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Li M, Chen S, Wang Y, Zhang S, Song D, Tian R, Geng J, Wang L. Label-free high-precise nanopore detection of endopeptidase activity of anthrax lethal factor regulated by diverse conditions. Biosens Bioelectron 2023; 219:114800. [PMID: 36274430 DOI: 10.1016/j.bios.2022.114800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/24/2022] [Accepted: 10/08/2022] [Indexed: 11/19/2022]
Abstract
Endopeptidase activity of anthrax lethal factor (aLF) prevents the destroy of anthracis spore intracellularly by host macrophages, meanwhile disables the signaling pathways extracellularly that leads to host lethality. Hence, inhibitory of this activity is expected to be an alternative option to cure anthrax infection. Herein, we fabricated a nanopore platform via transmembrane pore construction in vitro, which allows precise mimics, monitoring of intercellular proteinic transport and enables the quantitative detection of aLF endopeptidase activity towards MAPKK signaling protein at single molecule level. Next, we inhibited the aLF activity via screening approaches of protein-metal ion acquisition and other condition controlment (proton/hydroxide strength, adapted temperature, ionizing irradiation), which were identified by nanopore electrokinetic study. Upon the results, we found that Ca2+, Mg2+, Mn2+, Ni2+ collaborating with Zn2+ promote aLF activity efficiently. In contrary, Cd2+, Co2+, Cu2+ have great inhibitory effect. Result further revealed that, the speed of aLF endopeptidase activity with different ions functions as the nanopore signal frequency in linear manner, which enables evident distinction of those divalent ions using this proteinase assay. We also found the higher strength of the proton or hydroxide, the higher the inhibitory to aLF activity. Besides, adapted temperature and γ-ray also play integral roles in inhibiting this activity. Our results lay experimental basis for accurate detection of aLF activity, meanwhile provide new direction to screening novel stimuli-responsive inhibitors specific to aLF.
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Affiliation(s)
- Minghan Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China; Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Shanchuan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Shaoxia Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China; School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Dandan Song
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China; School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Rong Tian
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
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2
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Arshad JZ, Hanif M. Hydroxypyrone derivatives in drug discovery: from chelation therapy to rational design of metalloenzyme inhibitors. RSC Med Chem 2022; 13:1127-1149. [PMID: 36325396 PMCID: PMC9579940 DOI: 10.1039/d2md00175f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/28/2022] [Indexed: 07/31/2023] Open
Abstract
The versatile structural motif of hydroxypyrone is found in natural products and can be easily converted into hydroxypyridone and hydroxythiopyridone analogues. The favourable toxicity profile and ease of functionalization to access a vast library of compounds make them an ideal structural scaffold for drug design and discovery. This versatile scaffold possesses excellent metal chelating properties that can be exploited for chelation therapy in clinics. Deferiprone [1,2-dimethyl-3-hydroxy-4(1H)-one] was the first orally active chelator to treat iron overload in thalassemia major. Metal complexes of hydroxy-(thio)pyr(id)ones have been investigated as magnetic resonance imaging contrast agents, and anticancer and antidiabetic agents. In recent years, this compound class has demonstrated potential in discovering and developing metalloenzyme inhibitors. This review article summarizes recent literature on hydroxy-(thio)pyr(id)ones as inhibitors for metalloenzymes such as histone deacetylases, tyrosinase and metallo-β-lactamase. Different approaches to the design of hydroxy-(thio)pyr(id)ones and their biological properties against selected metalloenzymes are discussed.
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Affiliation(s)
- Jahan Zaib Arshad
- Department of Chemistry, Government College Women University Sialkot Sialkot Pakistan
| | - Muhammad Hanif
- School of Chemical Sciences, University of Auckland Private Bag 92019 Auckland 1142 New Zealand (+64) 9 373 7599 ext. 87422
- MacDiarmid Institute for Advanced Materials and Nanotechnology Wellington New Zealand
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Prosser KE, Kohlbrand AJ, Seo H, Kalaj M, Cohen SM. 19F-Tagged metal binding pharmacophores for NMR screening of metalloenzymes. Chem Commun (Camb) 2021; 57:4934-4937. [PMID: 33870988 PMCID: PMC8137660 DOI: 10.1039/d1cc01231b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study demonstrates the screening of a collection of twelve 19F-tagged metal-binding pharmacophores (MBPs) against the Zn(ii)-dependent metalloenzyme human carbonic anhydrase II (hCAII) by 19F NMR. The isomorphous replacement of Zn(ii) by Co(ii) in hCAII produces enhanced sensitivity and reveals the potential of 19F NMR-based techniques for metalloenzyme ligand discovery.
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Affiliation(s)
- Kathleen E Prosser
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Alysia J Kohlbrand
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Hyeonglim Seo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Mark Kalaj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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Kucerova-Chlupacova M, Halakova D, Majekova M, Treml J, Stefek M, Soltesova Prnova M. (4-Oxo-2-thioxothiazolidin-3-yl)acetic acids as potent and selective aldose reductase inhibitors. Chem Biol Interact 2020; 332:109286. [DOI: 10.1016/j.cbi.2020.109286] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/29/2020] [Accepted: 10/06/2020] [Indexed: 12/22/2022]
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5
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Dalvit C, Veronesi M, Vulpetti A. Fluorine NMR functional screening: from purified enzymes to human intact living cells. JOURNAL OF BIOMOLECULAR NMR 2020; 74:613-631. [PMID: 32347447 DOI: 10.1007/s10858-020-00311-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
The substrate- or cofactor-based fluorine NMR screening, also known as n-FABS (n fluorine atoms for biochemical screening), represents a powerful method for performing a direct functional assay in the search of inhibitors or enhancers of an enzymatic reaction. Although it suffers from the intrinsic low sensitivity compared to other biophysical techniques usually applied in functional assays, it has some distinctive features that makes it appealing for tackling complex chemical and biological systems. Its strengths are represented by the easy set-up, robustness, flexibility, lack of signal interference and rich information content resulting in the identification of bona fide inhibitors and reliable determination of their inhibitory strength. The versatility of the n-FABS allows its application to either purified enzymes, cell lysates or intact living cells. The principles, along with theoretical, technical and practical aspects, of the methodology are discussed. Furthermore, several applications of the technique to pharmaceutical projects are presented.
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Affiliation(s)
| | - Marina Veronesi
- D3-PharmaChemistry, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland
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Saxena M, Nandi S, Saxena AK. QSAR and molecular docking studies of lethal factor protease inhibitors against Bacillus anthracis. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:715-731. [PMID: 31556709 DOI: 10.1080/1062936x.2019.1658219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/18/2019] [Indexed: 06/10/2023]
Abstract
Bacillus anthracis is considered as a biological warfare agent because it is the causative agent of the serious infectious anthrax disease. Delay in treatment leads to lethal factor-mediated toxaemia which is very critical due to lack of therapeutic options. Consequently, attempts have been made to discover potent lethal factor (LF) protease inhibitors such as small-molecule synthetic 2-thio-1,3-thiazolidine-4-one (rhodanine) compounds. But computed descriptor-based quantitative structure-activity relationship (QSAR) and drug design studies on such aspect are poorly represented. Therefore, an attempt was made for developing QSAR models using structural descriptors for 1,3-thiazolidine-4-one compounds. The models were developed on a series of 49 LF protease inhibitors using the combination of constitutional, functional group, atom-centred fragment and molecular property descriptors. The best QSAR model included four variables, namely, C-040, nR05, GVWAI-80 and ALOGP that correlated well with the anti-LF protease activity with a good correlation coefficient (r = 0.870) of good statistical significance (F4, 29 = 14.09 (α = 0.001) F4, 29 = 6.19). This model was also validated and explained 58.1% of variances of the Bacillus anthracis inhibitory activities of the studied compounds with r2pred = 0.710 which denotes external predictability. Finally, molecular docking was carried out to predict the mode of binding of some highly active congeneric compounds. It was shown that VAL 1403 is an important residue for phenyl ring. TYR 1456 and HIS 1418 are responsible for interaction with the rhodanine nucleus. Therefore, these residues are considered responsible for the inhibition of LF protease anthrax and can predict significant dimension of essential structural features of these inhibitors to evaluate, screen and help priorities of the synthesis of the candidates against anthrax bioterrorism.
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Affiliation(s)
- M Saxena
- Department of Chemistry, Amity University , Lucknow , India
| | - S Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research, Affiliated to Uttarakhand Technical University , Kashipur , India
| | - A K Saxena
- Division of Medicinal and Process Chemistry, CSIR-Central Drug Research Institute , Lucknow , India
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Kotha S, Sreevani G. Diversity-Oriented Approach to Spirorhodanines via a [2+2+2] Cyclotrimerization. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sambasivarao Kotha
- Department of Chemistry; Indian Institute of Technology Bombay; 400076 Powai Mumbai India
| | - Gaddamedi Sreevani
- Department of Chemistry; Indian Institute of Technology Bombay; 400076 Powai Mumbai India
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8
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Dalvit C, Vulpetti A. Ligand-Based Fluorine NMR Screening: Principles and Applications in Drug Discovery Projects. J Med Chem 2018; 62:2218-2244. [DOI: 10.1021/acs.jmedchem.8b01210] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
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9
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Young CJ, Richard K, Beruar A, Lo SY, Siemann S. An investigation of the pH dependence of copper-substituted anthrax lethal factor and its mechanistic implications. J Inorg Biochem 2018; 182:1-8. [PMID: 29407865 DOI: 10.1016/j.jinorgbio.2018.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/18/2017] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
Abstract
Anthrax lethal factor (LF) is a zinc-dependent endopeptidase involved in the cleavage of proteins critical to the maintenance of host signaling pathways during anthrax infections. Although zinc is typically regarded as the native metal ion in vivo, LF is highly tolerant to metal substitution, with its replacement by copper yielding an enzyme (CuLF) 4.5-fold more active than the native zinc protein (at pH 7). The current study demonstrates that by careful choice of the buffer, ionic strength, pH and substrate, the activity ratio of CuLF and native LF can be increased to >40-fold. Using a fluorogenic LF substrate, such optimized assay conditions can be exploited to detect LF concentrations as low as 2 pM. In contrast to the zinc form, CuLF was found to be inhibited by bromide and iodide ions, to be resistant to metal loss under acidic conditions, and to display a sharp pH dependence with significantly shifted alkaline limb towards more acidic conditions. The alkaline limb in the enzyme's pH profile is suggested to originate from changes in the protonation state of the metal-bound water molecule which serves as the nucleophile in the catalytic mechanism. Based on these observations and studies on other zinc proteases, a minimal mechanism for LF is proposed.
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Affiliation(s)
- Calvin J Young
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Kaitlin Richard
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Ananya Beruar
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Suet Y Lo
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Stefan Siemann
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada.
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10
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S. Alneyadi S. Rhodanine as a Scaffold: A Short Review on Its Synthesis and Anti-Diabetic Activities. HETEROCYCLES 2018. [DOI: 10.3987/rev-17-878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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11
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Kaminskyy D, Kryshchyshyn A, Lesyk R. 5-Ene-4-thiazolidinones - An efficient tool in medicinal chemistry. Eur J Med Chem 2017; 140:542-594. [PMID: 28987611 PMCID: PMC7111298 DOI: 10.1016/j.ejmech.2017.09.031] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 07/14/2017] [Accepted: 09/17/2017] [Indexed: 02/02/2023]
Abstract
The presented review is an attempt to summarize a huge volume of data on 5-ene-4-thiazolidinones being a widely studied class of small molecules used in modern organic and medicinal chemistry. The manuscript covers approaches to the synthesis of 5-ene-4-thiazolidinone derivatives: modification of the C5 position of the basic core; synthesis of the target compounds in the one-pot or multistage reactions or transformation of other related heterocycles. The most prominent pharmacological profiles of 5-ene derivatives of different 4-thiazolidinone subtypes belonging to hit-, lead-compounds, drug-candidates and drugs as well as the most studied targets have been discussed. Currently target compounds (especially 5-en-rhodanines) are assigned as frequent hitters or pan-assay interference compounds (PAINS) within high-throughput screening campaigns. Nevertheless, the crucial impact of the presence/nature of C5 substituent (namely 5-ene) on the pharmacological effects of 5-ene-4-thiazolidinones was confirmed by the numerous listed findings from the original articles. The main directions for active 5-ene-4-thiazolidinones optimization have been shown: i) complication of the fragment in the C5 position; ii) introduction of the substituents in the N3 position (especially fragments with carboxylic group or its derivatives); iii) annealing in complex heterocyclic systems; iv) combination with other pharmacologically attractive fragments within hybrid pharmacophore approach. Moreover, the utilization of 5-ene-4-thiazolidinones in the synthesis of complex compounds with potent pharmacological application is described. The chemical transformations cover mainly the reactions which involve the exocyclic double bond in C5 position of the main core and correspond to the abovementioned direction of the 5-ene-4-thiazolidinone modification.
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Affiliation(s)
- Danylo Kaminskyy
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv-10, 79010, Ukraine
| | - Anna Kryshchyshyn
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv-10, 79010, Ukraine
| | - Roman Lesyk
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv-10, 79010, Ukraine.
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Targeting Bacillus anthracis toxicity with a genetically selected inhibitor of the PA/CMG2 protein-protein interaction. Sci Rep 2017; 7:3104. [PMID: 28596569 PMCID: PMC5465072 DOI: 10.1038/s41598-017-03253-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/25/2017] [Indexed: 11/23/2022] Open
Abstract
The protein-protein interaction between the human CMG2 receptor and the Bacillus anthracis protective antigen (PA) is essential for the transport of anthrax lethal and edema toxins into human cells. We used a genetically encoded high throughput screening platform to screen a SICLOPPS library of 3.2 million cyclic hexapeptides for inhibitors of this protein-protein interaction. Unusually, the top 3 hits all contained stop codons in the randomized region of the library, resulting in linear rather than cyclic peptides. These peptides disrupted the targeted interaction in vitro; two act by binding to CMG2 while one binds PA. The efficacy of the most potent CMG2-binding inhibitor was improved through the incorporation of non-natural phenylalanine analogues. Cell based assays demonstrated that the optimized inhibitor protects macrophages from the toxicity of lethal factor.
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El Khoury L, Naseem-Khan S, Kwapien K, Hobaika Z, Maroun RG, Piquemal JP, Gresh N. Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions. J Comput Chem 2017; 38:1897-1920. [DOI: 10.1002/jcc.24830] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/18/2017] [Accepted: 04/03/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Léa El Khoury
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC; UMR7616 CNRS Paris France
- Centre d'Analyses et de Recherche, UR EGFEM, LSIM, Faculté des Sciences, Saint Joseph University of Beirut; BP 11-514, Riad El Solh Beirut 1116-2050 Lebanon
| | - Sehr Naseem-Khan
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC; UMR7616 CNRS Paris France
| | - Karolina Kwapien
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale Paris France
- Institut Charles-Gerhardt, UMR 5253, CNRS-UM2-UM1-ENSM; Montpellier France
| | - Zeina Hobaika
- Centre d'Analyses et de Recherche, UR EGFEM, LSIM, Faculté des Sciences, Saint Joseph University of Beirut; BP 11-514, Riad El Solh Beirut 1116-2050 Lebanon
| | - Richard G. Maroun
- Centre d'Analyses et de Recherche, UR EGFEM, LSIM, Faculté des Sciences, Saint Joseph University of Beirut; BP 11-514, Riad El Solh Beirut 1116-2050 Lebanon
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC; UMR7616 CNRS Paris France
- Institut Universitaire de France; Paris Cedex 05 75231 France
- Department of Biomedical Engineering; The University of Texas at Austin; Texas 78712
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC; UMR7616 CNRS Paris France
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Affiliation(s)
- Megan Garland
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Sebastian Loscher
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Matthew Bogyo
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
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Goldberg AB, Cho E, Miller CJ, Lou HJ, Turk BE. Identification of a Substrate-selective Exosite within the Metalloproteinase Anthrax Lethal Factor. J Biol Chem 2016; 292:814-825. [PMID: 27909054 DOI: 10.1074/jbc.m116.761734] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/23/2016] [Indexed: 01/02/2023] Open
Abstract
The metalloproteinase anthrax lethal factor (LF) is secreted by Bacillus anthracis to promote disease virulence through disruption of host signaling pathways. LF is a highly specific protease, exclusively cleaving mitogen-activated protein kinase kinases (MKKs) and rodent NLRP1B (NACHT leucine-rich repeat and pyrin domain-containing protein 1B). How LF achieves such restricted substrate specificity is not understood. Previous studies have suggested the existence of an exosite interaction between LF and MKKs that promotes cleavage efficiency and specificity. Through a combination of in silico prediction and site-directed mutagenesis, we have mapped an exosite to a non-catalytic region of LF. Mutations within this site selectively impair proteolysis of full-length MKKs yet have no impact on cleavage of short peptide substrates. Although this region appears important for cleaving all LF protein substrates, we found that mutation of specific residues within the exosite differentially affects MKK and NLRP1B cleavage in vitro and in cultured cells. One residue in particular, Trp-271, is essential for cleavage of MKK3, MKK4, and MKK6 but dispensable for targeting of MEK1, MEK2, and NLRP1B. Analysis of chimeric substrates suggests that this residue interacts with the MKK catalytic domain. We found that LF-W271A blocked ERK phosphorylation and growth in a melanoma cell line, suggesting that it may provide a highly selective inhibitor of MEK1/2 for use as a cancer therapeutic. These findings provide insight into how a bacterial toxin functions to specifically impair host signaling pathways and suggest a general strategy for mapping protease exosite interactions.
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Affiliation(s)
- Allison B Goldberg
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Eunice Cho
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Chad J Miller
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Hua Jane Lou
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Benjamin E Turk
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
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16
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Ambrose EA. Botulinum Neurotoxin, Tetanus Toxin, and Anthrax Lethal Factor Countermeasures. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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17
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Zhang X, Amin EA. Highly predictive support vector machine (SVM) models for anthrax toxin lethal factor (LF) inhibitors. J Mol Graph Model 2016; 63:22-8. [PMID: 26615468 PMCID: PMC4713341 DOI: 10.1016/j.jmgm.2015.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 10/07/2015] [Accepted: 11/06/2015] [Indexed: 01/08/2023]
Abstract
Anthrax is a highly lethal, acute infectious disease caused by the rod-shaped, Gram-positive bacterium Bacillus anthracis. The anthrax toxin lethal factor (LF), a zinc metalloprotease secreted by the bacilli, plays a key role in anthrax pathogenesis and is chiefly responsible for anthrax-related toxemia and host death, partly via inactivation of mitogen-activated protein kinase kinase (MAPKK) enzymes and consequent disruption of key cellular signaling pathways. Antibiotics such as fluoroquinolones are capable of clearing the bacilli but have no effect on LF-mediated toxemia; LF itself therefore remains the preferred target for toxin inactivation. However, currently no LF inhibitor is available on the market as a therapeutic, partly due to the insufficiency of existing LF inhibitor scaffolds in terms of efficacy, selectivity, and toxicity. In the current work, we present novel support vector machine (SVM) models with high prediction accuracy that are designed to rapidly identify potential novel, structurally diverse LF inhibitor chemical matter from compound libraries. These SVM models were trained and validated using 508 compounds with published LF biological activity data and 847 inactive compounds deposited in the Pub Chem BioAssay database. One model, M1, demonstrated particularly favorable selectivity toward highly active compounds by correctly predicting 39 (95.12%) out of 41 nanomolar-level LF inhibitors, 46 (93.88%) out of 49 inactives, and 844 (99.65%) out of 847 Pub Chem inactives in external, unbiased test sets. These models are expected to facilitate the prediction of LF inhibitory activity for existing molecules, as well as identification of novel potential LF inhibitors from large datasets.
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Affiliation(s)
- Xia Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55414-2959, United States
| | - Elizabeth Ambrose Amin
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55414-2959, United States; Minnesota Supercomputing Institute for Advanced Computational Research, 117 Pleasant St SE, Minneapolis, MN, United States.
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18
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Fluorine nuclear magnetic resonance-based assay in living mammalian cells. Anal Biochem 2015; 495:52-9. [PMID: 26686030 DOI: 10.1016/j.ab.2015.11.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/17/2015] [Accepted: 11/24/2015] [Indexed: 12/18/2022]
Abstract
Nuclear magnetic resonance (NMR)-based screening has been recognized as a powerful approach for the identification and characterization of molecules interacting with pharmaceutical targets. Indeed, several NMR methods have been developed and successfully applied to many drug discovery projects. Whereas most of these approaches have targeted isolated biomolecular receptors, very few cases are reported with the screening performed in intact cells and cell extracts. Here we report the first successful application of the fluorine NMR-based assay n-FABS (n-fluorine atoms for biochemical screening) in living mammalian cells expressing the membrane protein fatty acid amide hydrolase (FAAH). This method allows the identification of both weak and potent inhibitors and the measurement of their potency in a physiological environment.
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Maize KM, Kurbanov EK, Johnson RL, Amin EA, Finzel BC. Ligand-induced expansion of the S1' site in the anthrax toxin lethal factor. FEBS Lett 2015; 589:3836-41. [PMID: 26578066 DOI: 10.1016/j.febslet.2015.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 10/27/2015] [Accepted: 11/02/2015] [Indexed: 12/31/2022]
Abstract
The Bacillus anthracis lethal factor (LF) is one component of a tripartite exotoxin partly responsible for persistent anthrax cytotoxicity after initial bacterial infection. Inhibitors of the zinc metalloproteinase have been investigated as potential therapeutic agents, but LF is a challenging target because inhibitors lack sufficient selectivity or possess poor pharmaceutical properties. These structural studies reveal an alternate conformation of the enzyme, induced upon binding of specific inhibitors, that opens a previously unobserved deep pocket termed S1'(∗) which might afford new opportunities to design selective inhibitors that target this subsite.
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Affiliation(s)
- Kimberly M Maize
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, United States
| | - Elbek K Kurbanov
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, United States
| | - Rodney L Johnson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, United States
| | - Elizabeth Ambrose Amin
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, United States
| | - Barry C Finzel
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, United States.
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20
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Kurbanov EK, Chiu TL, Solberg J, Francis S, Maize KM, Fernandez J, Johnson RL, Hawkinson JE, Walters MA, Finzel BC, Amin EA. Probing the S2′ Subsite of the Anthrax Toxin Lethal Factor Using Novel N-Alkylated Hydroxamates. J Med Chem 2015; 58:8723-33. [DOI: 10.1021/acs.jmedchem.5b01446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elbek K. Kurbanov
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Ting-Lan Chiu
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Jonathan Solberg
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Subhashree Francis
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Kimberly M. Maize
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Jenna Fernandez
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Rodney L. Johnson
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Jon E. Hawkinson
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Michael A. Walters
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Barry C. Finzel
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Elizabeth Ambrose Amin
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
- Minnesota
Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455, United States
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21
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Sharaf NG, Gronenborn AM. (19)F-modified proteins and (19)F-containing ligands as tools in solution NMR studies of protein interactions. Methods Enzymol 2015; 565:67-95. [PMID: 26577728 DOI: 10.1016/bs.mie.2015.05.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
(19)F solution NMR is a powerful and versatile tool to study protein structure and protein-ligand interactions due to the favorable NMR characteristics of the (19)F atom, its absence in naturally occurring biomolecules, and small size. Protocols to introduce (19)F atoms into both proteins and their ligands are readily available and offer the ability to conduct protein-observe (using (19)F-labeled proteins) or ligand-observe (using (19)F-containing ligands) NMR experiments. This chapter provides two protocols for the (19)F-labeling of proteins, using an Escherichia coli expression system: (i) amino acid type-specific incorporation of (19)F-modified amino acids and (ii) site-specific incorporation of (19)F-modified amino acids using recombinantly expressed orthogonal amber tRNA/tRNA synthetase pairs. In addition, we discuss several applications, involving (19)F-modified proteins and (19)F-containing ligands.
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Affiliation(s)
- Naima G Sharaf
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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22
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Effects of metalloprotease anthrax lethal factor on its peptide-based inhibitor R9LF-1. Mol Cell Biochem 2015; 406:293-9. [PMID: 25981534 DOI: 10.1007/s11010-015-2447-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 05/07/2015] [Indexed: 10/23/2022]
Abstract
The metalloprotease lethal factor (LF) from Bacillus anthracis plays a vital role in anthrax toxin action, and thus becomes a target for anti-anthrax therapy. Following the guidelines based on existing metalloprotease inhibitors, we designed a 'first-generation' LF inhibitor R9LF-1. This inhibitor was shown to be very stable by itself in a wide range of pH and temperature and able to inhibit LF activity in vitro. However, as we reported previously in the presence of LF, this inhibitor was degraded to a small molecular weight species, resulting in a significantly decreased ability to protect MAPKK from cleavage by LF as well as to protect murine macrophages from lethal toxin. In order to elucidate this unusual phenomenon to build solid basis for high-efficiency LF inhibitor development, we performed extensive research to study the effect of LF on its peptide-based inhibitor. Effects of temperature and incubation period of time on generation of the smaller peptide (short version R9LF-1) by LF as well as its catalytic domain were analyzed. We found that LF degraded R9LF-1 with maximum efficiency in the pH range of 7.0-8.5, which correlates well with the range of LF enzymatic activity with its native substrate. The degradation showed a deviation from normal hyperbolic kinetics but a similarity to the kinetics profile of an enzyme-catalyzed reaction with positive cooperativity. The short version R9LF-1 had decreased inhibitory activity toward LF; surprisingly, BIAcore results suggested a better affinity for its binding to LF. In addition, R9LF-1 was not hydrolyzed by other common proteases, such as chymotrypsin and pepsin, suggesting hydrolysis of the bond between amino acid and hydroxamate groups is unique to LF. This study calls for caution when designing peptide-based LF inhibitors and when interpreting effects of these types of inhibitors.
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Ohanjanian L, Remy KE, Li Y, Cui X, Eichacker PQ. An overview of investigational toxin-directed therapies for the adjunctive management of Bacillus anthracis infection and sepsis. Expert Opin Investig Drugs 2015; 24:851-65. [PMID: 25920540 DOI: 10.1517/13543784.2015.1041587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Sepsis with Bacillus anthracis infection has a very high mortality rate despite appropriate antibiotic and supportive therapies. Over the past 15 years, recent outbreaks in the US and in Europe, coupled with anthrax's bioterrorism weapon potential, have stimulated efforts to develop adjunctive therapies to improve clinical outcomes. Since lethal toxin and edema toxin (LT and ET) make central contributions to the pathogenesis of B. anthracis, these have been major targets in this effort. AREAS COVERED Here, the authors review different investigative biopharmaceuticals that have been recently identified for their therapeutic potential as inhibitors of LT or ET. Among these inhibitors are two antibody preparations that have been included in the Strategic National Stockpile (SNS) and several more that have reached Phase I testing. Presently, however, many of these candidate agents have only been studied in vitro and very few tested in bacteria-challenged models. EXPERT OPINION Although a large number of drugs have been identified as potential therapeutic inhibitors of LT and ET, in most cases their testing has been limited. The use of the two SNS antibody therapies during a large-scale exposure to B. anthracis will be difficult. Further testing and development of agents with oral bioavailability and relatively long shelf lives should be a focus for future research.
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Affiliation(s)
- Lernik Ohanjanian
- National Institutes of Health, Clinical Center, Critical Care Medicine Department , Building 10, Room 2C145, Bethesda, MD 20892 , USA +1 301 402 2914 ; +1 301 402 1213 ;
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24
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Maize KM, Zhang X, Amin EA. Statistical analysis, optimization, and prioritization of virtual screening parameters for zinc enzymes including the anthrax toxin lethal factor. Curr Top Med Chem 2014; 14:2105-14. [PMID: 25373478 DOI: 10.2174/1568026614666141106163011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 09/01/2014] [Accepted: 09/09/2014] [Indexed: 11/22/2022]
Abstract
The anthrax toxin lethal factor (LF) and matrix metalloproteinase-3 (MMP-3, stromelysin-1) are popular zinc metalloenzyme drug targets, with LF primarily responsible for anthrax-related toxicity and host death, while MMP-3 is involved in cancer- and rheumatic disease-related tissue remodeling. A number of in silico screening techniques, most notably docking and scoring, have proven useful for identifying new potential drug scaffolds targeting LF and MMP-3, as well as for optimizing lead compounds and investigating mechanisms of action. However, virtual screening outcomes can vary significantly depending on the specific docking parameters chosen, and systematic statistical significance analyses are needed to prioritize key parameters for screening small molecules against these zinc systems. In the current work, we present a series of chi-square statistical analyses of virtual screening outcomes for cocrystallized LF and MMP-3 inhibitors docked into their respective targets, evaluated by predicted enzyme-inhibitor dissociation constant and root-mean-square deviation (RMSD) between predicted and experimental bound configurations, and we present a series of preferred parameters for use with these systems in the industry-standard Surflex-Dock screening program, for use by researchers utilizing in silico techniques to discover and optimize new scaffolds.
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Affiliation(s)
| | | | - Elizabeth Ambrose Amin
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St SE, Minneapolis, MN 55416 USA.
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25
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Lo SY, Säbel CE, Webb MI, Walsby CJ, Siemann S. High metal substitution tolerance of anthrax lethal factor and characterization of its active copper-substituted analogue. J Inorg Biochem 2014; 140:12-22. [DOI: 10.1016/j.jinorgbio.2014.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/27/2014] [Accepted: 06/16/2014] [Indexed: 01/19/2023]
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26
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Maize KM, Kurbanov EK, De La Mora-Rey T, Geders TW, Hwang DJ, Walters MA, Johnson RL, Amin EA, Finzel BC. Anthrax toxin lethal factor domain 3 is highly mobile and responsive to ligand binding. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2813-22. [PMID: 25372673 PMCID: PMC4220970 DOI: 10.1107/s1399004714018161] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/07/2014] [Indexed: 12/30/2022]
Abstract
The secreted anthrax toxin consists of three components: the protective antigen (PA), edema factor (EF) and lethal factor (LF). LF, a zinc metalloproteinase, compromises the host immune system primarily by targeting mitogen-activated protein kinase kinases in macrophages. Peptide substrates and small-molecule inhibitors bind LF in the space between domains 3 and 4 of the hydrolase. Domain 3 is attached on a hinge to domain 2 via residues Ile300 and Pro385, and can move through an angular arc of greater than 35° in response to the binding of different ligands. Here, multiple LF structures including five new complexes with co-crystallized inhibitors are compared and three frequently populated LF conformational states termed `bioactive', `open' and `tight' are identified. The bioactive position is observed with large substrate peptides and leaves all peptide-recognition subsites open and accessible. The tight state is seen in unliganded and small-molecule complex structures. In this state, domain 3 is clamped over certain substrate subsites, blocking access. The open position appears to be an intermediate state between these extremes and is observed owing to steric constraints imposed by specific bound ligands. The tight conformation may be the lowest-energy conformation among the reported structures, as it is the position observed with no bound ligand, while the open and bioactive conformations are likely to be ligand-induced.
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Affiliation(s)
- Kimberly M. Maize
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Elbek K. Kurbanov
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Teresa De La Mora-Rey
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Todd W. Geders
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Dong-Jin Hwang
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Michael A. Walters
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Rodney L. Johnson
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Elizabeth A. Amin
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Barry C. Finzel
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
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27
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Trinh TN, Hizartzidis L, Lin AJS, Harman DG, McCluskey A, Gordon CP. An efficient continuous flow approach to furnish furan-based biaryls. Org Biomol Chem 2014; 12:9562-71. [PMID: 25333944 DOI: 10.1039/c4ob01641f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Suzuki cross-couplings of 5-formyl-2-furanylboronic acid with activated or neutral aryl bromides were performed under continuous flow conditions in the presence of (Bu)4N(+)F(-) and the immobilised t-butyl based palladium catalyst CatCart™ FC1032™. Deactivated aryl bromides and activated aryl chlorides were cross-coupled with 5-formyl-2-furanylboronic in the presence of (Bu)4N(+)OAc(-) using the bis-triphenylphosphine CatCart™ PdCl2(PPh3)2-DVB. Initial evidence indicates the latter method may serve as a universal approach to conduct Suzuki cross-couplings with the protocol successfully employed in the synthesis of the current gold standard Hedgehog pathway inhibitor LDE225.
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Affiliation(s)
- Trieu N Trinh
- Chemistry, Centre for Chemical Biology, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.
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28
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Chen Y, Tang H, Seibel W, Papoian R, Oh K, Li X, Zhang J, Golczak M, Palczewski K, Kiser PD. Identification and characterization of novel inhibitors of Mammalian aspartyl aminopeptidase. Mol Pharmacol 2014; 86:231-42. [PMID: 24913940 DOI: 10.1124/mol.114.093070] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Aspartyl aminopeptidase (DNPEP) has been implicated in the control of angiotensin signaling and endosome trafficking, but its precise biologic roles remain incompletely defined. We performed a high-throughput screen of ∼25,000 small molecules to identify inhibitors of DNPEP for use as tools to study its biologic functions. Twenty-three confirmed hits inhibited DNPEP-catalyzed hydrolysis of angiotensin II with micromolar potency. A counter screen against glutamyl aminopeptidase (ENPEP), an enzyme with substrate specificity similar to that of DNPEP, identified eight DNPEP-selective inhibitors. Structure-activity relationships and modeling studies revealed structural features common to the identified inhibitors, including a metal-chelating group and a charged or polar moiety that could interact with portions of the enzyme active site. The compounds identified in this study should be valuable tools for elucidating DNPEP physiology.
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Affiliation(s)
- Yuanyuan Chen
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Hong Tang
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - William Seibel
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Ruben Papoian
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Ki Oh
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Xiaoyu Li
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Jianye Zhang
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Marcin Golczak
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Philip D Kiser
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
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29
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Santiesteban OJ, Kaittanis C, Perez JM. Identification of toxin inhibitors using a magnetic nanosensor-based assay. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:1202-1211. [PMID: 24339142 DOI: 10.1002/smll.201301824] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 09/12/2013] [Indexed: 06/03/2023]
Abstract
A magnetic nanosensor-based method is described to screen a library of drugs for potential binding to toxins. Screening is performed by measuring changes in the magnetic relaxation signal of the nanosensors (bMR nanosensors) in aqueous suspension upon addition of the toxin. The Anthrax lethal factor (ALF) is selected as a model toxin to test the ability of our bMR nanosensor-based screening method to identify potential inhibitors of the toxin. Out of 30 molecules screened, sulindac, naproxen and fusaric acid are found to bind LF, with dissociation constants in the low micromolar range. Further biological analysis of the free molecules in solution indicate that sulindac and its metabolic products inhibited LF cytotoxicity to macrophages with IC50 values in the micromolar range. Meanwhile, fusaric acid is found to be less effective at inhibiting LF cytotoxicity, while naproxen does not inhibit LF toxicity. Most importantly, when the sulindac and fusaric acid-bMR nanosensors themselves are tested as LF inhibitors, as opposed to the corresponding free molecules, they are stronger inhibitors of LF with IC50 values in the nanomolar range. Taken together, these studies show that a bMR nanosensors-based assay can be used to screen known drugs and other small molecules for inhibitor of toxins. The method can be easily modified to screen for inhibitors of other molecular interactions and not only the selected free molecule can be study as potential inhibitors but also the bMR nanosensors themselves achieving greater inhibitory potential.
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Affiliation(s)
- Oscar J Santiesteban
- NanoScience Technology Center, 12424 Research Parway, Suite 400, University of Central Florida, Orlando, FL, 32826, USA; Department of Chemistry, 4111 Libra Drive, Physical Sciences Bld, Room 255, University of Central Florida, Orlando, FL, 32826, USA
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30
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Identification of exosite-targeting inhibitors of anthrax lethal factor by high-throughput screening. ACTA ACUST UNITED AC 2014; 19:875-82. [PMID: 22840775 DOI: 10.1016/j.chembiol.2012.05.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 05/10/2012] [Accepted: 05/17/2012] [Indexed: 12/24/2022]
Abstract
Protease inhibitor discovery has focused almost exclusively on compounds that bind to the active site. Inhibitors targeting protease exosites, regions outside of the active site that influence catalysis, offer potential advantages of increased specificity but are difficult to systematically discover. Here, we describe an assay suitable for detecting exosite-targeting inhibitors of the metalloproteinase anthrax lethal factor (LF) based on cleavage of a full-length mitogen-activated protein kinase kinase (MKK) substrate. We used this assay to screen a small-molecule library and then subjected hits to a secondary screen to exclude compounds that efficiently blocked cleavage of a peptide substrate. We identified a compound that preferentially inhibited cleavage of MKKs compared with peptide substrates and could suppress LF-induced macrophage cytolysis. This approach should be generally applicable to the discovery of exosite-targeting inhibitors of many additional proteases.
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31
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Structure-based pharmacophore modeling and virtual screening to identify novel inhibitors for anthrax lethal factor. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0947-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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32
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Bouzianas DG. Potential biological targets ofBacillus anthracisin anti-infective approaches against the threat of bioterrorism. Expert Rev Anti Infect Ther 2014; 5:665-84. [PMID: 17678429 DOI: 10.1586/14787210.5.4.665] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The terrorist attacks of 2001 involving anthrax underscore the imperative that safe and effective medical countermeasures should be readily available. Vaccination appears to be the most effective form of mass protection against a biological attack, but the current vaccines have drawbacks that justify the enormous amount of effort currently being put into developing more effective vaccines and other treatment modalities. After providing a comprehensive overview of the organism Bacillus anthracis as a biological weapon and its pathogenicity, this review briefly summarizes the current knowledge vital to the management of anthrax disease. This knowledge has been acquired since 2001 as a result of the progress on anthrax research and focuses on the possible development of improved human anti-infective strategies targeting B. anthracis spore components, as well as strategies based on host-pathogen interactions.
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Affiliation(s)
- Dimitrios G Bouzianas
- Department of Medical Laboratories, Faculty of Health and Care Professions, University-level Technological Educational Institute of Thessaloniki, Greece.
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33
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Veronesi M, Romeo E, Lambruschini C, Piomelli D, Bandiera T, Scarpelli R, Garau G, Dalvit C. Fluorine NMR-Based Screening on Cell Membrane Extracts. ChemMedChem 2013; 9:286-9. [DOI: 10.1002/cmdc.201300438] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Indexed: 11/12/2022]
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34
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Williams JD, Khan AR, Cardinale SC, Butler MM, Bowlin TL, Peet NP. Small molecule inhibitors of anthrax lethal factor toxin. Bioorg Med Chem 2013; 22:419-34. [PMID: 24290062 DOI: 10.1016/j.bmc.2013.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/29/2013] [Accepted: 11/05/2013] [Indexed: 10/26/2022]
Abstract
This manuscript describes the preparation of new small molecule inhibitors of Bacillus anthracis lethal factor. Our starting point was the symmetrical, bis-quinolinyl compound 1 (NSC 12155). Optimization of one half of this molecule led to new LF inhibitors that were desymmetrized to afford more drug-like compounds.
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Affiliation(s)
- John D Williams
- Microbiotix, Inc., Department of Medicinal Chemistry, One Innovation Drive, Worcester, MA 01605, United States; Microbiotix, Inc., Department of Molecular Biology, One Innovation Drive, Worcester, MA 01605, United States
| | - Atiyya R Khan
- Microbiotix, Inc., Department of Medicinal Chemistry, One Innovation Drive, Worcester, MA 01605, United States; Microbiotix, Inc., Department of Molecular Biology, One Innovation Drive, Worcester, MA 01605, United States
| | - Steven C Cardinale
- Microbiotix, Inc., Department of Medicinal Chemistry, One Innovation Drive, Worcester, MA 01605, United States; Microbiotix, Inc., Department of Molecular Biology, One Innovation Drive, Worcester, MA 01605, United States
| | - Michelle M Butler
- Microbiotix, Inc., Department of Medicinal Chemistry, One Innovation Drive, Worcester, MA 01605, United States; Microbiotix, Inc., Department of Molecular Biology, One Innovation Drive, Worcester, MA 01605, United States
| | - Terry L Bowlin
- Microbiotix, Inc., Department of Medicinal Chemistry, One Innovation Drive, Worcester, MA 01605, United States; Microbiotix, Inc., Department of Molecular Biology, One Innovation Drive, Worcester, MA 01605, United States
| | - Norton P Peet
- Microbiotix, Inc., Department of Medicinal Chemistry, One Innovation Drive, Worcester, MA 01605, United States; Microbiotix, Inc., Department of Molecular Biology, One Innovation Drive, Worcester, MA 01605, United States.
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35
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Holler TP, Evdokimov AG, Narasimhan L. Structural biology approaches to antibacterial drug discovery. Expert Opin Drug Discov 2013; 2:1085-101. [PMID: 23484874 DOI: 10.1517/17460441.2.8.1085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Antibacterial drug discovery has undertaken a major experiment in the 12 years since the first bacterial genomes were sequenced. Genome mining has identified hundreds of potential targets that have been distilled to a relatively small number of broad-spectrum targets ('low-hanging fruit') using the genetics tools of modern microbiology. Prosecuting these targets with high-throughput screens has led to a disappointingly small number of lead series that have mostly evaporated under closer scrutiny. In the meantime, multi-drug resistant pathogens are becoming a serious challenge in the clinic and the community and the number of pharmaceutical firms pursuing antibacterial discovery has declined. Filling the antibacterial development pipeline with novel chemical series is a significant challenge that will require the collaboration of scientists from many disciplines. Fortunately, advancements in the tools of structural biology and of in silico modeling are opening up new avenues of research that may help deal with the problems associated with discovering novel antibiotics.
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Affiliation(s)
- Tod P Holler
- Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor, MI 48105, USA +1 734 622 5954 ; +1 734 622 2963 ; Tod.Holler@pfizer. com
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36
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Small-molecule inhibitors of lethal factor protease activity protect against anthrax infection. Antimicrob Agents Chemother 2013; 57:4139-45. [PMID: 23774434 DOI: 10.1128/aac.00941-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax, manifests its pathogenesis through the action of two secreted toxins. The bipartite lethal and edema toxins, a combination of lethal factor or edema factor with the protein protective antigen, are important virulence factors for this bacterium. We previously developed small-molecule inhibitors of lethal factor proteolytic activity (LFIs) and demonstrated their in vivo efficacy in a rat lethal toxin challenge model. In this work, we show that these LFIs protect against lethality caused by anthrax infection in mice when combined with subprotective doses of either antibiotics or neutralizing monoclonal antibodies that target edema factor. Significantly, these inhibitors provided protection against lethal infection when administered as a monotherapy. As little as two doses (10 mg/kg) administered at 2 h and 8 h after spore infection was sufficient to provide a significant survival benefit in infected mice. Administration of LFIs early in the infection was found to inhibit dissemination of vegetative bacteria to the organs in the first 32 h following infection. In addition, neutralizing antibodies against edema factor also inhibited bacterial dissemination with similar efficacy. Together, our findings confirm the important roles that both anthrax toxins play in establishing anthrax infection and demonstrate the potential for small-molecule therapeutics targeting these proteins.
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37
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Thirumurugan P, Matosiuk D, Jozwiak K. Click Chemistry for Drug Development and Diverse Chemical–Biology Applications. Chem Rev 2013; 113:4905-79. [DOI: 10.1021/cr200409f] [Citation(s) in RCA: 1309] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Prakasam Thirumurugan
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Dariusz Matosiuk
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Krzysztof Jozwiak
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
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38
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Baell JB, Ferrins L, Falk H, Nikolakopoulos G. PAINS: Relevance to Tool Compound Discovery and Fragment-Based Screening. Aust J Chem 2013. [DOI: 10.1071/ch13551] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pan assay interference compounds (PAINS) are readily discovered in any bioassay and can appear to give selective and optimisable hits. The most common PAINS can be readily recognised by their structure. However, there are compounds that closely resemble PAINS that are not specifically recognised by the PAINS filters. In addition, highly reactive compounds are not encoded for in the PAINS filters because they were excluded from the high-throughput screening (HTS) library used to develop the filters and so were never present to provide indicting data. A compounding complication in the area is that very occasionally a PAINS compound may serve as a viable starting point for progression. Despite such an occasional example, the literature is littered with an overwhelming number of examples of compounds that fail to progress and were probably not optimisable in the first place, nor useful tool compounds. Thus it is with great caution and diligence that compounds possessing a known PAINS core should be progressed through to medicinal chemistry optimisation, if at all, as the chances are very high that the hits will be found to be non-progressable, often after a significant waste of resources.
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39
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Chiu TL, Maize KM, Amin EA. Identification of novel anthrax toxin countermeasures using in silico methods. Methods Mol Biol 2013; 993:177-84. [PMID: 23568471 PMCID: PMC4634872 DOI: 10.1007/978-1-62703-342-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Anthrax is an acute infectious disease caused by the spore-forming, gram-positive, rod-shaped bacterium Bacillus anthracis. The anthrax toxin lethal factor (LF) is the primary anthrax toxin component responsible for cytotoxicity and host death and has been a heavily researched target for design of postexposure therapeutics in the event of a bioterror attack. Various computer-aided drug design methodologies have proven useful for pinpointing new antianthrax drug scaffolds, optimizing existing leads and probes, and elucidating key mechanisms of action. We present a selection of in silico virtual screening protocols incorporating docking and scoring, shape-based searching, and pharmacophore mapping techniques to identify and prioritize small molecules with potential biological activity against LF. We also recommend screening parameters that have been shown to increase the accuracy and reliability of these computational results.
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Affiliation(s)
- Ting-Lan Chiu
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
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40
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Calugi C, Trabocchi A, Lalli C, Guarna A. d-Proline-based peptidomimetic inhibitors of anthrax lethal factor. Eur J Med Chem 2012; 56:96-107. [DOI: 10.1016/j.ejmech.2012.08.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 11/27/2022]
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41
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Vulpetti A, Dalvit C. Fluorine local environment: from screening to drug design. Drug Discov Today 2012; 17:890-7. [DOI: 10.1016/j.drudis.2012.03.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 02/19/2012] [Accepted: 03/26/2012] [Indexed: 12/21/2022]
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42
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Chiu TL, Amin EA. Development of a comprehensive, validated pharmacophore hypothesis for anthrax toxin lethal factor (LF) inhibitors using genetic algorithms, Pareto scoring, and structural biology. J Chem Inf Model 2012; 52:1886-97. [PMID: 22697455 PMCID: PMC3477282 DOI: 10.1021/ci300121p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Anthrax is an acute infectious disease caused by the spore-forming bacterium Bacillus anthracis. The anthrax toxin lethal factor (LF), an 89-kDa zinc hydrolase secreted by the bacilli, is the toxin component chiefly responsible for pathogenesis and has been a popular target for rational and structure-based drug design. Although hundreds of small-molecule compounds have been designed to target the LF active site, relatively few reported inhibitors have exhibited activity in cell-based assays, and no LF inhibitor is currently available to treat or prevent anthrax. This study presents a new pharmacophore map assembly, validated by experiment, designed to rapidly identify and prioritize promising LF inhibitor scaffolds from virtual compound libraries. The new hypothesis incorporates structural information from all five available LF enzyme-inhibitor complexes deposited in the Protein Data Bank (PDB) and is the first LF pharmacophore map reported to date that includes features representing interactions involving all three key subsites of the LF catalytic binding region. In a wide-ranging validation study on all 546 compounds for which published LF biological activity data exist, this model displayed strong selectivity toward nanomolar-level LF inhibitors, successfully identifying 72.1% of existing nanomolar-level compounds in an unbiased test set, while rejecting 100% of weakly active (>100 μM) compounds. In addition to its capabilities as a database searching tool, this comprehensive model points to a number of key design principles and previously unidentified ligand-receptor interactions that are likely to influence compound potency.
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Affiliation(s)
- Ting-Lan Chiu
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Elizabeth A. Amin
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
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43
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Tomašić T, Peterlin Mašič L. Rhodanine as a scaffold in drug discovery: a critical review of its biological activities and mechanisms of target modulation. Expert Opin Drug Discov 2012; 7:549-60. [PMID: 22607309 DOI: 10.1517/17460441.2012.688743] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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44
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Park HC, Sung SR, Lim SM, Lee JS, Kim SK, Yoon MY. Proteolytic assay-based screening identifies a potent inhibitor of anthrax lethal factor. Microb Pathog 2012; 53:109-12. [PMID: 22561400 DOI: 10.1016/j.micpath.2012.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 04/09/2012] [Accepted: 04/18/2012] [Indexed: 10/28/2022]
Abstract
Anthrax lethal factor (LF), a Zn(2+)-dependent metalloprotease, is a key virulence component of anthrax toxin. Here, we used proteolytic assay-based screening to identify novel LF inhibitors from a naturally extracted chemical library. The screening identified four compounds that inhibited in vitro proteolytic activity of LF with an IC(50) of low micromolar range (11-20 μM). Three of these compounds were toxic to the mouse macrophage-like cell line, RAW 264.7. Compound 200 was non-toxic, however, and successfully protected Raw 264.7 cells from a lethal toxin challenge with an IC(50) of 39.2 μM. We also identified possible binding modes of compound 200 by molecular docking.
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Affiliation(s)
- Hae-Chul Park
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul 133-761, Republic of Korea
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45
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Ivarsson ME, Leroux JC, Castagner B. Targeting bacterial toxins. Angew Chem Int Ed Engl 2012; 51:4024-45. [PMID: 22441768 DOI: 10.1002/anie.201104384] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/21/2011] [Indexed: 12/18/2022]
Abstract
Protein toxins constitute the main virulence factors of several species of bacteria and have proven to be attractive targets for drug development. Lead candidates that target bacterial toxins range from small molecules to polymeric binders, and act at each of the multiple steps in the process of toxin-mediated pathogenicity. Despite recent and significant advances in the field, a rationally designed drug that targets toxins has yet to reach the market. This Review presents the state of the art in bacterial toxin targeted drug development with a critical consideration of achieved breakthroughs and withstanding challenges. The discussion focuses on A-B-type protein toxins secreted by four species of bacteria, namely Clostridium difficile (toxins A and B), Vibrio cholerae (cholera toxin), enterohemorrhagic Escherichia coli (Shiga toxin), and Bacillus anthracis (anthrax toxin), which are the causative agents of diseases for which treatments need to be improved.
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Affiliation(s)
- Mattias E Ivarsson
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology Zurich, Wolfgang-Pauli-Strasse 10, Zurich, Switzerland
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46
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47
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Finch KE, Knezevic CE, Nottbohm AC, Partlow KC, Hergenrother PJ. Selective small molecule inhibition of poly(ADP-ribose) glycohydrolase (PARG). ACS Chem Biol 2012; 7:563-70. [PMID: 22220926 DOI: 10.1021/cb200506t] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The poly(ADP-ribose) (PAR) post-translational modification is essential for diverse cellular functions, including regulation of transcription, response to DNA damage, and mitosis. Cellular PAR is predominantly synthesized by the enzyme poly(ADP-ribose) polymerase-1 (PARP-1). PARP-1 is a critical node in the DNA damage response pathway, and multiple potent PARP-1 inhibitors have been described, some of which show considerable promise in the clinic for the treatment of certain cancers. Cellular PAR is efficiently degraded by poly(ADP-ribose) glycohydrolase (PARG), an enzyme for which no potent, readily accessible, and specific inhibitors exist. Herein we report the discovery of small molecules that effectively inhibit PARG in vitro and in cellular lysates. These potent PARG inhibitors can be produced in two chemical steps from commercial starting materials and have complete specificity for PARG over the other known PAR glycohydrolase (ADP-ribosylhydrolase 3, ARH3) and over PARP-1 and thus will be useful tools for studying the biochemistry of PAR signaling.
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Affiliation(s)
- Kristin E. Finch
- Department of Chemistry, University of Illinois, 600 S. Mathews, Urbana, Illinois 61801, United
States
| | - Claire E. Knezevic
- Department of Chemistry, University of Illinois, 600 S. Mathews, Urbana, Illinois 61801, United
States
| | - Amanda C. Nottbohm
- Department of Chemistry, University of Illinois, 600 S. Mathews, Urbana, Illinois 61801, United
States
| | - Kathryn C. Partlow
- Department of Chemistry, University of Illinois, 600 S. Mathews, Urbana, Illinois 61801, United
States
| | - Paul J. Hergenrother
- Department of Chemistry, University of Illinois, 600 S. Mathews, Urbana, Illinois 61801, United
States
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48
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Huang D, Caflisch A. Fragment-Based Approaches in Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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49
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Kim J, Park HC, Gedi V, Park HY, Roberts AG, Atkins WM, Yoon MY. Yeast-hybrid based high-throughput assay for identification of anthrax lethal factor inhibitors. Biochem Biophys Res Commun 2010; 404:517-22. [PMID: 21144836 DOI: 10.1016/j.bbrc.2010.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 12/02/2010] [Indexed: 10/18/2022]
Abstract
Inhibitors of anthrax lethal factor (LF) are currently being sought as effective therapeutics for the treatment of anthrax. Here we report a novel screening approach for inhibitors of LF, a yeast-hybrid-based assay system in which the expression of reporter genes from a Gal4 promoter is repressed by LF proteolytic activity. Yeast cells were co-transformed with LF and a chimeric transcription factor that contains an LF substrate sequence inserted between the DNA-binding and activation domains of Gal4. In the resulting yeast cells, LF cleaves the substrate, thus inactivating the chimeric Gal4 and resulting in lack of expression of reporter genes. Compounds that inhibit LF cleavage of its substrate are identified by changes in reporter gene activity. Relative to in vitro screens for inhibitors of LF proteolytic activity, this screen has the advantage of excluding compounds that are toxic or non-permeable to eukaryotic cells. Additionally, the screen has the advantage of being fast, easy and cheap because exogenous LF and substrate are not needed. An initial chemical library screen with this system has identified four candidate inhibitors which were confirmed to inhibit LF protease activity in an in vitro assay. Furthermore, FBS-00831, one of the compounds identified, protects Raw 264.7 macrophages from anthrax lethal toxin and the possible binding site on LF was also evaluated by molecular docking.
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Affiliation(s)
- Joungmok Kim
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul 133-761, South Korea
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50
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Drag M, Salvesen GS. Emerging principles in protease-based drug discovery. Nat Rev Drug Discov 2010; 9:690-701. [PMID: 20811381 DOI: 10.1038/nrd3053] [Citation(s) in RCA: 397] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteases have an important role in many signalling pathways, and represent potential drug targets for diseases ranging from cardiovascular disorders to cancer, as well as for combating many parasites and viruses. Although inhibitors of well-established protease targets such as angiotensin-converting enzyme and HIV protease have shown substantial therapeutic success, developing drugs for new protease targets has proved challenging in recent years. This in part could be due to issues such as the difficulty of achieving selectivity when targeting protease active sites. This Perspective discusses the general principles in protease-based drug discovery, highlighting the lessons learned and the emerging strategies, such as targeting allosteric sites, which could help harness the therapeutic potential of new protease targets.
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Affiliation(s)
- Marcin Drag
- Program in Apoptosis and Cell Death Research, Burnham Institute for Medical Research, La Jolla, California 92037, USA.
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