID: 26034337 PMCID: PMC4448728 DOI: 10.1016/j.tetlet.2015.01.189] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A tandem arylation/oxidation of diarylmethanes for the convenient synthesis of unsymmetrical triarylmethanols bearing different aryl and heteroaryl groups is described. A Pd(OAc)2-NiXantphos catalyst system efficiently catalyzed arylation of weakly acidic sp3-hybridized C-H bonds of diarylmethanes with aryl bromides, and the arylation products were then oxidized in situ to carbinols by simply opening the reaction flasks to air. The triarylmethanol products were obtained in 35-98% yield.
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Affiliation(s)
- Jianyou Mao
- Department of Applied Chemistry, China Agricultural University, 2 West Yuanmingyuan Road, Beijing 100193, P. R. China
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104–6323, United States
| | - Kelly Eberle
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104–6323, United States
| | - Jiadi Zhang
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104–6323, United States
| | - Carles Rodriguez
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Zhenfeng Xi
- Beijing National Laboratory for Molecular Sciences, and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, China
| | - Miquel A. Pericàs
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain
- Departament de Química Orgànica, Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Patrick J. Walsh
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104–6323, United States
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18
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Unzippers, resolvers and sensors: a structural and functional biochemistry tale of RNA helicases. Int J Mol Sci 2015; 16:2269-93. [PMID: 25622248 PMCID: PMC4346836 DOI: 10.3390/ijms16022269] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/09/2015] [Accepted: 01/12/2015] [Indexed: 12/28/2022] Open
Abstract
The centrality of RNA within the biological world is an irrefutable fact that currently attracts increasing attention from the scientific community. The panoply of functional RNAs requires the existence of specific biological caretakers, RNA helicases, devoted to maintain the proper folding of those molecules, resolving unstable structures. However, evolution has taken advantage of the specific position and characteristics of RNA helicases to develop new functions for these proteins, which are at the interface of the basic processes for transference of information from DNA to proteins. RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Structural biology studies during the last decade, founded in X-ray crystallography, have characterized in detail several RNA-helicases. This comprehensive review summarizes the structural knowledge accumulated in the last two decades within this family of proteins, with special emphasis on the structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes.
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19
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Docking studies of Pakistani HCV NS3 helicase: a possible antiviral drug target. PLoS One 2014; 9:e106339. [PMID: 25188400 PMCID: PMC4154687 DOI: 10.1371/journal.pone.0106339] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 07/19/2014] [Indexed: 01/02/2023] Open
Abstract
The nonstructural protein 3 (NS3) of hepatitis C virus (HCV) helicase is believed to be essential for viral replication and has become an attractive target for the development of antiviral drugs. The study of helicase is useful for elucidating its involvement in positive sense single-stranded RNA virus replication and to serve as templates for the design of novel antiviral drugs. In recent years, several models have been proposed on the conformational change leading to protein movement and RNA unwinding. Some compounds have been recently reported to inhibit the helicase and these include small molecules, RNA aptamers and antibodies. The current study is designed to help gain insights for the consideration of potential inhibitors for Pakistani HCV NS3 helicase protein. We have cloned, expressed and purified HCV NS3 helicase from Pakistani HCV serum samples and determined its 3D structure and employed it further in computational docking analysis to identify inhibitors against HCV genotype 3a (GT3a),including six antiviral key molecules such as quercetin, beta-carotene, resveratrol, catechins, lycopene and lutein. The conformation obtained after docking showed good hydrogen bond (HBond) interactions with best docking energy for quercetin and catechins followed by resveratrol and lutein. These anti-helicase key molecules will offer an alternative attraction to target the viral helicase, due to the current limitation with the interferon resistance treatment and presences of high rate of resistance in anti-protease inhibitor classes.
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20
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Unique helicase determinants in the essential conjugative TraI factor from Salmonella enterica serovar Typhimurium plasmid pCU1. J Bacteriol 2014; 196:3082-90. [PMID: 24936053 DOI: 10.1128/jb.01496-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The widespread development of multidrug-resistant bacteria is a major health emergency. Conjugative DNA plasmids, which harbor a wide range of antibiotic resistance genes, also encode the protein factors necessary to orchestrate the propagation of plasmid DNA between bacterial cells through conjugative transfer. Successful conjugative DNA transfer depends on key catalytic components to nick one strand of the duplex DNA plasmid and separate the DNA strands while cell-to-cell transfer occurs. The TraI protein from the conjugative Salmonella plasmid pCU1 fulfills these key catalytic roles, as it contains both single-stranded DNA-nicking relaxase and ATP-dependent helicase domains within a single, 1,078-residue polypeptide. In this work, we unraveled the helicase determinants of Salmonella pCU1 TraI through DNA binding, ATPase, and DNA strand separation assays. TraI binds DNA substrates with high affinity in a manner influenced by nucleic acid length and the presence of a DNA hairpin structure adjacent to the nick site. TraI selectively hydrolyzes ATP, and mutations in conserved helicase motifs eliminate ATPase activity. Surprisingly, the absence of a relatively short (144-residue) domain at the extreme C terminus of the protein severely diminishes ATP-dependent strand separation. Collectively, these data define the helicase motifs of the conjugative factor TraI from Salmonella pCU1 and reveal a previously uncharacterized C-terminal functional domain that uncouples ATP hydrolysis from strand separation activity.
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21
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Coutard B, Decroly E, Li C, Sharff A, Lescar J, Bricogne G, Barral K. Assessment of Dengue virus helicase and methyltransferase as targets for fragment-based drug discovery. Antiviral Res 2014; 106:61-70. [DOI: 10.1016/j.antiviral.2014.03.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/14/2014] [Accepted: 03/18/2014] [Indexed: 12/18/2022]
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22
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Lou Z, Sun Y, Rao Z. Current progress in antiviral strategies. Trends Pharmacol Sci 2014; 35:86-102. [PMID: 24439476 PMCID: PMC7112804 DOI: 10.1016/j.tips.2013.11.006] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/23/2013] [Accepted: 11/26/2013] [Indexed: 02/07/2023]
Abstract
Antiviral agents function as either viral targets or host factors. Virus-targeting antivirals (VTAs) function through a direct (DVTAs) or an indirect (InDVTAs) method in the viral life cycle. Host-targeting antivirals (HTAs) include reagents that target the host proteins that are involved in the viral life cycle.
The prevalence of chronic viral infectious diseases, such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus; the emergence and re-emergence of new viral infections, such as picornaviruses and coronaviruses; and, particularly, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Increased understanding of the molecular mechanisms of viral infection has provided great potential for the discovery of new antiviral agents that target viral proteins or host factors. Virus-targeting antivirals can function directly or indirectly to inhibit the biological functions of viral proteins, mostly enzymatic activities, or to block viral replication machinery. Host-targeting antivirals target the host proteins that are involved in the viral life cycle, regulating the function of the immune system or other cellular processes in host cells. Here we review key targets and considerations for the development of both antiviral strategies.
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Affiliation(s)
- Zhiyong Lou
- Laboratory of Structural Biology and MOE Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, 100084, China.
| | - Yuna Sun
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China
| | - Zihe Rao
- Laboratory of Structural Biology and MOE Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, 100084, China; National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China.
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23
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Hepatitis C virus NS3 inhibitors: current and future perspectives. BIOMED RESEARCH INTERNATIONAL 2013; 2013:467869. [PMID: 24282816 PMCID: PMC3825274 DOI: 10.1155/2013/467869] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 09/08/2013] [Indexed: 12/24/2022]
Abstract
Currently, hepatitis C virus (HCV) infection is considered a serious health-care problem all over the world. A good number of direct-acting antivirals (DAAs) against HCV infection are in clinical progress including NS3-4A protease inhibitors, RNA-dependent RNA polymerase inhibitors, and NS5A inhibitors as well as host targeted inhibitors. Two NS3-4A protease inhibitors (telaprevir and boceprevir) have been recently approved for the treatment of hepatitis C in combination with standard of care (pegylated interferon plus ribavirin). The new therapy has significantly improved sustained virologic response (SVR); however, the adverse effects associated with this therapy are still the main concern. In addition to the emergence of viral resistance, other targets must be continually developed. One such underdeveloped target is the helicase portion of the HCV NS3 protein. This review article summarizes our current understanding of HCV treatment, particularly with those of NS3 inhibitors.
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Shadrick WR, Mukherjee S, Hanson AM, Sweeney NL, Frick DN. Aurintricarboxylic acid modulates the affinity of hepatitis C virus NS3 helicase for both nucleic acid and ATP. Biochemistry 2013; 52:6151-9. [PMID: 23947785 DOI: 10.1021/bi4006495] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aurintricarboxylic acid (ATA) is a potent inhibitor of many enzymes needed for cell and virus replication, such as polymerases, helicases, nucleases, and topoisomerases. This study examines how ATA interacts with the helicase encoded by the hepatitis C virus (HCV) and reveals that ATA interferes with both nucleic acid and ATP binding to the enzyme. We show that ATA directly binds HCV helicase to prevent the enzyme from interacting with nucleic acids and to modulate the affinity of HCV helicase for ATP, the fuel for helicase action. Amino acid substitutions in the helicase DNA binding cleft or its ATP binding site alter the ability of ATA to disrupt helicase-DNA interactions. These data, along with molecular modeling results, support the notion that an ATA polymer binds between Arg467 and Glu493 to prevent the helicase from binding either ATP or nucleic acids. We also characterize how ATA affects the kinetics of helicase-catalyzed ATP hydrolysis, and thermodynamic parameters describing the direct interaction between HCV helicase and ATA using microcalorimetry. The thermodynamics of ATA binding to HCV helicase reveal that ATA binding does not mimic nucleic acid binding in that ATA binding is driven by a smaller enthalpy change and an increase in entropy.
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Affiliation(s)
- William R Shadrick
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
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25
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Zhu T, Cao S, Su PC, Patel R, Shah D, Chokshi HB, Szukala R, Johnson ME, Hevener KE. Hit identification and optimization in virtual screening: practical recommendations based on a critical literature analysis. J Med Chem 2013; 56:6560-72. [PMID: 23688234 DOI: 10.1021/jm301916b] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A critical analysis of virtual screening results published between 2007 and 2011 was performed. The activity of reported hit compounds from over 400 studies was compared to their hit identification criteria. Hit rates and ligand efficiencies were calculated to assist in these analyses, and the results were compared with factors such as the size of the virtual library and the number of compounds tested. A series of promiscuity, druglike, and ADMET filters were applied to the reported hits to assess the quality of compounds reported, and a careful analysis of a subset of the studies that presented hit optimization was performed. These data allowed us to make several practical recommendations with respect to selection of compounds for experimental testing, definition of hit identification criteria, and general virtual screening hit criteria to allow for realistic hit optimization. A key recommendation is the use of size-targeted ligand efficiency values as hit identification criteria.
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Affiliation(s)
- Tian Zhu
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago , 900 S. Ashland Avenue, Suite 3100, Chicago, Illinois 60607-7173, United States
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26
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Sweeney NL, Shadrick WR, Mukherjee S, Li K, Frankowski KJ, Schoenen FJ, Frick DN. Primuline derivatives that mimic RNA to stimulate hepatitis C virus NS3 helicase-catalyzed ATP hydrolysis. J Biol Chem 2013; 288:19949-57. [PMID: 23703611 DOI: 10.1074/jbc.m113.463166] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ATP hydrolysis fuels the ability of helicases and related proteins to translocate on nucleic acids and separate base pairs. As a consequence, nucleic acid binding stimulates the rate at which a helicase catalyzes ATP hydrolysis. In this study, we searched a library of small molecule helicase inhibitors for compounds that stimulate ATP hydrolysis catalyzed by the hepatitis C virus (HCV) NS3 helicase, which is an important antiviral drug target. Two compounds were found that stimulate HCV helicase-catalyzed ATP hydrolysis, both of which are amide derivatives synthesized from the main component of the yellow dye primuline. Both compounds possess a terminal pyridine moiety, which was critical for stimulation. Analogs lacking a terminal pyridine inhibited HCV helicase catalyzed ATP hydrolysis. Unlike other HCV helicase inhibitors, the stimulatory compounds differentiate between helicases isolated from various HCV genotypes and related viruses. The compounds only stimulated ATP hydrolysis catalyzed by NS3 purified from HCV genotype 1b. They inhibited helicases from other HCV genotypes (e.g. 1a and 2a) or related flaviviruses (e.g. Dengue virus). The stimulatory compounds interacted with HCV helicase in the absence of ATP with dissociation constants of about 2 μM. Molecular modeling and site-directed mutagenesis studies suggest that the stimulatory compounds bind in the HCV helicase RNA-binding cleft near key residues Arg-393, Glu-493, and Ser-231.
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Affiliation(s)
- Noreena L Sweeney
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA
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Shadrick WR, Ndjomou J, Kolli R, Mukherjee S, Hanson AM, Frick DN. Discovering new medicines targeting helicases: challenges and recent progress. ACTA ACUST UNITED AC 2013; 18:761-81. [PMID: 23536547 PMCID: PMC4427233 DOI: 10.1177/1087057113482586] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Helicases are ubiquitous motor proteins that separate and/or rearrange nucleic acid duplexes in reactions fueled by adenosine triphosphate (ATP) hydrolysis. Helicases encoded by bacteria, viruses, and human cells are widely studied targets for new antiviral, antibiotic, and anticancer drugs. This review summarizes the biochemistry of frequently targeted helicases. These proteins include viral enzymes from herpes simplex virus, papillomaviruses, polyomaviruses, coronaviruses, the hepatitis C virus, and various flaviviruses. Bacterial targets examined include DnaB-like and RecBCD-like helicases. The human DEAD-box protein DDX3 is the cellular antiviral target discussed, and cellular anticancer drug targets discussed are the human RecQ-like helicases and eIF4A. We also review assays used for helicase inhibitor discovery and the most promising and common helicase inhibitor chemotypes, such as nucleotide analogues, polyphenyls, metal ion chelators, flavones, polycyclic aromatic polymers, coumarins, and various DNA binding pharmacophores. Also discussed are common complications encountered while searching for potent helicase inhibitors and possible solutions for these problems.
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Affiliation(s)
- William R Shadrick
- Department of Chemistry & Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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28
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Salam KA, Furuta A, Noda N, Tsuneda S, Sekiguchi Y, Yamashita A, Moriishi K, Nakakoshi M, Tsubuki M, Tani H, Tanaka J, Akimitsu N. Psammaplin A inhibits hepatitis C virus NS3 helicase. J Nat Med 2013; 67:765-72. [PMID: 23359228 DOI: 10.1007/s11418-013-0742-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 01/06/2013] [Indexed: 01/04/2023]
Abstract
Hepatitis C virus (HCV) is the causative agent of hepatitis C, a chronic infectious disease that can lead to development of hepatocellular carcinoma. The NS3 nucleoside triphosphatase (NTPase)/helicase has an essential role in HCV replication, and is therefore an attractive target for direct-acting antiviral strategies. In this study, we employed high-throughput screening using a photo-induced electron transfer (PET) system to identify an inhibitor of NS3 helicase from marine organism extracts. We successfully identified psammaplin A as a novel NS3 inhibitor. The dose-response relationship clearly demonstrates the inhibition of NS3 RNA helicase and ATPase activities by psammaplin A, with IC₅₀ values of 17 and 32 μM, respectively. Psammaplin A has no influence on the apparent Km value (0.4 mM) of NS3 ATPase activity, and acts as a non-competitive inhibitor. Additionally, it inhibits the binding of NS3 to single-stranded RNA in a dose-dependent manner. Furthermore, psammaplin A shows an inhibitory effect on viral replication, with EC₅₀ values of 6.1 and 6.3 μM in subgenomic replicon cells derived from genotypes 1b and 2a, respectively. We postulate that psammaplin A is a potential anti-viral agent through the inhibition of ATPase, RNA binding and helicase activities of NS3.
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Affiliation(s)
- Kazi Abdus Salam
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
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29
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Mukherjee S, Hanson AM, Shadrick WR, Ndjomou J, Sweeney NL, Hernandez JJ, Bartczak D, Li K, Frankowski KJ, Heck JA, Arnold LA, Schoenen FJ, Frick DN. Identification and analysis of hepatitis C virus NS3 helicase inhibitors using nucleic acid binding assays. Nucleic Acids Res 2012; 40:8607-21. [PMID: 22740655 PMCID: PMC3458564 DOI: 10.1093/nar/gks623] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Typical assays used to discover and analyze small molecules that inhibit the hepatitis C virus (HCV) NS3 helicase yield few hits and are often confounded by compound interference. Oligonucleotide binding assays are examined here as an alternative. After comparing fluorescence polarization (FP), homogeneous time-resolved fluorescence (HTRF®; Cisbio) and AlphaScreen® (Perkin Elmer) assays, an FP-based assay was chosen to screen Sigma’s Library of Pharmacologically Active Compounds (LOPAC) for compounds that inhibit NS3-DNA complex formation. Four LOPAC compounds inhibited the FP-based assay: aurintricarboxylic acid (ATA) (IC50 = 1.4 μM), suramin sodium salt (IC50 = 3.6 μM), NF 023 hydrate (IC50 = 6.2 μM) and tyrphostin AG 538 (IC50 = 3.6 μM). All but AG 538 inhibited helicase-catalyzed strand separation, and all but NF 023 inhibited replication of subgenomic HCV replicons. A counterscreen using Escherichia coli single-stranded DNA binding protein (SSB) revealed that none of the new HCV helicase inhibitors were specific for NS3h. However, when the SSB-based assay was used to analyze derivatives of another non-specific helicase inhibitor, the main component of the dye primuline, it revealed that some primuline derivatives (e.g. PubChem CID50930730) are up to 30-fold more specific for HCV NS3h than similarly potent HCV helicase inhibitors.
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Affiliation(s)
- Sourav Mukherjee
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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Abstract
RNA helicases unwind their RNA substrates in an ATP-dependent reaction, and are central to all cellular processes involving RNA. They have important roles in viral life cycles, where RNA helicases are either virus-encoded or recruited from the host. Vertebrate RNA helicases sense viral infections, and trigger the innate antiviral immune response. RNA helicases have been implicated in protozoic, bacterial and fungal infections. They are also linked to neurological disorders, cancer, and aging processes. Genome-wide studies continue to identify helicase genes that change their expression patterns after infection or disease outbreak, but the mechanism of RNA helicase action has been defined for only a few diseases. RNA helicases are prognostic and diagnostic markers and suitable drug targets, predominantly for antiviral and anti-cancer therapies. This review summarizes the current knowledge on RNA helicases in infection and disease, and their growing potential as drug targets.
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Affiliation(s)
- Lenz Steimer
- University of Muenster, Institute for Physical Chemistry, Muenster, Germany
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31
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Tang J, Huang ZM, Chen YY, Zhang ZH, Liu GL, Zhang J. A novel inhibitor of human La protein with anti-HBV activity discovered by structure-based virtual screening and in vitro evaluation. PLoS One 2012; 7:e36363. [PMID: 22558448 PMCID: PMC3338670 DOI: 10.1371/journal.pone.0036363] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 04/05/2012] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Over 350 million people worldwide are infected with hepatitis B virus (HBV), a major cause of liver failure and hepatocellular carcinoma. Current therapeutic agents are highly effective, but are also associated with development of viral resistance. Therefore, strategies for identifying other anti-HBV agents with specific, but distinctive mechanisms of action are needed. The human La (hLa) protein, which forms a stabilizing complex with HBV RNA ribonucleoprotein to promote HBV replication, is a promising target of molecular therapy. AIMS This study aimed to discover novel inhibitors of hLa that could inhibit HBV replication and expression. METHODS A multistage molecular docking approach was used to screen a Specs database and an in-house library against hLa binding sites. Sequential in vitro evaluations were performed to detect potential compounds with high scores in HepG2.2.15 cells. RESULTS Of the 26 potential compounds with high scores chosen for experimental verification, 12 had HBV DNA inhibition ratios of less than 50% with P<0.05. Six had significant inhibition of HBV e antigen (HBeAg) levels, and 13 had significant inhibition of HBV surface antigen (HBsAg) levels by in vitro assays. Compounds HBSC-11, HBSC-15 and HBSC-34 (HBSC is system prefix for active compounds screened by the library) were selected for evaluation. HBSC-11 was found to have an obvious inhibitory effect on hLa transcription and expression. CONCLUSIONS Our findings suggest that anti-HBV activity of HBSC-11 may be mediated by a reduction in hLa levels. In addition, our data suggest the potential clinical use of hLa inhibitors, such as HBSC-11, for treating HBV infection.
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Affiliation(s)
- Jing Tang
- Department of Pharmacy, First People's Hospital Affiliated with Shanghai JiaoTong University, Shanghai, China
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Li K, Frankowski KJ, Belon CA, Neuenswander B, Ndjomou J, Hanson AM, Shanahan MA, Schoenen FJ, Blagg BSJ, Aubé J, Frick DN. Optimization of potent hepatitis C virus NS3 helicase inhibitors isolated from the yellow dyes thioflavine S and primuline. J Med Chem 2012; 55:3319-30. [PMID: 22409723 DOI: 10.1021/jm300021v] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A screen for hepatitis C virus (HCV) NS3 helicase inhibitors revealed that the commercial dye thioflavine S was the most potent inhibitor of NS3-catalyzed DNA and RNA unwinding in the 827-compound National Cancer Institute Mechanistic Set. Thioflavine S and the related dye primuline were separated here into their pure components, all of which were oligomers of substituted benzothiazoles. The most potent compound (P4), a benzothiazole tetramer, inhibited unwinding >50% at 2 ± 1 μM, inhibited the subgenomic HCV replicon at 10 μM, and was not toxic at 100 μM. Because P4 also interacted with DNA, more specific analogues were synthesized from the abundant dimeric component of primuline. Some of the 32 analogues prepared retained ability to inhibit HCV helicase but did not appear to interact with DNA. The most potent of these specific helicase inhibitors (compound 17) was active against the replicon and inhibited the helicase more than 50% at 2.6 ± 1 μM.
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Affiliation(s)
- Kelin Li
- University of Kansas Specialized Chemistry Center, University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, USA
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Deore RR, Chen GS, Chang PT, Chern TR, Lai SY, Chuang MH, Lin JH, Kung FL, Chen CS, Chiou CT, Chern JW. Discovery of N-Arylalkyl-3-hydroxy-4-oxo-3,4-dihydroquinazolin-2-carboxamide Derivatives as HCV NS5B Polymerase Inhibitors. ChemMedChem 2012; 7:850-60. [DOI: 10.1002/cmdc.201200058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Indexed: 11/06/2022]
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Peng HK, Lin CK, Yang SY, Tseng CK, Tzeng CC, Lee JC, Yang SC. Synthesis and anti-HCV activity evaluation of anilinoquinoline derivatives. Bioorg Med Chem Lett 2012; 22:1107-10. [DOI: 10.1016/j.bmcl.2011.11.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 11/25/2011] [Accepted: 11/28/2011] [Indexed: 12/12/2022]
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Rehman S, Ashfaq UA, Javed T. Antiviral drugs against hepatitis C virus. GENETIC VACCINES AND THERAPY 2011; 9:11. [PMID: 21699699 PMCID: PMC3136400 DOI: 10.1186/1479-0556-9-11] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 06/23/2011] [Indexed: 12/20/2022]
Abstract
Hepatitis C virus (HCV) infection is a major worldwide problem causes acute and chronic HCV infection. Current treatment of HCV includes pegylated interferon-α (PEG IFN- α) plus ribavirin (RBV) which has significant side effects depending upon the type of genotype. Currently, there is a need to develop antiviral agents, both from synthetic chemistry and Herbal sources. In the last decade, various novel HCV replication, helicase and entry inhibitors have been synthesized and some of which have been entered in different phases of clinical trials. Successful results have been acquired by executing combinational therapy of compounds with standard regime in different HCV replicons. Even though, diverse groups of compounds have been described as antiviral targets against HCV via Specifically Targeted Antiviral Therapy for hepatitis C (STAT-C) approach (in which compounds are designed to directly block HCV or host proteins concerned in HCV replication), still there is a need to improve the properties of existing antiviral compounds. In this review, we sum up potent antiviral compounds against entry, unwinding and replication of HCV and discussed their activity in combination with standard therapy. Conclusively, further innovative research on chemical compounds will lead to consistent standard therapy with fewer side effects.
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Affiliation(s)
- Sidra Rehman
- Division of Molecular Medicine, National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Usman A Ashfaq
- Division of Molecular Medicine, National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tariq Javed
- Division of Molecular Medicine, National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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Hwu JR, Lin SY, Tsay SC, De Clercq E, Leyssen P, Neyts J. Coumarin−Purine Ribofuranoside Conjugates as New Agents against Hepatitis C Virus. J Med Chem 2011; 54:2114-26. [DOI: 10.1021/jm101337v] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jih Ru Hwu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C
- Department of Chemistry, National Central University, Jhongli City, Taiwan 32001, R.O.C
| | - Shu-Yu Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C
| | - Shwu-Chen Tsay
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C
| | - Erik De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Pieter Leyssen
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Johan Neyts
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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Lee YH, Wei CW, Wang JJ, Chiou CT. Rana catesbeiana ribonuclease inhibits Japanese encephalitis virus (JEV) replication and enhances apoptosis of JEV-infected BHK-21 cells. Antiviral Res 2011; 89:193-8. [DOI: 10.1016/j.antiviral.2011.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 12/20/2010] [Accepted: 01/10/2011] [Indexed: 02/03/2023]
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Kesel AJ. Broad-spectrum antiviral activity including human immunodeficiency and hepatitis C viruses mediated by a novel retinoid thiosemicarbazone derivative. Eur J Med Chem 2011; 46:1656-64. [PMID: 21376429 DOI: 10.1016/j.ejmech.2011.02.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 02/06/2011] [Accepted: 02/09/2011] [Indexed: 12/18/2022]
Abstract
Aromatic aldehyde-derived thiosemicarbazones 4-6, the S-substituted modified thiosemicarbazones 7/8, and a vitamin A-derived (retinoid) thiosemicarbazone derivative 12 were investigated as inhibitors of human hepatitis C virus (HCV) subgenomic RNA replicon Huh7 ET (luc-ubi-neo/ET) replication. Compounds 4-6 and 12 were found to be potent suppressors of HCV RNA replicon replication. The trifluoromethoxy-substituted thiosemicarbazone 6 and the retinoid thiosemicarbazone derivative 12 were even superior in selectivity to the included reference agent recombinant human alpha-interferon-2b, showing potencies in the nanomolar range of concentration. In addition, compounds 5, 6, 8 and 12 were tested as inhibitors of cytopathic effect (CPE) induced by human varicella-zoster virus (VZV) and/or human cytomegalovirus (HCMV). Compounds 4-6, 8 and 12 were additionally examined as inhibitors of CPE induced by cowpox virus and vaccinia virus. Thiosemicarbazone 4 was inhibitory on cowpox and vaccinia virus replication comparable in potency and selectivity to the reference agent cidofovir. Retinoid thiosemicarbazone derivative 12 was active as micromolar inhibitor of VZV, HCMV, and, in addition, human immunodeficiency virus type 1 (HIV-1) replication. These results indicate that thiosemicarbazone derivatives are appropriate lead structures to be evaluated in targeted antiviral therapies for hepatitis C (STAT-C), and that the vitamin A-related thiosemicarbazone derivative 12 emerges as a broad-spectrum antiviral agent, co-suppressing the multiplication of important RNA and DNA viruses.
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Briguglio I, Piras S, Corona P, Carta A. Inhibition of RNA Helicases of ssRNA(+) Virus Belonging to Flaviviridae, Coronaviridae and Picornaviridae Families. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2010; 2011:213135. [PMID: 27516903 PMCID: PMC4970650 DOI: 10.1155/2011/213135] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 10/03/2010] [Accepted: 10/25/2010] [Indexed: 01/13/2023]
Abstract
Many viral pathogens encode the motor proteins named RNA helicases which display various functions in genome replication. General strategies to design specific and selective drugs targeting helicase for the treatment of viral infections could act via one or more of the following mechanisms: inhibition of the NTPase activity, by interferences with ATP binding and therefore by limiting the energy required for the unwinding and translocation, or by allosteric mechanism and therefore by stabilizing the conformation of the enzyme in low helicase activity state; inhibition of nucleic acids binding to the helicase; inhibition of coupling of ATP hydrolysis to unwinding; inhibition of unwinding by sterically blocking helicase translocation. Recently, by in vitro screening studies, it has been reported that several benzotriazole, imidazole, imidazodiazepine, phenothiazine, quinoline, anthracycline, triphenylmethane, tropolone, pyrrole, acridone, small peptide, and Bananin derivatives are endowed with helicase inhibition of pathogen viruses belonging to Flaviviridae, Coronaviridae, and Picornaviridae families.
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Affiliation(s)
- Irene Briguglio
- Department of Medicinal and Toxicological Chemistry, University of Sassari, Via Muroni 23/a, 07100 Sassari, Italy
| | - Sandra Piras
- Department of Medicinal and Toxicological Chemistry, University of Sassari, Via Muroni 23/a, 07100 Sassari, Italy
| | - Paola Corona
- Department of Medicinal and Toxicological Chemistry, University of Sassari, Via Muroni 23/a, 07100 Sassari, Italy
| | - Antonio Carta
- Department of Medicinal and Toxicological Chemistry, University of Sassari, Via Muroni 23/a, 07100 Sassari, Italy
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Gemma S, Butini S, Campiani G, Brindisi M, Zanoli S, Romano MP, Tripaldi P, Savini L, Fiorini I, Borrelli G, Novellino E, Maga G. Discovery of potent nucleotide-mimicking competitive inhibitors of hepatitis C virus NS3 helicase. Bioorg Med Chem Lett 2010; 21:2776-9. [PMID: 20880703 DOI: 10.1016/j.bmcl.2010.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 08/31/2010] [Accepted: 09/01/2010] [Indexed: 02/04/2023]
Abstract
Among the enzymes involved in the life cycle of HCV, the non-structural protein NS3, with its double function of protease and NTPase/helicase, is essential for the virus replication. Exploiting our previous knowledge in the development of nucleotide-mimicking NS3 helicase (NS3h) inhibitors endowed with key structural and electronic features necessary for an optimal ligand-enzyme interaction, we developed the tetrahydroacridinyl derivative 3a as the most potent NS3h competitive inhibitor reported to date (HCV NS3h K(i)=20 nM).
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Affiliation(s)
- Sandra Gemma
- European Research Centre for Drug Discovery and Development, Università di Siena, via Aldo Moro, 53100 Siena, Italy
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Lemon SM, McKeating JA, Pietschmann T, Frick DN, Glenn JS, Tellinghuisen TL, Symons J, Furman PA. Development of novel therapies for hepatitis C. Antiviral Res 2010; 86:79-92. [PMID: 20417376 DOI: 10.1016/j.antiviral.2010.02.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 01/30/2010] [Accepted: 02/01/2010] [Indexed: 10/19/2022]
Abstract
The current standard of care for the treatment of hepatitis C virus (HCV) infection is a combination of pegylated IFN and ribavirin (Peg-IFN/RBV). Because of the adverse effects associated with both IFN and ribavirin and because Peg-IFN/RBV provides only about a 45-50% sustained virological response (SVR, undetectable HCV RNA for greater than 24 weeks after cessation of therapy) in genotype 1-infected individuals, there is a need for more potent anti-HCV compounds with fewer adverse effects. The twenty-first International Conference on Antiviral Research held in May 2009 in Miami Beach, Florida, featured a special session focused on novel targets for HCV therapy. The session included presentations by world-renowned experts in HCV virology and covered a diverse array of potential targets for the development of new classes of HCV therapies. This review contains concise summaries of discussed topics that included the innate immune response, virus entry, the NS2 protease, the NS3 helicase, NS4B, and NS5A. Each presenter discussed the current knowledge of these targets and provided examples of recent scientific breakthroughs that are enhancing our understanding of these targets. As our understanding of the role of these novel anti-HCV targets increases so will our ability to discover new, more safe and effective anti-HCV therapies.
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Affiliation(s)
- Stanley M Lemon
- Center for Hepatitis Research, Institute for Human Infections and Immunity, University of Texas Medical Branch at Galveston, Galveston, TX, USA
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Najda-Bernatowicz A, Krawczyk M, Stankiewicz-Drogoń A, Bretner M, Boguszewska-Chachulska AM. Studies on the anti-hepatitis C virus activity of newly synthesized tropolone derivatives: identification of NS3 helicase inhibitors that specifically inhibit subgenomic HCV replication. Bioorg Med Chem 2010; 18:5129-36. [PMID: 20579888 DOI: 10.1016/j.bmc.2010.05.066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 05/21/2010] [Accepted: 05/25/2010] [Indexed: 10/19/2022]
Abstract
We synthesized new tropolone derivatives substituted with cyclic amines: piperidine, piperazine or pyrrolidine. The most active anti-helicase compound (IC50=3.4 microM), 3,5,7-tri[(4'-methylpiperazin-1'-yl)methyl]tropolone (2), inhibited RNA replication by 50% at 46.9 microM (EC50) and exhibited the lowest cytotoxicity (CC50)>1 mM resulting in a selectivity index (SI=CC50/EC50)>21. The most efficient replication inhibitor, 3,5,7-tri[(4'-methylpiperidin-1'-yl)methyl]tropolone (6), inhibited RNA replication with an EC50 of 32.0 microM and a SI value of 17.4, whereas 3,5,7-tri[(3'-methylpiperidin-1'-yl)methyl]tropolone (7) exhibited a slightly lower activity with an EC50 of 35.6 microM and a SI of 9.8.
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Belon CA, High YD, Lin TI, Pauwels F, Frick DN. Mechanism and specificity of a symmetrical benzimidazolephenylcarboxamide helicase inhibitor. Biochemistry 2010; 49:1822-32. [PMID: 20108979 DOI: 10.1021/bi901974a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This study examines the effects of 1-N,4-N-bis[4-(1H-benzimidazol-2-yl)phenyl]benzene-1,4-dicarboxamide ((BIP)(2)B) on the NS3 helicase encoded by the hepatitis C virus (HCV). Molecular beacon-based helicase assays were used to show that (BIP)(2)B inhibits the ability of HCV helicase to separate a variety of RNA and DNA duplexes with half-maximal inhibitory concentrations ranging from 0.7 to 5 microM, depending on the nature of the substrate. In single turnover assays, (BIP)(2)B only inhibited unwinding reactions when it was preincubated with the helicase-nucleic acid complex. (BIP)(2)B quenched NS3 intrinsic protein fluorescence with an apparent dissociation constant of 5 microM, and in the presence of (BIP)(2)B, HCV helicase did not appear to interact with a fluorescent DNA oligonucleotide. In assays monitoring HCV helicase-catalyzed ATP hydrolysis, (BIP)(2)B only inhibited helicase-catalyzed ATP hydrolysis in the presence of intermediate concentrations of RNA, suggesting RNA and (BIP)(2)B compete for the same binding site. HCV helicases isolated from various HCV genotypes were similarly sensitive to (BIP)(2)B, with half-maximal inhibitory concentrations ranging from 0.7 to 2.4 microM. (BIP)(2)B also inhibited ATP hydrolysis catalyzed by related helicases from Dengue virus, Japanese encephalitis virus, and humans. (BIP)(2)B appeared to bind the HCV and human proteins with similar affinity (K(i) = 7 and 8 microM, respectively), but it bound the flavivirus proteins up to 270 times more tightly. Results are discussed in light of a molecular model of a (BIP)(2)B-HCV helicase complex, which is unable to bind nucleic acid, thus preventing the enzyme from separating double-stranded nucleic acid.
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Affiliation(s)
- Craig A Belon
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
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Delang L, Coelmont L, Neyts J. Antiviral therapy for hepatitis C virus: beyond the standard of care. Viruses 2010; 2:826-866. [PMID: 21994657 PMCID: PMC3185663 DOI: 10.3390/v2040826] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 03/09/2010] [Accepted: 03/17/2010] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) represents a major health burden, with an estimated 180 million chronically infected individuals worldwide. These patients are at increased risk of developing liver cirrhosis and hepatocellular carcinoma. Infection with HCV is the leading cause of liver transplantation in the Western world. Currently, the standard of care (SoC) consists of pegylated interferon alpha (pegIFN-α) and ribavirin (RBV). However this therapy has a limited efficacy and is associated with serious side effects. Therefore more tolerable, highly potent inhibitors of HCV replication are urgently needed. Both Specifically Targeted Antiviral Therapy for HCV (STAT-C) and inhibitors that are believed to interfere with the host-viral interaction are discussed.
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Affiliation(s)
| | | | - Johan Neyts
- Rega Institute for Medical Research, KULeuven, Minderbroedersstraat 10, 3000 Leuven, Belgium; E-Mails: (L.D.); (L.C.)
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Abstract
Current HCV therapy presents many side effects, is inadequate in treating all patients infected with the disease, and it is likely that future therapy will involve the specific targeting of multiple viral enzymes. The HCV NS2/3 protease is a dimeric autocatalytic protease that cleaves the viral polyprotein between NS2 and NS3. NS2/3 cleavage has been shown to be absolutely required for genome replication and viral infectivity in a chimpanzee and, therefore, NS2/3 has been suggested to be a promising target for future HCV drug development. This article focuses on the characterization of NS2/3 processing, the methods developed and progress achieved towards the generation of NS2/3 cleavage inhibitors. The challenges involved in developing active site inhibitors of this enzyme, as well as alternative approaches to inhibiting HCV replication through the NS2/3 and NS2 proteins, are also discussed.
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Affiliation(s)
- Sarah Welbourn
- Goodman Cancer Centre & Department of Biochemistry, McGill University, Montréal, Québec, Canada, H3A 1A3
| | - Arnim Pause
- Goodman Cancer Centre & Department of Biochemistry, McGill University, Cancer Pavilion, room 618, 1160 av. des Pins Ouest, Montréal, Québec, Canada, H3A 1A3
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