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Latendresse M, Malerich JP, Herson J, Krummenacker M, Szeto J, Vu VA, Collins N, Madrid PB. SynRoute: A Retrosynthetic Planning Software. J Chem Inf Model 2023; 63:5484-5495. [PMID: 37635298 PMCID: PMC10498441 DOI: 10.1021/acs.jcim.3c00491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Indexed: 08/29/2023]
Abstract
Computer-assisted synthetic planning has seen major advancements that stem from the availability of large reaction databases and artificial intelligence methodologies. SynRoute is a new retrosynthetic planning software tool that uses a relatively small number of general reaction templates, currently 263, along with a literature-based reaction database to find short, practical synthetic routes for target compounds. For each reaction template, a machine learning classifier is trained using data from the Pistachio reaction database to predict whether new computer-generated reactions based on the template are likely to work experimentally in the laboratory. This reaction generation methodology is used together with a vectorized Dijkstra-like search of top-scoring routes organized by synthetic strategies for easy browsing by a synthetic chemist. SynRoute was able to find routes for an average of 83% of compounds based on selection of random subsets of drug-like compounds from the ChEMBL database. Laboratory evaluation of 12 routes produced by SynRoute, to synthesize compounds not from the previous random subsets, demonstrated the ability to produce feasible overall synthetic strategies for all compounds evaluated.
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Affiliation(s)
| | | | - James Herson
- SRI International, 333 Ravenswood Ave, Menlo Park, California 94025, United States
| | - Markus Krummenacker
- SRI International, 333 Ravenswood Ave, Menlo Park, California 94025, United States
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2
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McNaughton AD, Joshi RP, Knutson CR, Fnu A, Luebke KJ, Malerich JP, Madrid PB, Kumar N. Machine Learning Models for Predicting Molecular UV-Vis Spectra with Quantum Mechanical Properties. J Chem Inf Model 2023; 63:1462-1471. [PMID: 36847578 DOI: 10.1021/acs.jcim.2c01662] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Accurate understanding of ultraviolet-visible (UV-vis) spectra is critical for the high-throughput synthesis of compounds for drug discovery. Experimentally determining UV-vis spectra can become expensive when dealing with a large quantity of novel compounds. This provides us an opportunity to drive computational advances in molecular property predictions using quantum mechanics and machine learning methods. In this work, we use both quantum mechanically (QM) predicted and experimentally measured UV-vis spectra as input to devise four different machine learning architectures, UVvis-SchNet, UVvis-DTNN, UVvis-Transformer, and UVvis-MPNN, and assess the performance of each method. We find that the UVvis-MPNN model outperforms the other models when using optimized 3D coordinates and QM predicted spectra as input features. This model has the highest performance for predicting UV-vis spectra with a training RMSE of 0.06 and validation RMSE of 0.08. Most importantly, our model can be used for the challenging task of predicting differences in the UV-vis spectral signatures of regioisomers.
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Affiliation(s)
- Andrew D McNaughton
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Rajendra P Joshi
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Carter R Knutson
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Anubhav Fnu
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kevin J Luebke
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jeremiah P Malerich
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Peter B Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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3
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Madrid PB, Chang PY. Accelerating space radiation countermeasure development through drug repurposing. Life Sci Space Res (Amst) 2022; 35:30-35. [PMID: 36336366 DOI: 10.1016/j.lssr.2022.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/06/2022] [Accepted: 07/10/2022] [Indexed: 06/16/2023]
Abstract
The discovery of safe and effective radiation countermeasures (MCM) for long-duration spaceflight is challenging due to the complexity of the space radiation biology and high safety requirements. There are few if any clinically-validated molecular targets for this use case, and preclinical models have several known limitations. These challenges make the evaluation of existing FDA-approved drugs for this indication, or drug repurposing, an attractive strategy to accelerate space radiation countermeasure development. Drug repurposing offers several advantages over de novo drug discovery including established manufacturing methods, human clinical safety data, and well-understood dosing and pharmacokinetic considerations. There are limitations working with a fixed set of possible candidate compounds, but some properties of repurposed drugs can be tailored for well-defined new indications through reformulation and development of drug combinations. Drug repurposing is thus an attractive strategy for mitigating the high risks and costs of drug development and delivering new countermeasures to protect human from space radiation in long-term missions.
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Affiliation(s)
- P B Madrid
- SRI International, Biosciences Division, Menlo Park CA United States
| | - P Y Chang
- SRI International, Biosciences Division, Menlo Park CA United States.
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4
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Avital-Shmilovici M, Liu X, Shaler T, Lowenthal A, Bourbon P, Snider J, Tambo-Ong A, Repellin C, Yniguez K, Sambucetti L, Madrid PB, Collins N. Mega-High-Throughput Screening Platform for the Discovery of Biologically Relevant Sequence-Defined Non-Natural Polymers. ACS Cent Sci 2022; 8:86-101. [PMID: 35106376 PMCID: PMC8796305 DOI: 10.1021/acscentsci.1c01041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 06/14/2023]
Abstract
Combinatorial methods enable the synthesis of chemical libraries on scales of millions to billions of compounds, but the ability to efficiently screen and sequence such large libraries has remained a major bottleneck for molecular discovery. We developed a novel technology for screening and sequencing libraries of synthetic molecules of up to a billion compounds in size. This platform utilizes the fiber-optic array scanning technology (FAST) to screen bead-based libraries of synthetic compounds at a rate of 5 million compounds per minute (∼83 000 Hz). This ultra-high-throughput screening platform has been used to screen libraries of synthetic "self-readable" non-natural polymers that can be sequenced at the femtomole scale by chemical fragmentation and high-resolution mass spectrometry. The versatility and throughput of the platform were demonstrated by screening two libraries of non-natural polyamide polymers with sizes of 1.77M and 1B compounds against the protein targets K-Ras, asialoglycoprotein receptor 1 (ASGPR), IL-6, IL-6 receptor (IL-6R), and TNFα. Hits with low nanomolar binding affinities were found against all targets, including competitive inhibitors of K-Ras binding to Raf and functionally active uptake ligands for ASGPR facilitating intracellular delivery of a nonglycan ligand.
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5
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Urbina F, Batra K, Luebke KJ, White JD, Matsiev D, Olson LL, Malerich JP, Hupcey MAZ, Madrid PB, Ekins S. UV-adVISor: Attention-Based Recurrent Neural Networks to Predict UV-Vis Spectra. Anal Chem 2021; 93:16076-16085. [PMID: 34812602 DOI: 10.1021/acs.analchem.1c03741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet-visible (UV-Vis) absorption spectra are routinely collected as part of high-performance liquid chromatography (HPLC) analysis systems and can be used to identify chemical reaction products by comparison to the reference spectra. Here, we present UV-adVISor as a new computational tool for predicting the UV-Vis spectra from a molecule's structure alone. UV-Vis prediction was approached as a sequence-to-sequence problem. We utilized Long-Short Term Memory and attention-based neural networks with Extended Connectivity Fingerprint Diameter 6 or molecule SMILES to generate predictive models for the UV spectra. We have produced two spectrum datasets (dataset I, N = 949, and dataset II, N = 2222) using different compound collections and spectrum acquisition methods to train, validate, and test our models. We evaluated the prediction accuracy of the complete spectra by the correspondence of wavelengths of absorbance maxima and with a series of statistical measures (the best test set median model parameters are in parentheses for model II), including RMSE (0.064), R2 (0.71), and dynamic time warping (DTW, 0.194) of the entire spectrum curve. Scrambling molecule structures with the experimental spectra during training resulted in a degraded R2, confirming the utility of the approaches for prediction. UV-adVISor is able to provide fast and accurate predictions for libraries of compounds.
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Affiliation(s)
- Fabio Urbina
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Kushal Batra
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States.,Computer Science, NC State University, Raleigh, North Carolina 27606, United States
| | - Kevin J Luebke
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jason D White
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Daniel Matsiev
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Lori L Olson
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jeremiah P Malerich
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Maggie A Z Hupcey
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Peter B Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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6
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Gawriljuk VO, Zin PPK, Puhl AC, Zorn KM, Foil DH, Lane TR, Hurst B, Tavella TA, Costa FTM, Lakshmanane P, Bernatchez J, Godoy AS, Oliva G, Siqueira-Neto JL, Madrid PB, Ekins S. Machine Learning Models Identify Inhibitors of SARS-CoV-2. J Chem Inf Model 2021; 61:4224-4235. [PMID: 34387990 DOI: 10.1021/acs.jcim.1c00683] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
With the rapidly evolving SARS-CoV-2 variants of concern, there is an urgent need for the discovery of further treatments for the coronavirus disease (COVID-19). Drug repurposing is one of the most rapid strategies for addressing this need, and numerous compounds have already been selected for in vitro testing by several groups. These have led to a growing database of molecules with in vitro activity against the virus. Machine learning models can assist drug discovery through prediction of the best compounds based on previously published data. Herein, we have implemented several machine learning methods to develop predictive models from recent SARS-CoV-2 in vitro inhibition data and used them to prioritize additional FDA-approved compounds for in vitro testing selected from our in-house compound library. From the compounds predicted with a Bayesian machine learning model, lumefantrine, an antimalarial was selected for testing and showed limited antiviral activity in cell-based assays while demonstrating binding (Kd 259 nM) to the spike protein using microscale thermophoresis. Several other compounds which we prioritized have since been tested by others and were also found to be active in vitro. This combined machine learning and in vitro testing approach can be expanded to virtually screen available molecules with predicted activity against SARS-CoV-2 reference WIV04 strain and circulating variants of concern. In the process of this work, we have created multiple iterations of machine learning models that can be used as a prioritization tool for SARS-CoV-2 antiviral drug discovery programs. The very latest model for SARS-CoV-2 with over 500 compounds is now freely available at www.assaycentral.org.
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Affiliation(s)
- Victor O Gawriljuk
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100-Santa Angelina, São Carlos, São Paulo 13563-120, Brazil
| | - Phyo Phyo Kyaw Zin
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Ana C Puhl
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Kimberley M Zorn
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Daniel H Foil
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Thomas R Lane
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Brett Hurst
- Institute for Antiviral Research, Utah State University, Logan, Utah 84322-5600, United States.,Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah 84322-4815, United States
| | - Tatyana Almeida Tavella
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacinto da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo, Brazil
| | - Fabio Trindade Maranhão Costa
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacinto da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo, Brazil
| | - Premkumar Lakshmanane
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill North Carolina 27599, United States
| | - Jean Bernatchez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Andre S Godoy
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100-Santa Angelina, São Carlos, São Paulo 13563-120, Brazil
| | - Glaucius Oliva
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100-Santa Angelina, São Carlos, São Paulo 13563-120, Brazil
| | - Jair L Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Peter B Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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7
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Puhl AC, Fritch EJ, Lane TR, Tse LV, Yount BL, Sacramento CQ, Fintelman-Rodrigues N, Tavella TA, Maranhão Costa FT, Weston S, Logue J, Frieman M, Premkumar L, Pearce KH, Hurst BL, Andrade CH, Levi JA, Johnson NJ, Kisthardt SC, Scholle F, Souza TML, Moorman NJ, Baric RS, Madrid PB, Ekins S. Repurposing the Ebola and Marburg Virus Inhibitors Tilorone, Quinacrine, and Pyronaridine: In Vitro Activity against SARS-CoV-2 and Potential Mechanisms. ACS Omega 2021; 6:7454-7468. [PMID: 33778258 PMCID: PMC7992063 DOI: 10.1021/acsomega.0c05996] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/02/2021] [Indexed: 05/11/2023]
Abstract
Severe acute respiratory coronavirus 2 (SARS-CoV-2) is a newly identified virus that has resulted in over 2.5 million deaths globally and over 116 million cases globally in March, 2021. Small-molecule inhibitors that reverse disease severity have proven difficult to discover. One of the key approaches that has been widely applied in an effort to speed up the translation of drugs is drug repurposing. A few drugs have shown in vitro activity against Ebola viruses and demonstrated activity against SARS-CoV-2 in vivo. Most notably, the RNA polymerase targeting remdesivir demonstrated activity in vitro and efficacy in the early stage of the disease in humans. Testing other small-molecule drugs that are active against Ebola viruses (EBOVs) would appear a reasonable strategy to evaluate their potential for SARS-CoV-2. We have previously repurposed pyronaridine, tilorone, and quinacrine (from malaria, influenza, and antiprotozoal uses, respectively) as inhibitors of Ebola and Marburg viruses in vitro in HeLa cells and mouse-adapted EBOV in mice in vivo. We have now tested these three drugs in various cell lines (VeroE6, Vero76, Caco-2, Calu-3, A549-ACE2, HUH-7, and monocytes) infected with SARS-CoV-2 as well as other viruses (including MHV and HCoV 229E). The compilation of these results indicated considerable variability in antiviral activity observed across cell lines. We found that tilorone and pyronaridine inhibited the virus replication in A549-ACE2 cells with IC50 values of 180 nM and IC50 198 nM, respectively. We used microscale thermophoresis to test the binding of these molecules to the spike protein, and tilorone and pyronaridine bind to the spike receptor binding domain protein with K d values of 339 and 647 nM, respectively. Human Cmax for pyronaridine and quinacrine is greater than the IC50 observed in A549-ACE2 cells. We also provide novel insights into the mechanism of these compounds which is likely lysosomotropic.
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Affiliation(s)
- Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Ethan J. Fritch
- Department
of Microbiology and Immunology, University
of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Thomas R. Lane
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Longping V. Tse
- Department
of Epidemiology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Boyd L. Yount
- Department
of Epidemiology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Carolina Q. Sacramento
- Laboratório
de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ 21040-900, Brazil
- Centro
De Desenvolvimento Tecnológico Em Saúde (CDTS), Fiocruz, Rio de
Janeiro 21040-900, Brazil
| | - Natalia Fintelman-Rodrigues
- Laboratório
de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ 21040-900, Brazil
- Centro
De Desenvolvimento Tecnológico Em Saúde (CDTS), Fiocruz, Rio de
Janeiro 21040-900, Brazil
| | - Tatyana Almeida Tavella
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacinto da Silva, Department
of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Fabio Trindade Maranhão Costa
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacinto da Silva, Department
of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Stuart Weston
- Department
of Microbiology and Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - James Logue
- Department
of Microbiology and Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Matthew Frieman
- Department
of Microbiology and Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Lakshmanane Premkumar
- Department
of Microbiology and Immunology, University
of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H. Pearce
- Center
for Integrative Chemical Biology and Drug Discovery, Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- UNC
Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, United States
| | - Brett L. Hurst
- Institute
for Antiviral Research, Utah State University, Logan, Utah 84322, United States
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah 84322, United States
| | - Carolina Horta Andrade
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacinto da Silva, Department
of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo 13083-970, Brazil
- LabMol—Laboratory of Molecular Modeling
and Drug Design, Faculdade
de Farmácia, Universidade Federal
de Goiás, Goiânia,
GO 74605-170, Brazil
| | - James A. Levi
- Department of Biological Sciences, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Nicole J. Johnson
- Department of Biological Sciences, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Samantha C. Kisthardt
- Department of Biological Sciences, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Frank Scholle
- Department of Biological Sciences, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thiago Moreno L. Souza
- Laboratório
de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ 21040-900, Brazil
- Centro
De Desenvolvimento Tecnológico Em Saúde (CDTS), Fiocruz, Rio de
Janeiro 21040-900, Brazil
| | - Nathaniel John Moorman
- Department
of Microbiology and Immunology, University
of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
- Center
for Integrative Chemical Biology and Drug Discovery, Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Rapidly Emerging Antiviral Drug Discovery
Initiative, University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Ralph S. Baric
- Department
of Microbiology and Immunology, University
of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department
of Epidemiology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
- Rapidly Emerging Antiviral Drug Discovery
Initiative, University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Peter B. Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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8
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Vignaux PA, Minerali E, Lane TR, Foil DH, Madrid PB, Puhl AC, Ekins S. The Antiviral Drug Tilorone Is a Potent and Selective Inhibitor of Acetylcholinesterase. Chem Res Toxicol 2021; 34:1296-1307. [PMID: 33400519 DOI: 10.1021/acs.chemrestox.0c00466] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Acetylcholinesterase (AChE) is an important drug target in neurological disorders like Alzheimer's disease, Lewy body dementia, and Parkinson's disease dementia as well as for other conditions like myasthenia gravis and anticholinergic poisoning. In this study, we have used a combination of high-throughput screening, machine learning, and docking to identify new inhibitors of this enzyme. Bayesian machine learning models were generated with literature data from ChEMBL for eel and human AChE inhibitors as well as butyrylcholinesterase inhibitors (BuChE) and compared with other machine learning methods. High-throughput screens for the eel AChE inhibitor model identified several molecules including tilorone, an antiviral drug that is well-established outside of the United States, as a newly identified nanomolar AChE inhibitor. We have described how tilorone inhibits both eel and human AChE with IC50's of 14.4 nM and 64.4 nM, respectively, but does not inhibit the closely related BuChE IC50 > 50 μM. We have docked tilorone into the human AChE crystal structure and shown that this selectivity is likely due to the reliance on a specific interaction with a hydrophobic residue in the peripheral anionic site of AChE that is absent in BuChE. We also conducted a pharmacological safety profile (SafetyScreen44) and kinase selectivity screen (SelectScreen) that showed tilorone (1 μM) only inhibited AChE out of 44 toxicology target proteins evaluated and did not appreciably inhibit any of the 485 kinases tested. This study suggests there may be a potential role for repurposing tilorone or its derivatives in conditions that benefit from AChE inhibition.
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Affiliation(s)
- Patricia A Vignaux
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Eni Minerali
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Thomas R Lane
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Daniel H Foil
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Peter B Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Ana C Puhl
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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9
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Lane TR, Dyall J, Mercer L, Goodin C, Foil DH, Zhou H, Postnikova E, Liang JY, Holbrook MR, Madrid PB, Ekins S. Repurposing Pyramax®, quinacrine and tilorone as treatments for Ebola virus disease. Antiviral Res 2020; 182:104908. [PMID: 32798602 PMCID: PMC7425680 DOI: 10.1016/j.antiviral.2020.104908] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/03/2020] [Accepted: 08/04/2020] [Indexed: 12/15/2022]
Abstract
We have recently identified three molecules (tilorone, quinacrine and pyronaridine tetraphosphate) which all demonstrated efficacy in the mouse model of infection with mouse-adapted Ebola virus (EBOV) model of disease and had similar in vitro inhibition of an Ebola pseudovirus (VSV-EBOV-GP), suggesting they interfere with viral entry. Using a machine learning model to predict lysosomotropism these compounds were evaluated for their ability to possess a lysosomotropic mechanism in vitro. We now demonstrate in vitro that pyronaridine tetraphosphate is an inhibitor of Lysotracker accumulation in lysosomes (IC50 = 0.56 μM). Further, we evaluated antiviral synergy between pyronaridine and artesunate (Pyramax®), which are used in combination to treat malaria. Artesunate was not found to have lysosomotropic activity in vitro and the combination effect on EBOV inhibition was shown to be additive. Pyramax® may represent a unique example of the repurposing of a combination product for another disease.
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Affiliation(s)
- Thomas R Lane
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, 27606, USA
| | - Julie Dyall
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Luke Mercer
- Cambrex, 3501 Tricenter Blvd, Suite C, Durham, NC, 27713, USA
| | - Caleb Goodin
- Cambrex, 3501 Tricenter Blvd, Suite C, Durham, NC, 27713, USA
| | - Daniel H Foil
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, 27606, USA
| | - Huanying Zhou
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | | | - Janie Y Liang
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Peter B Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, CA, 94025, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, 27606, USA.
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10
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Lane TR, Massey C, Comer JE, Freiberg AN, Zhou H, Dyall J, Holbrook MR, Anantpadma M, Davey RA, Madrid PB, Ekins S. Pyronaridine tetraphosphate efficacy against Ebola virus infection in guinea pig. Antiviral Res 2020; 181:104863. [PMID: 32682926 PMCID: PMC8194506 DOI: 10.1016/j.antiviral.2020.104863] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 12/22/2022]
Abstract
The recent outbreaks of the Ebola virus (EBOV) in Africa have brought global visibility to the shortage of available therapeutic options to treat patients infected with this or closely related viruses. We have recently computationally identified three molecules which have all demonstrated statistically significant efficacy in the mouse model of infection with mouse adapted Ebola virus (ma-EBOV). One of these molecules is the antimalarial pyronaridine tetraphosphate (IC50 range of 0.82-1.30 μM against three strains of EBOV and IC50 range of 1.01-2.72 μM against two strains of Marburg virus (MARV)) which is an approved drug in the European Union and used in combination with artesunate. To date, no small molecule drugs have shown statistically significant efficacy in the guinea pig model of EBOV infection. Pharmacokinetics and range-finding studies in guinea pigs directed us to a single 300 mg/kg or 600 mg/kg oral dose of pyronaridine 1hr after infection. Pyronaridine resulted in statistically significant survival of 40% at 300 mg/kg and protected from a lethal challenge with EBOV. In comparison, oral favipiravir (300 mg/kg dosed once a day) had 43.5% survival. All animals in the vehicle treatment group succumbed to disease by study day 12 (100% mortality). The in vitro metabolism and metabolite identification of pyronaridine and another of our EBOV active molecules, tilorone, suggested significant species differences which may account for the efficacy or lack thereof, respectively in guinea pig. In summary, our studies with pyronaridine demonstrates its utility for repurposing as an antiviral against EBOV and MARV.
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Affiliation(s)
- Thomas R. Lane
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Christopher Massey
- Institutional Office of Regulated Nonclinical Studies, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
| | - Jason E. Comer
- Institutional Office of Regulated Nonclinical Studies, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
| | - Alexander N. Freiberg
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
| | - Huanying Zhou
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Julie Dyall
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Michael R. Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Manu Anantpadma
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Robert A. Davey
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Peter B. Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
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11
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Collins N, Stout D, Lim JP, Malerich JP, White JD, Madrid PB, Latendresse M, Krieger D, Szeto J, Vu VA, Rucker K, Deleo M, Gorfu Y, Krummenacker M, Hokama LA, Karp P, Mallya S. Fully Automated Chemical Synthesis: Toward the Universal Synthesizer. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00143] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Nathan Collins
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - David Stout
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jin-Ping Lim
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jeremiah P. Malerich
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jason D. White
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Peter B. Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Mario Latendresse
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - David Krieger
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Judy Szeto
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Vi-Anh Vu
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Kristina Rucker
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Michael Deleo
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Yonael Gorfu
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Markus Krummenacker
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Leslie A. Hokama
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Peter Karp
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Sahana Mallya
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
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12
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Ekins S, Lane TR, Madrid PB. Tilorone: a Broad-Spectrum Antiviral Invented in the USA and Commercialized in Russia and beyond. Pharm Res 2020; 37:71. [PMID: 32215760 PMCID: PMC7100484 DOI: 10.1007/s11095-020-02799-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/10/2020] [Indexed: 12/05/2022]
Abstract
For the last 50 years we have known of a broad-spectrum agent tilorone dihydrochloride (Tilorone). This is a small-molecule orally bioavailable drug that was originally discovered in the USA and is currently used clinically as an antiviral in Russia and the Ukraine. Over the years there have been numerous clinical and non-clinical reports of its broad spectrum of antiviral activity. More recently we have identified additional promising antiviral activities against Middle East Respiratory Syndrome, Chikungunya, Ebola and Marburg which highlights that this old drug may have other uses against new viruses. This may in turn inform the types of drugs that we need for virus outbreaks such as for the new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Tilorone has been long neglected by the west in many respects but it deserves further reassessment in light of current and future needs for broad-spectrum antivirals.
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Affiliation(s)
- Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC27606, USA.
| | - Thomas R Lane
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC27606, USA
| | - Peter B Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California, 94025, USA
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13
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Lane TR, Massey C, Comer JE, Anantpadma M, Freundlich JS, Davey RA, Madrid PB, Ekins S. Repurposing the antimalarial pyronaridine tetraphosphate to protect against Ebola virus infection. PLoS Negl Trop Dis 2019; 13:e0007890. [PMID: 31751347 PMCID: PMC6894882 DOI: 10.1371/journal.pntd.0007890] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/05/2019] [Accepted: 10/29/2019] [Indexed: 12/28/2022] Open
Abstract
Recent outbreaks of the Ebola virus (EBOV) have focused attention on the dire need for antivirals to treat these patients. We identified pyronaridine tetraphosphate as a potential candidate as it is an approved drug in the European Union which is currently used in combination with artesunate as a treatment for malaria (EC50 between 420 nM—1.14 μM against EBOV in HeLa cells). Range-finding studies in mice directed us to a single 75 mg/kg i.p. dose 1 hr after infection which resulted in 100% survival and statistically significantly reduced viremia at study day 3 from a lethal challenge with mouse-adapted EBOV (maEBOV). Further, an EBOV window study suggested we could dose pyronaridine 2 or 24 hrs post-exposure to result in similar efficacy. Analysis of cytokine and chemokine panels suggests that pyronaridine may act as an immunomodulator during an EBOV infection. Our studies with pyronaridine clearly demonstrate potential utility for its repurposing as an antiviral against EBOV and merits further study in larger animal models with the added benefit of already being used as a treatment against malaria. To date there is no approved drug for Ebola Virus infection. Our approach has been to assess drugs that are already approved for other uses in various countries. Using computational models, we have previously identified three such drugs and demonstrated their activity against the Ebola virus in vitro. We now report on the in vitro absorption, metabolism, distribution, excretion and pharmacokinetic properties of one of these molecules, namely the antimalarial pyronaridine. We justify efficacy testing in the mouse model of ebola infection. We also demonstrate that a single dose of this drug is 100% effective against the virus. This study provides important preclinical evaluation of this already approved drug and justifies its selection for larger animal efficacy studies.
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Affiliation(s)
- Thomas R. Lane
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, United States of America
| | - Christopher Massey
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Jason E. Comer
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
- Institutional Office of Regulated Nonclinical Studies, University of Texas Medical Branch, Galveston, TX, United States of America
- Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Joel S. Freundlich
- Departments of Pharmacology, Physiology, and Neuroscience & Medicine, Center for Emerging and Reemerging Pathogens, Rutgers University–New Jersey Medical School, NJ, United States of America
| | - Robert A. Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | | | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, United States of America
- * E-mail:
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14
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Anantpadma M, Lane T, Zorn KM, Lingerfelt MA, Clark AM, Freundlich JS, Davey RA, Madrid PB, Ekins S. Ebola Virus Bayesian Machine Learning Models Enable New in Vitro Leads. ACS Omega 2019; 4:2353-2361. [PMID: 30729228 PMCID: PMC6356859 DOI: 10.1021/acsomega.8b02948] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/17/2019] [Indexed: 05/08/2023]
Abstract
We have previously described the first Bayesian machine learning models from FDA-approved drug screens, for identifying compounds active against the Ebola virus (EBOV). These models led to the identification of three active molecules in vitro: tilorone, pyronaridine, and quinacrine. A follow-up study demonstrated that one of these compounds, tilorone, has 100% in vivo efficacy in mice infected with mouse-adapted EBOV at 30 mg/kg/day intraperitoneal. This suggested that we can learn from the published data on EBOV inhibition and use it to select new compounds for testing that are active in vivo. We used these previously built Bayesian machine learning EBOV models alongside our chemical insights for the selection of 12 molecules, absent from the training set, to test for in vitro EBOV inhibition. Nine molecules were directly selected using the model, and eight of these molecules possessed a promising in vitro activity (EC50 < 15 μM). Three further compounds were selected for an in vitro evaluation because they were antimalarials, and compounds of this class like pyronaridine and quinacrine have previously been shown to inhibit EBOV. We identified the antimalarial drug arterolane (IC50 = 4.53 μM) and the anticancer clinical candidate lucanthone (IC50 = 3.27 μM) as novel compounds that have EBOV inhibitory activity in HeLa cells and generally lack cytotoxicity. This work provides further validation for using machine learning and medicinal chemistry expertize to prioritize compounds for testing in vitro prior to more costly in vivo tests. These studies provide further corroboration of this strategy and suggest that it can likely be applied to other pathogens in the future.
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Affiliation(s)
- Manu Anantpadma
- Department
of Virology and Immunology, Texas Biomedical
Research Institute, 8715
West Military Drive, San Antonio, Texas 78227, United
States
| | - Thomas Lane
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Kimberley M. Zorn
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Mary A. Lingerfelt
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Alex M. Clark
- Molecular
Materials Informatics, Inc., 1900 St. Jacques #302, Montreal H3J 2S1, Quebec, Canada
| | - Joel S. Freundlich
- Departments
of Pharmacology, Physiology, and Neuroscience & Medicine, Center
for Emerging and Reemerging Pathogens, Rutgers
University—New Jersey Medical School, 185 South Orange Avenue, Newark, New Jersey 07103, United States
| | - Robert A. Davey
- Department
of Virology and Immunology, Texas Biomedical
Research Institute, 8715
West Military Drive, San Antonio, Texas 78227, United
States
| | - Peter B. Madrid
- SRI
International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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15
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Prantner AM, Yin C, Kamat K, Sharma K, Lowenthal AC, Madrid PB, Scholler N. Molecular Imaging of Mesothelin-Expressing Ovarian Cancer with a Human and Mouse Cross-Reactive Nanobody. Mol Pharm 2018; 15:1403-1411. [PMID: 29462558 DOI: 10.1021/acs.molpharmaceut.7b00789] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Mesothelin is an epithelial marker highly expressed at the cell surface of cancer cells from diverse origins, including ovarian and pancreatic adenocarcinomas and mesotheliomas. Previously, we identified and characterized an antimesothelin nanobody (NbG3a) for in vitro diagnostic applications. The main goal of this research was to establish the potential of NbG3a as a molecular imaging agent. Site-specific biotinylated NbG3a (bNbG3a) was bound to streptavidin-conjugated reagents for in vitro and in vivo assays. Initially, we performed microscale thermophoresis to determine the binding affinity between bNbG3a and human ( Kd = 46 ± 8 nM) or mouse ( Kd = 4.8 ± 0.4 nM) mesothelin protein. The human and mouse cross-reactivity was confirmed by in vivo optical imaging using bNbG3a bound to fluorescent streptavidin. We also localized the binding site of nNbG3a on human mesothelin using overlapping peptide scan. NbG3a recognized an epitope within residues 21-65 of the mature membrane bound form of human mesothelin, which is part of the N-terminal region of mesothelin that is important for interactions between mesothelin on peritoneal cells and CA125 on tumor cells. Next, the bNbG3a in vivo half-life after intravenous injection in healthy mice was estimated by ELISA assay to be 5.3 ± 1.3 min. In tumor-bearing animals, fluorescent bNbG3a accumulated in a subcutaneous ovarian xenograft (A1847) and in two syngeneic, orthotopic ovarian tumors (intraovary and intraperitoneal ID8) within an hour of intravenous injection that peaked by 4 h and persisted up to 48 h. MRI analysis of bNbG3a-targeted streptavidin-labeled iron oxides showed that the MRI signal intensity decreased 1 h after injection for a subcutaneous xenograft model of ovarian cancer for bNbG3a-labeled iron oxides compared to unlabeled iron oxides. The signal intensity differences continued up to the final time point at 24 h post injection. Finally, in vivo immunofluorescence 24 or 48 h after bNbG3a intravenous injection showed bNbG3a diffuse distribution of both xenograft and syngeneic ovarian tumors, with local areas of high concentration throughout A1847 human tumor. The data support the use of NbG3a for continued preclinical development and translation to human applications for cancers that overexpress mesothelin.
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Affiliation(s)
- Andrew M Prantner
- Biosciences Division , SRI International , 333 Ravenswood Avenue , Menlo Park , California 94025 , United States
| | - Catherine Yin
- Biosciences Division , SRI International , 333 Ravenswood Avenue , Menlo Park , California 94025 , United States
| | - Kalika Kamat
- Biosciences Division , SRI International , 333 Ravenswood Avenue , Menlo Park , California 94025 , United States
| | - Khushboo Sharma
- Biosciences Division , SRI International , 333 Ravenswood Avenue , Menlo Park , California 94025 , United States
| | - Andrew C Lowenthal
- Biosciences Division , SRI International , 333 Ravenswood Avenue , Menlo Park , California 94025 , United States
| | - Peter B Madrid
- Biosciences Division , SRI International , 333 Ravenswood Avenue , Menlo Park , California 94025 , United States
| | - Nathalie Scholler
- Biosciences Division , SRI International , 333 Ravenswood Avenue , Menlo Park , California 94025 , United States
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16
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Abstract
Due to growing problems with drug resistance, there is an outstanding need for new, cost-effective drugs for the treatment of malaria. The 4-aminoquinolines have provided a number of useful antimalarials, and Plasmodium falciparum, the causative organism for the most deadly form of human malaria, is generally slow to develop resistance to these drugs. Therefore, diverse screening libraries of quinolines continue to be useful for antimalarial drug discovery. We report herein the development of an efficient method for producing libraries of 4-aminoquinolines variant in the side chain portion of the molecule. The effects of these substitutions were evaluated by screening this library for activity against P. falciparum, revealing four potent compounds active against drug-resistant strains.
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Affiliation(s)
- Peter B Madrid
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-2280, USA
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17
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Ekins S, Madrid PB, Sarker M, Li SG, Mittal N, Kumar P, Wang X, Stratton TP, Zimmerman M, Talcott C, Bourbon P, Travers M, Yadav M, Freundlich JS. Combining Metabolite-Based Pharmacophores with Bayesian Machine Learning Models for Mycobacterium tuberculosis Drug Discovery. PLoS One 2015; 10:e0141076. [PMID: 26517557 PMCID: PMC4627656 DOI: 10.1371/journal.pone.0141076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/05/2015] [Indexed: 12/15/2022] Open
Abstract
Integrated computational approaches for Mycobacterium tuberculosis (Mtb) are useful to identify new molecules that could lead to future tuberculosis (TB) drugs. Our approach uses information derived from the TBCyc pathway and genome database, the Collaborative Drug Discovery TB database combined with 3D pharmacophores and dual event Bayesian models of whole-cell activity and lack of cytotoxicity. We have prioritized a large number of molecules that may act as mimics of substrates and metabolites in the TB metabolome. We computationally searched over 200,000 commercial molecules using 66 pharmacophores based on substrates and metabolites from Mtb and further filtering with Bayesian models. We ultimately tested 110 compounds in vitro that resulted in two compounds of interest, BAS 04912643 and BAS 00623753 (MIC of 2.5 and 5 μg/mL, respectively). These molecules were used as a starting point for hit-to-lead optimization. The most promising class proved to be the quinoxaline di-N-oxides, evidenced by transcriptional profiling to induce mRNA level perturbations most closely resembling known protonophores. One of these, SRI58 exhibited an MIC = 1.25 μg/mL versus Mtb and a CC50 in Vero cells of >40 μg/mL, while featuring fair Caco-2 A-B permeability (2.3 x 10−6 cm/s), kinetic solubility (125 μM at pH 7.4 in PBS) and mouse metabolic stability (63.6% remaining after 1 h incubation with mouse liver microsomes). Despite demonstration of how a combined bioinformatics/cheminformatics approach afforded a small molecule with promising in vitro profiles, we found that SRI58 did not exhibit quantifiable blood levels in mice.
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Affiliation(s)
- Sean Ekins
- Collaborative Drug Discovery Inc., 1633 Bayshore Highway, Suite 342, Burlingame, CA, 94010, United States of America
- Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, NC, 27526, United States of America
- * E-mail: (SE); (PBM); (JSF)
| | - Peter B. Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, CA, 94025, United States of America
- * E-mail: (SE); (PBM); (JSF)
| | - Malabika Sarker
- SRI International, 333 Ravenswood Avenue, Menlo Park, CA, 94025, United States of America
| | - Shao-Gang Li
- Departments of Pharmacology & Physiology and Medicine, Center for Emerging and Reemerging Pathogens, Rutgers University–New Jersey Medical School, 185 South Orange Avenue, Newark, NJ, 07103, United States of America
| | - Nisha Mittal
- Departments of Pharmacology & Physiology and Medicine, Center for Emerging and Reemerging Pathogens, Rutgers University–New Jersey Medical School, 185 South Orange Avenue, Newark, NJ, 07103, United States of America
| | - Pradeep Kumar
- Department of Medicine, Center for Emerging and Reemerging Pathogens, Rutgers University–New Jersey Medical School, 185 South Orange Avenue, Newark, NJ, 07103, United States of America
| | - Xin Wang
- Departments of Pharmacology & Physiology and Medicine, Center for Emerging and Reemerging Pathogens, Rutgers University–New Jersey Medical School, 185 South Orange Avenue, Newark, NJ, 07103, United States of America
| | - Thomas P. Stratton
- Departments of Pharmacology & Physiology and Medicine, Center for Emerging and Reemerging Pathogens, Rutgers University–New Jersey Medical School, 185 South Orange Avenue, Newark, NJ, 07103, United States of America
| | - Matthew Zimmerman
- Public Health Research Institute, Rutgers University–New Jersey Medical School, Newark, NJ, 07103, United States of America
| | - Carolyn Talcott
- SRI International, 333 Ravenswood Avenue, Menlo Park, CA, 94025, United States of America
| | - Pauline Bourbon
- SRI International, 333 Ravenswood Avenue, Menlo Park, CA, 94025, United States of America
| | - Mike Travers
- Collaborative Drug Discovery Inc., 1633 Bayshore Highway, Suite 342, Burlingame, CA, 94010, United States of America
| | - Maneesh Yadav
- SRI International, 333 Ravenswood Avenue, Menlo Park, CA, 94025, United States of America
| | - Joel S. Freundlich
- Departments of Pharmacology & Physiology and Medicine, Center for Emerging and Reemerging Pathogens, Rutgers University–New Jersey Medical School, 185 South Orange Avenue, Newark, NJ, 07103, United States of America
- * E-mail: (SE); (PBM); (JSF)
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18
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Madrid PB, Panchal RG, Warren TK, Shurtleff AC, Endsley AN, Green CE, Kolokoltsov A, Davey R, Manger ID, Gilfillan L, Bavari S, Tanga MJ. Evaluation of Ebola Virus Inhibitors for Drug Repurposing. ACS Infect Dis 2015; 1:317-26. [PMID: 27622822 DOI: 10.1021/acsinfecdis.5b00030] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A systematic screen of FDA-approved drugs was performed to identify compounds with in vitro antiviral activities against Ebola virus (EBOV). Compounds active (>50% viral inhibition and <30% cellular toxicity) at a single concentration were tested in dose-response assays to quantitate the antiviral activities in replication and viral entry assays as well as cytotoxicity in the Vero cell line used to conduct these assays. On the basis of the approved human dosing, toxicity/tolerability, and pharmacokinetic data, seven of these in vitro hits from different pharmacological classes (chloroquine (CQ), amiodarone, prochlorperazine, benztropine, azithromycin, chlortetracycline, and clomiphene) were evaluated for their in vivo efficacy at a single dose and were administered via either intraperitoneal (ip) or oral route. Initially, azithromycin (100 mg/kg, twice daily, ip), CQ (90 mg/kg, twice daily, ip), and amiodarone (60 mg/kg, twice daily, ip) demonstrated significant increases in survival in the mouse model. After repeat evaluation, only CQ was found to reproducibly give significant efficacy in the mouse model with this dosing regimen. Azithromycin and CQ were also tested in a guinea pig model of EBOV infection over a range of doses, but none of the doses increased survival, and drug-related toxicity was observed at lower doses than in the mouse. These results show the benefits and specific challenges associated with drug repurposing and highlight the need for careful evaluation of approved drugs as rapidly deployable countermeasures against future pandemics.
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Affiliation(s)
- Peter B. Madrid
- Biosciences
Division, SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Rekha G. Panchal
- U.S.
Army Medical Research Institute of Infectious Diseases, Fort Detrick, 1425 Porter Street, Frederick, Maryland 21702, United States
| | - Travis K. Warren
- U.S.
Army Medical Research Institute of Infectious Diseases, Fort Detrick, 1425 Porter Street, Frederick, Maryland 21702, United States
| | - Amy C. Shurtleff
- U.S.
Army Medical Research Institute of Infectious Diseases, Fort Detrick, 1425 Porter Street, Frederick, Maryland 21702, United States
| | - Aaron N. Endsley
- Biosciences
Division, SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Carol E. Green
- Biosciences
Division, SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Andrey Kolokoltsov
- University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Robert Davey
- University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Ian D. Manger
- Biosciences
Division, SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Lynne Gilfillan
- Biosciences
Division, SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Sina Bavari
- U.S.
Army Medical Research Institute of Infectious Diseases, Fort Detrick, 1425 Porter Street, Frederick, Maryland 21702, United States
| | - Mary J. Tanga
- Biosciences
Division, SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
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Madrid PB, Chopra S, Manger ID, Gilfillan L, Keepers TR, Shurtleff AC, Green CE, Iyer LV, Dilks HH, Davey RA, Kolokoltsov AA, Carrion R, Patterson JL, Bavari S, Panchal RG, Warren TK, Wells JB, Moos WH, Burke RL, Tanga MJ. A systematic screen of FDA-approved drugs for inhibitors of biological threat agents. PLoS One 2013; 8:e60579. [PMID: 23577127 PMCID: PMC3618516 DOI: 10.1371/journal.pone.0060579] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 02/28/2013] [Indexed: 12/15/2022] Open
Abstract
Background The rapid development of effective medical countermeasures against potential biological threat agents is vital. Repurposing existing drugs that may have unanticipated activities as potential countermeasures is one way to meet this important goal, since currently approved drugs already have well-established safety and pharmacokinetic profiles in patients, as well as manufacturing and distribution networks. Therefore, approved drugs could rapidly be made available for a new indication in an emergency. Methodology/Principal Findings A large systematic effort to determine whether existing drugs can be used against high containment bacterial and viral pathogens is described. We assembled and screened 1012 FDA-approved drugs for off-label broad-spectrum efficacy against Bacillus anthracis; Francisella tularensis; Coxiella burnetii; and Ebola, Marburg, and Lassa fever viruses using in vitro cell culture assays. We found a variety of hits against two or more of these biological threat pathogens, which were validated in secondary assays. As expected, antibiotic compounds were highly active against bacterial agents, but we did not identify any non-antibiotic compounds with broad-spectrum antibacterial activity. Lomefloxacin and erythromycin were found to be the most potent compounds in vivo protecting mice against Bacillus anthracis challenge. While multiple virus-specific inhibitors were identified, the most noteworthy antiviral compound identified was chloroquine, which disrupted entry and replication of two or more viruses in vitro and protected mice against Ebola virus challenge in vivo. Conclusions/Significance The feasibility of repurposing existing drugs to face novel threats is demonstrated and this represents the first effort to apply this approach to high containment bacteria and viruses.
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Affiliation(s)
- Peter B Madrid
- Center for Infectious Disease and Biodefense Research, SRI International, Menlo Park, California, USA.
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20
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Chopra S, Koolpe GA, Tambo-Ong AA, Matsuyama KN, Ryan KJ, Tran TB, Doppalapudi RS, Riccio ES, Iyer LV, Green CE, Wan B, Franzblau SG, Madrid PB. Discovery and optimization of benzotriazine di-N-oxides targeting replicating and nonreplicating Mycobacterium tuberculosis. J Med Chem 2012; 55:6047-60. [PMID: 22691154 DOI: 10.1021/jm300123s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Compounds bactericidal against both replicating and nonreplicating Mtb may shorten the length of TB treatment regimens by eliminating infections more rapidly. Screening of a panel of antimicrobial and anticancer drug classes that are bioreduced into cytotoxic species revealed that 1,2,4-benzotriazine di-N-oxides (BTOs) are potently bactericidal against replicating and nonreplicating Mtb. Medicinal chemistry optimization, guided by semiempirical molecular orbital calculations, identified a new lead compound (20q) from this series with an MIC of 0.31 μg/mL against H37Rv and a cytotoxicity (CC(50)) against Vero cells of 25 μg/mL. 20q also had equivalent potency against a panel of single-drug resistant strains of Mtb and remarkably selective activity for Mtb over a panel of other pathogenic bacterial strains. 20q was also negative in a L5178Y MOLY assay, indicating low potential for genetic toxicity. These data along with measurements of the physiochemical properties and pharmacokinetic profile demonstrate that BTOs have the potential to be developed into a new class of antitubercular drugs.
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Affiliation(s)
- Sidharth Chopra
- Center for Infectious Disease and Biodefense Research, Bioscience Division, SRI International, Menlo Park, CA 94025-3493, USA
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Culyba M, Hwang Y, Attar S, Madrid PB, Bupp J, Huryn D, Sanchez L, Grobler J, Miller MD, Bushman FD. Bulged DNA substrates for identifying poxvirus resolvase inhibitors. Nucleic Acids Res 2012; 40:e124. [PMID: 22581770 PMCID: PMC3439875 DOI: 10.1093/nar/gks325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Resolvase enzymes that cleave DNA four-way (Holliday) junctions are required for poxvirus replication, but clinically useful inhibitors have not been developed. Here, we report an assay for resolvase cleavage activity based on fluorescence polarization (FP) for high-throughput screening and mechanistic studies. Initial analysis showed that cleavage of a fluorescently labeled Holliday junction substrate did not yield an appreciable change in FP, probably because the cleavage product did not have sufficiently increased mobility to yield a strong FP signal. Iterative optimization yielded a substrate with an off-center DNA bulge, which after cleavage released a labeled short stand and yielded a greatly reduced FP signal. Using this assay, 133,000 compounds were screened, identifying 1-hydroxy-1,8-naphthyridin-2(1H)-one compounds as inhibitors. Structure-activity studies revealed functional parallels to Food and Drug Administration (FDA)-approved drugs targeting the related human immunodeficiency virus integrase enzyme. Some 1-hydroxy-1,8-naphthyridin-2(1H)-one compounds showed anti-poxvirus activity.
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Affiliation(s)
- Matthew Culyba
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA
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22
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Chopra S, Matsuyama K, Tran T, Malerich JP, Wan B, Franzblau SG, Lun S, Guo H, Maiga MC, Bishai WR, Madrid PB. Evaluation of gyrase B as a drug target in Mycobacterium tuberculosis. J Antimicrob Chemother 2012; 67:415-21. [PMID: 22052686 PMCID: PMC3254195 DOI: 10.1093/jac/dkr449] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 09/28/2011] [Accepted: 10/03/2011] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES New classes of drugs are needed to treat tuberculosis (TB) in order to combat the emergence of resistance to existing agents and shorten the duration of therapy. Targeting DNA gyrase is a clinically validated therapeutic approach using fluoroquinolone antibiotics to target the gyrase subunit A (GyrA) of the heterotetramer. Increasing resistance to fluoroquinolones has driven interest in targeting the gyrase subunit B (GyrB), which has not been targeted for TB. The biological activities of two potent small-molecule inhibitors of GyrB have been characterized to validate its targeting as a therapeutic strategy for treating TB. MATERIALS AND METHODS Novobiocin and aminobenzimidazole 1 (AB-1) were tested for their activity against Mycobacterium tuberculosis (Mtb) H37Rv and other mycobacteria. AB-1 and novobiocin were also evaluated for their interaction with rifampicin and isoniazid as well as their potential for cytotoxicity. Finally, AB-1 was tested for in vivo efficacy in a murine model of TB. RESULTS Novobiocin and AB-1 have both been shown to be active against Mtb with MIC values of 4 and 1 mg/L, respectively. Only AB-1 exhibited time-dependent bactericidal activity against drug-susceptible and drug-resistant mycobacteria, including a fluoroquinolone-resistant strain. AB-1 had potent activity in the low oxygen recovery assay model for non-replicating persistent Mtb. Additionally, AB-1 has no interaction with isoniazid and rifampicin, and has no cross-resistance with fluoroquinolones. In a murine model of TB, AB-1 significantly reduced lung cfu counts in a dose-dependent manner. CONCLUSIONS Aminobenzimidazole inhibitors of GyrB exhibit many of the characteristics required for their consideration as a potential front-line antimycobacterial therapeutic.
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Affiliation(s)
- Sidharth Chopra
- Center for Infectious Disease and Biodefense Research, Bioscience Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA
| | - Karen Matsuyama
- Center for Infectious Disease and Biodefense Research, Bioscience Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA
| | - Tran Tran
- Center for Infectious Disease and Biodefense Research, Bioscience Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA
| | - Jeremiah P. Malerich
- Center for Infectious Disease and Biodefense Research, Bioscience Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA
| | - Baojie Wan
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, USA
| | - Scott G. Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, USA
| | - Shichun Lun
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, 1550 Orleans St., Baltimore, MD, USA
| | - Haidan Guo
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, 1550 Orleans St., Baltimore, MD, USA
| | - Mariama C. Maiga
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, 1550 Orleans St., Baltimore, MD, USA
| | - William R. Bishai
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, 1550 Orleans St., Baltimore, MD, USA
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Suite Z310 Doris Duke Building, 719 Umbilo Road, Durban, 4001, Republic of South Africa
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA
| | - Peter B. Madrid
- Center for Infectious Disease and Biodefense Research, Bioscience Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA
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Tambo-ong A, Chopra S, Glaser BT, Matsuyama K, Tran T, Madrid PB. Mannich reaction derivatives of novobiocin with modulated physiochemical properties and their antibacterial activities. Bioorg Med Chem Lett 2011; 21:5697-700. [PMID: 21871799 DOI: 10.1016/j.bmcl.2011.08.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 08/05/2011] [Accepted: 08/05/2011] [Indexed: 11/30/2022]
Abstract
Synthetic derivatives of the natural product antibiotic novobiocin were synthesized in order to improve their physiochemical properties. A Mannich reaction was used to introduce new side chains at a solvent-exposed position of the molecule, and a diverse panel of functional groups was evaluated at this position. Novobiocin and the new derivatives were tested for their binding to gyrase B and their antibacterial activities against Staphylococcus aureus, Mycobacterium tuberculosis, Francisella tularensis and Escherichia coli. While the new derivatives still bound the gyrase B protein potently (0.07-1.8 μM, IC(50)), they had significantly less antibacterial activity. Two compounds were identified with increased antibacterial activity against M. tuberculosis, with a minimum inhibitory concentration of 2.5 μg/ml.
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Affiliation(s)
- Arlyn Tambo-ong
- Center for Infectious Disease and Biodefense Research, Biosciences Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
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24
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Klöck C, Jin X, Choi K, Khosla C, Madrid PB, Spencer A, Raimundo BC, Boardman P, Lanza G, Griffin JH. Acylideneoxoindoles: a new class of reversible inhibitors of human transglutaminase 2. Bioorg Med Chem Lett 2011; 21:2692-6. [PMID: 21215619 PMCID: PMC3081996 DOI: 10.1016/j.bmcl.2010.12.037] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Revised: 12/04/2010] [Accepted: 12/07/2010] [Indexed: 01/03/2023]
Abstract
Inhibitors of human transglutaminase 2 (TG2) are anticipated to be useful in the therapy of a variety of diseases including celiac sprue as well as certain CNS disorders and cancers. A class of 3-acylidene-2-oxoindoles was identified as potent reversible inhibitors of human TG2. Structure-activity relationship analysis of a lead compound led to the generation of several potent, competitive inhibitors. Analogs with significant non-competitive character were also identified, suggesting that the compounds bind at one or more allosteric regulatory sites on this multidomain enzyme. The most active compounds had K(i) values below 1.0 μM in two different kinetic assays for human TG2, and may therefore be suitable for investigations into the role of TG2 in physiology and disease in animals.
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Affiliation(s)
- Cornelius Klöck
- Department of Chemistry, Stanford University, Stanford CA 94305, USA
| | - Xi Jin
- Department of Chemistry, Stanford University, Stanford CA 94305, USA
| | - Kihang Choi
- Department of Chemistry, Stanford University, Stanford CA 94305, USA
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford CA 94305, USA
- Deparment of Chemical Engineering, Stanford University, Stanford CA 94305, USA
| | - Peter B. Madrid
- Department of Medicinal Chemistry SRI International, Menlo Park CA 94025, USA
| | - Andrew Spencer
- Celiac Sprue Research Foundation, P.O. Box 61193, Palo Alto CA 94306-1193, USA
| | - Brian C. Raimundo
- Numerate, Inc., 1150 Bayhill Drive, Ste 203, San Bruno CA 94066, USA
| | - Paul Boardman
- Numerate, Inc., 1150 Bayhill Drive, Ste 203, San Bruno CA 94066, USA
| | - Guido Lanza
- Numerate, Inc., 1150 Bayhill Drive, Ste 203, San Bruno CA 94066, USA
| | - John H. Griffin
- Numerate, Inc., 1150 Bayhill Drive, Ste 203, San Bruno CA 94066, USA
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Glaser BT, Malerich JP, Duellman SJ, Fong J, Hutson C, Fine RM, Keblansky B, Tang MJ, Madrid PB. A high-throughput fluorescence polarization assay for inhibitors of gyrase B. ACTA ACUST UNITED AC 2011; 16:230-8. [PMID: 21245469 DOI: 10.1177/1087057110392038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
DNA gyrase, a type II topoisomerase that introduces negative supercoils into DNA, is a validated antibacterial drug target. The holoenzyme is composed of 2 subunits, gyrase A (GyrA) and gyrase B (GyrB), which form a functional A(2)B(2) heterotetramer required for bacterial viability. A novel fluorescence polarization (FP) assay has been developed and optimized to detect inhibitors that bind to the adenosine triphosphate (ATP) binding domain of GyrB. Guided by the crystal structure of the natural product novobiocin bound to GyrB, a novel novobiocin-Texas Red probe (Novo-TRX) was designed and synthesized for use in a high-throughput FP assay. The binding kinetics of the interaction of Novo-TRX with GyrB from Francisella tularensis has been characterized, as well as the effect of common buffer additives on the interaction. The assay was developed into a 21-µL, 384-well assay format and has been validated for use in high-throughput screening against a collection of Food and Drug Administration-approved compounds. The assay performed with an average Z' factor of 0.80 and was able to identify GyrB inhibitors from a screening library.
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Laderoute KR, Calaoagan JM, Madrid PB, Klon AE, Ehrlich PJ. SU11248 (sunitinib) directly inhibits the activity of mammalian 5'-AMP-activated protein kinase (AMPK). Cancer Biol Ther 2010; 10:68-76. [PMID: 20495370 DOI: 10.4161/cbt.10.1.12162] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AMPK has been termed the fuel sensor of mammalian cells because it directly responds to the depletion of the fuel molecule ATP. In previous work, we found that AMPK is strongly activated by tumor-like hypoxia and glucose deprivation, independently of the oxygen response system associated with HIF-1. We also observed high levels of AMPK activity in tumor cells in vivo, using different model tumors. These findings suggested the hypothesis that modulation of AMPK activity could have therapeutic value for the treatment of solid tumors. To investigate this hypothesis, we have been conducting a SAR study of potential small-molecule modulators of AMPK activity. Here we report that the chemotherapeutic drug SU11248 (sunitinib) is at least as potent an inhibitor of AMPK as compound C, which is a commonly used experimental direct inhibitor of the enzyme. We also provide a computational model of the binding pose of SU11248 to an AMPKα subunit, which suggests a structural basis for the affinity of the drug for the ATP site of the catalytic domain. The ability of SU11248 to inhibit AMPK has potential clinical significance--there may be populations of SU11248-treated patients in which AMPK activity is inhibited in normal as well as in tumor tissue.
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Ray S, Madrid PB, Catz P, LeValley SE, Furniss MJ, Rausch LL, Guy RK, DeRisi JL, Iyer LV, Green CE, Mirsalis JC. Development of a new generation of 4-aminoquinoline antimalarial compounds using predictive pharmacokinetic and toxicology models. J Med Chem 2010; 53:3685-95. [PMID: 20361799 DOI: 10.1021/jm100057h] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Among the known antimalarial drugs, chloroquine (CQ) and other 4-aminoquinolines have shown high potency and good bioavailability. Yet complications associated with drug resistance necessitate the discovery of effective new antimalarial agents. ADMET prediction studies were employed to evaluate a library of new molecules based on the 4-aminoquinolone-related structure of CQ. Extensive in vitro screening and in vivo pharmacokinetic studies in mice helped to identify two lead molecules, 18 and 4, with promising in vitro therapeutic efficacy, improved ADMET properties, low risk for drug-drug interactions, and desirable pharmacokinetic profiles. Both 18 and 4 are highly potent antimalarial compounds, with IC(50) values of 5.6 and 17.3 nM, respectively, against the W2 (CQ-resistant) strain of Plasmodium falciparum (for CQ, IC(50) = 382 nM). When tested in mice, these compounds were found to have biological half-lives and plasma exposure values similar to or higher than those of CQ; they are therefore desirable candidates to pursue in future clinical trials.
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Affiliation(s)
- Sunetra Ray
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, USA
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Madrid PB, Liou AP, DeRisi JL, Guy RK. Incorporation of an Intramolecular Hydrogen-Bonding Motif in the Side Chain of 4-Aminoquinolines Enhances Activity against Drug-Resistant P. falciparum. J Med Chem 2008. [DOI: 10.1021/jm701572a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Warhurst DC, Craig JC, Adagu IS, Guy RK, Madrid PB, Fivelman QL. Activity of piperaquine and other 4-aminoquinoline antiplasmodial drugs against chloroquine-sensitive and resistant blood-stages of Plasmodium falciparum. Biochem Pharmacol 2007; 73:1910-26. [PMID: 17466277 DOI: 10.1016/j.bcp.2007.03.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 03/05/2007] [Accepted: 03/12/2007] [Indexed: 10/23/2022]
Abstract
Chloroquine (CQ), a 4-aminoquinoline, accumulates in acidic digestive vacuoles of the malaria parasite, preventing conversion of toxic haematin to beta-haematin. We examine how bis 4-aminoquinoline piperaquine (PQ) and its hydroxy-modification (OH-PQ) retain potency on chloroquine-resistant (CQ-R) Plasmodium falciparum. For CQ, PQ, OH-PQ and 4 and 5, representing halves of PQ, beta-haematin inhibitory activity (BHIA) was assayed, while potency was determined in CQ-sensitive (CQ-S) and CQ-R P. falciparum. From measured pK(a)s and the pH-modulated distribution of base between water and lipid (logD), the vacuolar accumulation ratio (VAR) of charged drug from plasma water (pH 7.4) into vacuolar water (pH 4.8) and lipid accumulation ratio (LAR) were calculated. All agents were active in BHIA. In CQ-S, PQ, OH-PQ and CQ were equally potent while 4 and 5 were 100 times less potent. CQ with two basic centres has a VAR of 143,482, while 4 and 5, with two basic centres of lower pK(a)s have VARs of 1287 and 1966. In contrast PQ and OH-PQ have four basic centres and achieve VARs of 104,378 and 19,874. This confirms the importance of VAR for potency against CQ-S parasites. Contrasting results were seen in CQ-R. 5, PQ and OH-PQ with LARs of 693; 973,492 and 398,118 (compared with 8.25 for CQ) showed similar potency in CQ-S and CQ-R. Importance of LAR for potency against CQ-R parasites probably reflects ability to block efflux by hydrophobic interaction with PfCRT but may relate to beta-haematin inhibition in vacuolar lipid.
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Affiliation(s)
- David C Warhurst
- Pathogen Molecular Biology Unit, Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, University of London, Keppel Street, London WC1E 7HT, UK.
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Madrid PB, Polgar WE, Toll L, Tanga MJ. Synthesis and antitubercular activity of phenothiazines with reduced binding to dopamine and serotonin receptors. Bioorg Med Chem Lett 2007; 17:3014-7. [PMID: 17407813 DOI: 10.1016/j.bmcl.2007.03.064] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 03/19/2007] [Accepted: 03/19/2007] [Indexed: 11/28/2022]
Abstract
Analogs of the psychotropic phenothiazines were synthesized and examined as antitubercular agents against Mycobacterium tuberculosis H37Rv. The compounds were subsequently counter-screened for binding to the dopaminergic-receptor subtypes D1, D2, D3 and the serotonergic-receptor subtypes 5-HT(1A), 5-HT(2A), and 5-HT(2C). The most active compounds showed MICs from 2 to 4 microg/mL and had overall reduced binding to the dopamine and serotonin receptors compared to chlorpromazine and trifluoperazine.
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Affiliation(s)
- Peter B Madrid
- Biosciences Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA.
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31
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Mayer M, Lang PT, Gerber S, Madrid PB, Pinto IG, Guy RK, James TL. Synthesis and testing of a focused phenothiazine library for binding to HIV-1 TAR RNA. ACTA ACUST UNITED AC 2006; 13:993-1000. [PMID: 16984889 DOI: 10.1016/j.chembiol.2006.07.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 07/12/2006] [Accepted: 07/25/2006] [Indexed: 11/25/2022]
Abstract
We have synthesized a series of phenothiazine derivatives, which were used to test the structure-activity relationship of binding to HIV-1 TAR RNA. Variations from our initial compound, 2-acetylphenothiazine, focused on two moieties: ring substitutions and n-alkyl substitutions. Binding characteristics were ascertained via NMR, principally by saturation transfer difference spectra of the ligand and imino proton resonance shifts of the RNA. Both ring and alkyl substitutions manifested NMR changes upon binding. In general, the active site, while somewhat flexible, has regions that can be capitalized for increased binding through van der Waals interactions and others that can be optimized for solubility in subsequent stages of development. However, binding can be nontrivially enhanced several-fold through optimization of van der Waals and hydrophilic sites of the scaffold.
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Affiliation(s)
- Moriz Mayer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA
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May BCH, Witkop J, Sherrill J, Anderson MO, Madrid PB, Zorn JA, Prusiner SB, Cohen FE, Guy RK. Structure–activity relationship study of 9-aminoacridine compounds in scrapie-infected neuroblastoma cells. Bioorg Med Chem Lett 2006; 16:4913-6. [PMID: 16860557 DOI: 10.1016/j.bmcl.2006.06.050] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Accepted: 06/14/2006] [Indexed: 11/26/2022]
Abstract
A focused library of variously substituted 9-aminoacridine compounds was screened for bioactivity against accumulation of the infectious prion protein isoform, denoted PrP(Sc), in a cell model of prion replication. The efficacy of compounds against PrP(Sc) accumulation was influenced by both substituents of the distal tertiary amine and acridine heterocycle, while cellular cytotoxicity was encoded in the acridine heterocycle substituents.
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Affiliation(s)
- Barnaby C H May
- Institute for Neurodegenerative Diseases, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143, USA.
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Madrid PB, Liou AP, DeRisi JL, Guy RK. Incorporation of an intramolecular hydrogen-bonding motif in the side chain of 4-aminoquinolines enhances activity against drug-resistant P. falciparum. J Med Chem 2006; 49:4535-43. [PMID: 16854059 PMCID: PMC1524878 DOI: 10.1021/jm0600951] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous data showing that several chloroquine analogues containing an intramolecular hydrogen-bonding motif were potent against multidrug-resistant P. falciparum led to the exploration of the importance of this motif. A series of 116 compounds containing four different alkyl linkers and various aromatic substitutions with hydrogen bond accepting capability was synthesized. The series showed broad potency against the drug-resistant W2 strain of P. falciparum. In particular, a novel series containing variations of the alpha-aminocresol motif gave eight compounds with IC50 values more potent than 5 nM against the W2 strain. Such simple modifications, significantly altering the pKa and sterics of the basic side chain in chloroquine analogues, may prove to be part of a strategy for overcoming the problem of worldwide resistance to affordable antimalarial drugs.
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Affiliation(s)
- Peter B Madrid
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-2280, USA
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Anderson MO, Sherrill J, Madrid PB, Liou AP, Weisman JL, DeRisi JL, Guy RK. Parallel synthesis of 9-aminoacridines and their evaluation against chloroquine-resistant Plasmodium falciparum. Bioorg Med Chem 2005; 14:334-43. [PMID: 16216519 PMCID: PMC1474025 DOI: 10.1016/j.bmc.2005.08.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Revised: 08/04/2005] [Accepted: 08/05/2005] [Indexed: 10/25/2022]
Abstract
A parallel synthetic strategy to the 9-aminoacridine scaffold of the classical anti-malarial drug quinacrine (2) is presented. The method features a new route to 9-chloroacridines that utilizes triflates of salicylic acid derivatives, which are commercially available in a variety of substitution patterns. The route allows ready variation of the two diversity elements present in this class of molecules: the tricyclic aromatic heterocyclic core, and the disubstituted diamine sidechain. In this study, a library of 175 compounds was designed, although only 93 of the final products had purities acceptable for screening. Impurity was generally due to incomplete removal of 9-acridones (18), a degradation product of the 9-chloroacridine synthetic intermediates. The library was screened against two strains of Plasmodium falciparum, including a model of the drug-resistant parasite, and six novel compounds were found to have IC(50) values in the low nanomolar range.
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Affiliation(s)
- Marc O Anderson
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA 94143-2280, USA
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Madrid PB, Sherrill J, Liou AP, Weisman JL, Derisi JL, Guy RK. Synthesis of ring-substituted 4-aminoquinolines and evaluation of their antimalarial activities. Bioorg Med Chem Lett 2005; 15:1015-8. [PMID: 15686903 DOI: 10.1016/j.bmcl.2004.12.037] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2004] [Revised: 12/10/2004] [Accepted: 12/14/2004] [Indexed: 11/26/2022]
Abstract
A simple two-step synthesis method was used to make 51 B-ring-substituted 4-hydroxyquinolines allowing analysis of the effect of ring substitutions on inhibition of growth of chloroquine sensitive and resistant strains of Plasmodium falciparum, the dominant cause of malaria morbidity. Substituted quinoline rings other than the 7-chloroquinoline ring found in chloroquine were found to have significant activity against the drug-resistant strain of P. falciparum W2.
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Affiliation(s)
- Peter B Madrid
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143-2280, USA
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