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Moiketsi BN, Makale KPP, Rantong G, Rahube TO, Makhzoum A. Potential of Selected African Medicinal Plants as Alternative Therapeutics against Multi-Drug-Resistant Bacteria. Biomedicines 2023; 11:2605. [PMID: 37892979 PMCID: PMC10604549 DOI: 10.3390/biomedicines11102605] [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: 05/30/2023] [Revised: 09/04/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
Antimicrobial resistance is considered a "One-Health" problem, impacting humans, animals, and the environment. The problem of the rapid development and spread of bacteria resistant to multiple antibiotics is a rising global health threat affecting both rich and poor nations. Low- and middle-income countries are at highest risk, in part due to the lack of innovative research on the surveillance and discovery of novel therapeutic options. Fast and effective drug discovery is crucial towards combatting antimicrobial resistance and reducing the burden of infectious diseases. African medicinal plants have been used for millennia in folk medicine to cure many diseases and ailments. Over 10% of the Southern African vegetation is applied in traditional medicine, with over 15 species being partially or fully commercialized. These include the genera Euclea, Ficus, Aloe, Lippia. And Artemisia, amongst many others. Bioactive compounds from indigenous medicinal plants, alone or in combination with existing antimicrobials, offer promising solutions towards overcoming multi-drug resistance. Secondary metabolites have different mechanisms and modes of action against bacteria, such as the inhibition and disruption of cell wall synthesis; inhibition of DNA replication and ATP synthesis; inhibition of quorum sensing; inhibition of AHL or oligopeptide signal generation, broadcasting, and reception; inhibition of the formation of biofilm; disruption of pathogenicity activities; and generation of reactive oxygen species. The aim of this review is to highlight some promising traditional medicinal plants found in Africa and provide insights into their secondary metabolites as alternative options in antibiotic therapy against multi-drug-resistant bacteria. Additionally, synergism between plant secondary metabolites and antibiotics has been discussed.
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Affiliation(s)
| | | | | | - Teddie O. Rahube
- Department of Biological Sciences and Biotechnology, Faculty of Science, Botswana International University of Science and Technology (BIUST), Private Bag 16, Palapye, Botswana; (B.N.M.); (K.P.P.M.); (G.R.)
| | - Abdullah Makhzoum
- Department of Biological Sciences and Biotechnology, Faculty of Science, Botswana International University of Science and Technology (BIUST), Private Bag 16, Palapye, Botswana; (B.N.M.); (K.P.P.M.); (G.R.)
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2
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Cai S, Kumar R, Singh BR. Clostridial Neurotoxins: Structure, Function and Implications to Other Bacterial Toxins. Microorganisms 2021; 9:2206. [PMID: 34835332 PMCID: PMC8618262 DOI: 10.3390/microorganisms9112206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 01/20/2023] Open
Abstract
Gram-positive bacteria are ancient organisms. Many bacteria, including Gram-positive bacteria, produce toxins to manipulate the host, leading to various diseases. While the targets of Gram-positive bacterial toxins are diverse, many of those toxins use a similar mechanism to invade host cells and exert their functions. Clostridial neurotoxins produced by Clostridial tetani and Clostridial botulinum provide a classical example to illustrate the structure-function relationship of bacterial toxins. Here, we critically review the recent progress of the structure-function relationship of clostridial neurotoxins, including the diversity of the clostridial neurotoxins, the mode of actions, and the flexible structures required for the activation of toxins. The mechanism clostridial neurotoxins use for triggering their activity is shared with many other Gram-positive bacterial toxins, especially molten globule-type structures. This review also summarizes the implications of the molten globule-type flexible structures to other Gram-positive bacterial toxins. Understanding these highly dynamic flexible structures in solution and their role in the function of bacterial toxins not only fills in the missing link of the high-resolution structures from X-ray crystallography but also provides vital information for better designing antidotes against those toxins.
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Affiliation(s)
- Shuowei Cai
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA
| | - Raj Kumar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA 02747, USA; (R.K.); (B.R.S.)
| | - Bal Ram Singh
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA 02747, USA; (R.K.); (B.R.S.)
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3
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Patel KB, Kononova O, Cai S, Barsegov V, Parmar VS, Kumar R, Singh BR. Botulinum neurotoxin inhibitor binding dynamics and kinetics relevant for drug design. Biochim Biophys Acta Gen Subj 2021; 1865:129933. [PMID: 34023445 DOI: 10.1016/j.bbagen.2021.129933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND A natural product analog, 3-(4-nitrophenyl)-7H-furo[3,2-g]chromen-7-one, which is a nitrophenyl psoralen (NPP) was found to be an effective inhibitor of botulinum neurotoxin type A (BoNT/A). METHODS In this work, we performed enzyme inhibition kinetics and employed biochemical techniques such as isothermal calorimetry (ITC) and fluorescence spectroscopy as well as molecular modeling to examine the kinetics and binding mechanism of NPP inhibitor with BoNT/A LC. RESULTS Studies of inhibition mechanism and binding dynamics of NPP to BoNT/A light chain (BoNT/A LC) showed that NPP is a mixed type inhibitor for the zinc endopeptidase activity, implying that at least part of the inhibitor-enzyme binding site may be different from the substrate-enzyme binding site. By using biochemical techniques, we demonstrated NPP forms a stable complex with BoNT/A LC. These observations were confirmed by Molecular Dynamics (MD) simulation, which demonstrates that NPP binds to the site near the active site. CONCLUSION The NPP binding interferes with BoNT/A LC binding to the SNAP-25, hence, inhibits its cleavage. Based on these results, we propose a modified strategy for designing a molecule to enhance the efficiency of the inhibition against the neurotoxic effect of BoNT. GENERAL SIGNIFICANCE Insights into the interactions of NPP with BoNT/A LC using biochemical and computational approaches will aid in the future development of effective countermeasures and better pharmacological strategies against botulism.
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Affiliation(s)
- Kruti B Patel
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA; Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, USA
| | - Olga Kononova
- Department of Chemistry and Biochemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - Shuowei Cai
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, USA
| | - Valeri Barsegov
- Department of Chemistry and Biochemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - Virinder S Parmar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA; Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Raj Kumar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA
| | - Bal Ram Singh
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA; Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, USA; Prime Bio Inc., Dartmouth, MA, USA.
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4
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Bompiani KM, Caglič D, Krutein MC, Benoni G, Hrones M, Lairson LL, Bian H, Smith GR, Dickerson TJ. High-Throughput Screening Uncovers Novel Botulinum Neurotoxin Inhibitor Chemotypes. ACS COMBINATORIAL SCIENCE 2016; 18:461-74. [PMID: 27314875 DOI: 10.1021/acscombsci.6b00033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Botulism is caused by potent and specific bacterial neurotoxins that infect host neurons and block neurotransmitter release. Treatment for botulism is limited to administration of an antitoxin within a short time window, before the toxin enters neurons. Alternatively, current botulism drug development targets the toxin light chain, which is a zinc-dependent metalloprotease that is delivered into neurons and mediates long-term pathology. Several groups have identified inhibitory small molecules, peptides, or aptamers, although no molecule has advanced to the clinic due to a lack of efficacy in advanced models. Here we used a homogeneous high-throughput enzyme assay to screen three libraries of drug-like small molecules for new chemotypes that modulate recombinant botulinum neurotoxin light chain activity. High-throughput screening of 97088 compounds identified numerous small molecules that activate or inhibit metalloprotease activity. We describe four major classes of inhibitory compounds identified, detail their structure-activity relationships, and assess their relative inhibitory potency. A previously unreported chemotype in any context of enzyme inhibition is described with potent submicromolar inhibition (Ki = 200-300 nM). Additional detailed kinetic analyses and cellular cytotoxicity assays indicate the best compound from this series is a competitive inhibitor with cytotoxicity values around 4-5 μM. Given the potency and drug-like character of these lead compounds, further studies, including cellular activity assays and DMPK analysis, are justified.
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Affiliation(s)
- Kristin M. Bompiani
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dejan Caglič
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michelle C. Krutein
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Galit Benoni
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Morgan Hrones
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Luke L. Lairson
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Haiyan Bian
- Fox Chase Chemical Diversity Center, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Garry R. Smith
- Fox Chase Chemical Diversity Center, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Tobin J. Dickerson
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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5
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Wang F, Wan H, Hu JP, Chang S. Molecular dynamics simulations of wild type and mutants of botulinum neurotoxin A complexed with synaptic vesicle protein 2C. MOLECULAR BIOSYSTEMS 2015; 11:223-31. [DOI: 10.1039/c4mb00383g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Using molecular dynamics simulations, we investigate the relationship between the conformational changes of BoNT/A-RBD:SV2C-LD and the interfacial interactions.
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Affiliation(s)
- Feng Wang
- School of Information Science & Engineering
- Changzhou University
- Changzhou
- China
| | - Hua Wan
- College of Informatics
- South China Agricultural University
- Guangzhou
- China
| | - Jian-ping Hu
- Faculty of Biotechnology Industry
- Chengdu University
- Chengdu
- China
| | - Shan Chang
- College of Informatics
- South China Agricultural University
- Guangzhou
- China
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6
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Upadhyay A, Upadhyaya I, Kollanoor-Johny A, Venkitanarayanan K. Combating pathogenic microorganisms using plant-derived antimicrobials: a minireview of the mechanistic basis. BIOMED RESEARCH INTERNATIONAL 2014; 2014:761741. [PMID: 25298964 PMCID: PMC4178913 DOI: 10.1155/2014/761741] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/05/2014] [Accepted: 08/08/2014] [Indexed: 12/19/2022]
Abstract
The emergence of antibiotic resistance in pathogenic bacteria has led to renewed interest in exploring the potential of plant-derived antimicrobials (PDAs) as an alternative therapeutic strategy to combat microbial infections. Historically, plant extracts have been used as a safe, effective, and natural remedy for ailments and diseases in traditional medicine. Extensive research in the last two decades has identified a plethora of PDAs with a wide spectrum of activity against a variety of fungal and bacterial pathogens causing infections in humans and animals. Active components of many plant extracts have been characterized and are commercially available; however, research delineating the mechanistic basis of their antimicrobial action is scanty. This review highlights the potential of various plant-derived compounds to control pathogenic bacteria, especially the diverse effects exerted by plant compounds on various virulence factors that are critical for pathogenicity inside the host. In addition, the potential effect of PDAs on gut microbiota is discussed.
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Affiliation(s)
- Abhinav Upadhyay
- Department of Animal Science, University of Connecticut, 3636 Horsebarn Hill Road Extension, Unit 4040, Storrs, CT 06269, USA
| | - Indu Upadhyaya
- Department of Animal Science, University of Connecticut, 3636 Horsebarn Hill Road Extension, Unit 4040, Storrs, CT 06269, USA
| | - Anup Kollanoor-Johny
- Department of Animal Science, University of Connecticut, 3636 Horsebarn Hill Road Extension, Unit 4040, Storrs, CT 06269, USA
| | - Kumar Venkitanarayanan
- Department of Animal Science, University of Connecticut, 3636 Horsebarn Hill Road Extension, Unit 4040, Storrs, CT 06269, USA
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7
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Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening. J Comput Aided Mol Des 2014; 28:765-78. [PMID: 24958623 DOI: 10.1007/s10822-014-9758-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 05/26/2014] [Indexed: 01/25/2023]
Abstract
Botulinum neurotoxin serotype A (BoNT/A) is the most lethal toxin among the Tier 1 Select Agents. Development of potent and selective small molecule inhibitors against BoNT/A zinc metalloprotease remains a challenging problem due to its exceptionally large substrate binding surface and conformational plasticity. The exosites of the catalytic domain of BoNT/A are intriguing alternative sites for small molecule intervention, but their suitability for inhibitor design remains largely unexplored. In this study, we employed two recently identified exosite inhibitors, D-chicoric acid and lomofungin, to probe the structural features of the exosites and molecular mechanisms of synergistic inhibition. The results showed that D-chicoric acid favors binding at the α-exosite, whereas lomofungin preferentially binds at the β-exosite by mimicking the substrate β-sheet binding interaction. Molecular dynamics simulations and binding interaction analysis of the exosite inhibitors with BoNT/A revealed key elements and hotspots that likely contribute to the inhibitor binding and synergistic inhibition. Finally, we performed database virtual screening for novel inhibitors of BoNT/A targeting the exosites. Hits C1 and C2 showed non-competitive inhibition and likely target the α- and β-exosites, respectively. The identified exosite inhibitors may provide novel candidates for structure-based development of therapeutics against BoNT/A intoxication.
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8
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Videnović M, Opsenica DM, Burnett J, Gomba L, Nuss JE, Selaković Ž, Konstantinović J, Krstić M, Šegan S, Zlatović M, Sciotti RJ, Bavari S, Šolaja BA. Second generation steroidal 4-aminoquinolines are potent, dual-target inhibitors of the botulinum neurotoxin serotype A metalloprotease and P. falciparum malaria. J Med Chem 2014; 57:4134-53. [PMID: 24742203 PMCID: PMC4032193 DOI: 10.1021/jm500033r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Indexed: 01/25/2023]
Abstract
Significantly more potent second generation 4-amino-7-chloroquinoline (4,7-ACQ) based inhibitors of the botulinum neurotoxin serotype A (BoNT/A) light chain were synthesized. Introducing an amino group at the C(3) position of the cholate component markedly increased potency (IC50 values for such derivatives ranged from 0.81 to 2.27 μM). Two additional subclasses were prepared: bis(steroidal)-4,7-ACQ derivatives and bis(4,7-ACQ)cholate derivatives; both classes provided inhibitors with nanomolar-range potencies (e.g., the Ki of compound 67 is 0.10 μM). During BoNT/A challenge using primary neurons, select derivatives protected SNAP-25 by up to 89%. Docking simulations were performed to rationalize the compounds' in vitro potencies. In addition to specific residue contacts, coordination of the enzyme's catalytic zinc and expulsion of the enzyme's catalytic water were a consistent theme. With respect to antimalarial activity, the compounds provided better IC90 activities against chloroquine resistant (CQR) malaria than CQ, and seven compounds were more active than mefloquine against CQR strain W2.
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Affiliation(s)
- Milica Videnović
- Faculty
of Chemistry, University of Belgrade, Studentski trg 16, P.O. Box 51, 11158, Belgrade, Serbia
| | - Dejan M. Opsenica
- Institute
of Chemistry, Technology, and Metallurgy, University of Belgrade, Njegoseva 12, 11000 Belgrade, Serbia
| | - James
C. Burnett
- Computational
Drug Development Group, Leidos Biomedical
Research, Inc., FNLCR at Frederick, P.O.
Box B, Frederick, Maryland 21701, United States
| | - Laura Gomba
- Department
of Bacteriology, United States Army Medical
Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, Maryland 21702, United States
| | - Jonathan E. Nuss
- Department
of Bacteriology, United States Army Medical
Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, Maryland 21702, United States
| | - Života Selaković
- Faculty
of Chemistry, University of Belgrade, Studentski trg 16, P.O. Box 51, 11158, Belgrade, Serbia
| | - Jelena Konstantinović
- Faculty
of Chemistry Innovative Centre, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Maja Krstić
- Faculty
of Chemistry, University of Belgrade, Studentski trg 16, P.O. Box 51, 11158, Belgrade, Serbia
| | - Sandra Šegan
- Institute
of Chemistry, Technology, and Metallurgy, University of Belgrade, Njegoseva 12, 11000 Belgrade, Serbia
| | - Mario Zlatović
- Faculty
of Chemistry, University of Belgrade, Studentski trg 16, P.O. Box 51, 11158, Belgrade, Serbia
| | - Richard J. Sciotti
- Division
of Experimental Therapeutics, Walter Reed
Army Institute of Research, Silver
Spring, Maryland 20910, United States
| | - Sina Bavari
- Target
Discovery and Experimental Microbiology, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, Maryland 21702, United States
| | - Bogdan A. Šolaja
- Faculty
of Chemistry, University of Belgrade, Studentski trg 16, P.O. Box 51, 11158, Belgrade, Serbia
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9
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Patel K, Cai S, Singh BR. Current strategies for designing antidotes against botulinum neurotoxins. Expert Opin Drug Discov 2014; 9:319-33. [DOI: 10.1517/17460441.2014.884066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kruti Patel
- University of Massachusetts Dartmouth, Department of Chemistry and Biochemistry, North Dartmouth, MA 02747, USA
| | - Shuowei Cai
- University of Massachusetts Dartmouth, Department of Chemistry and Biochemistry, North Dartmouth, MA 02747, USA
| | - Bal Ram Singh
- University of Massachusetts Dartmouth, Department of Chemistry and Biochemistry, North Dartmouth, MA 02747, USA
- Institute of Advanced Sciences and Prime Bio, Inc., Botulinum Research Center, 166 Chase Road, North Dartmouth, MA 02747, USA
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10
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Caglič D, Krutein MC, Bompiani KM, Barlow DJ, Benoni G, Pelletier JC, Reitz AB, Lairson LL, Houseknecht KL, Smith GR, Dickerson TJ. Identification of clinically viable quinolinol inhibitors of botulinum neurotoxin A light chain. J Med Chem 2014; 57:669-76. [PMID: 24387280 PMCID: PMC3983388 DOI: 10.1021/jm4012164] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Botulinum neurotoxins (BoNT) are the most potent toxins known and a significant bioterrorist threat. Few small molecule compounds have been identified that are active in cell-based or animal models, potentially due to toxin enzyme plasticity. Here we screened commercially available quinolinols, as well as synthesized hydroxyquinolines. Seventy-two compounds had IC50 values below 10 μM, with the best compound exhibiting submicromolar inhibition (IC50 = 0.8 μM). Structure-activity relationship trends showed that the enzyme tolerates various substitutions at R1 but has a clear preference for bulky aryl amide groups at R2, while methylation at R3 increased inhibitor potency. Evaluation of the most potent compounds in an ADME panel showed that these compounds possess poor solubility at pH 6.8, but display excellent solubility at low pH, suggesting that oral dosing may be possible. Our data show the potential of quinolinol compounds as BoNT therapeutics due to their good in vitro potencies and favorable ADME properties.
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Affiliation(s)
- Dejan Caglič
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Kumar R, Kukreja RV, Li L, Zhmurov A, Kononova O, Cai S, Ahmed SA, Barsegov V, Singh BR. Botulinum neurotoxin: unique folding of enzyme domain of the most-poisonous poison. J Biomol Struct Dyn 2013; 32:804-15. [DOI: 10.1080/07391102.2013.791878] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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The thioredoxin reductase-thioredoxin system is involved in the entry of tetanus and botulinum neurotoxins in the cytosol of nerve terminals. FEBS Lett 2012. [DOI: 10.1016/j.febslet.2012.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Singh P, Singh MK, Chaudhary D, Chauhan V, Bharadwaj P, Pandey A, Upadhyay N, Dhaked RK. Small-molecule quinolinol inhibitor identified provides protection against BoNT/A in mice. PLoS One 2012; 7:e47110. [PMID: 23071727 PMCID: PMC3469547 DOI: 10.1371/journal.pone.0047110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 09/10/2012] [Indexed: 11/18/2022] Open
Abstract
Botulinum neurotoxins (BoNTs), etiological agents of the life threatening neuroparalytic disease botulism, are the most toxic substances currently known. The potential for the use as bioweapon makes the development of small-molecule inhibitor against these deadly toxins is a top priority. Currently, there are no approved pharmacological treatments for BoNT intoxication. Although an effective vaccine/immunotherapy is available for immuno-prophylaxis but this cannot reverse the effects of toxin inside neurons. A small-molecule pharmacological intervention, especially one that would be effective against the light chain protease, would be highly desirable. Similarity search was carried out from ChemBridge and NSC libraries to the hit (7-(phenyl(8-quinolinylamino)methyl)-8-quinolinol; NSC 84096) to mine its analogs. Several hits obtained were screened for in silico inhibition using AutoDock 4.1 and 19 new molecules selected based on binding energy and Ki. Among these, eleven quinolinol derivatives potently inhibited in vitro endopeptidase activity of botulinum neurotoxin type A light chain (rBoNT/A-LC) on synaptosomes isolated from rat brain which simulate the in vivo system. Five of these inhibitor molecules exhibited IC(50) values ranging from 3.0 nM to 10.0 µM. NSC 84087 is the most potent inhibitor reported so far, found to be a promising lead for therapeutic development, as it exhibits no toxicity, and is able to protect animals from pre and post challenge of botulinum neurotoxin type A (BoNT/A).
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Affiliation(s)
- Padma Singh
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Manglesh Kumar Singh
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Dilip Chaudhary
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Vinita Chauhan
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Pranay Bharadwaj
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Apurva Pandey
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Nisha Upadhyay
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
| | - Ram Kumar Dhaked
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, India
- * E-mail:
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14
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Time-dependent botulinum neurotoxin serotype A metalloprotease inhibitors. Bioorg Med Chem 2011; 19:7338-48. [PMID: 22082667 DOI: 10.1016/j.bmc.2011.10.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 10/13/2011] [Accepted: 10/19/2011] [Indexed: 11/21/2022]
Abstract
Botulinum neurotoxins (BoNTs) are the most lethal of biological substances, and are categorized as class A biothreat agents by the Centers for Disease Control and Prevention. There are currently no drugs to treat the deadly flaccid paralysis resulting from BoNT intoxication. Among the seven BoNT serotypes, the development of therapeutics to counter BoNT/A is a priority (due to its long half-life in the neuronal cytosol and its ease of production). In this regard, the BoNT/A enzyme light chain (LC) component, a zinc metalloprotease responsible for the intracellular cleavage of synaptosomal-associated protein of 25 kDa, is a desirable target for developing post-BoNT/A intoxication rescue therapeutics. In an earlier study, we reported the high throughput screening of a library containing 70,000 compounds, and uncovered a novel class of benzimidazole acrylonitrile-based BoNT/A LC inhibitors. Herein, we present both structure-activity relationships and a proposed mechanism of action for this novel inhibitor chemotype.
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Abstract
The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here.
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16
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Thompson AA, Jiao GS, Kim S, Thai A, Cregar-Hernandez L, Margosiak SA, Johnson AT, Han GW, O’Malley S, Stevens RC. Structural characterization of three novel hydroxamate-based zinc chelating inhibitors of the Clostridium botulinum serotype A neurotoxin light chain metalloprotease reveals a compact binding site resulting from 60/70 loop flexibility. Biochemistry 2011; 50:4019-28. [PMID: 21434688 PMCID: PMC3092028 DOI: 10.1021/bi2001483] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Neurotoxins synthesized by Clostridium botulinum bacteria (BoNT), the etiological agent of human botulism, are extremely toxic proteins making them high-risk agents for bioterrorism. Small molecule inhibitor development has been focused on the light chain zinc-dependent metalloprotease domain of the neurotoxin, an effort that has been hampered by its relatively flexible active site. Developed in concert with structure--activity relationship studies, the X-ray crystal structures of the complex of BoNT serotype A light chain (BoNT/A LC) with three different micromolar-potency hydroxamate-based inhibitors are reported here. Comparison with an unliganded BoNT/A LC structure reveals significant changes in the active site as a result of binding by the unique inhibitor scaffolds. The 60/70 loop at the opening of the active site pocket undergoes the largest conformational change, presumably through an induced-fit mechanism, resulting in the most compact catalytic pocket observed in all known BoNT/A LC structures.
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Affiliation(s)
- Aaron A. Thompson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Guan-Sheng Jiao
- Department of Chemistry, PanThera Biopharma LLC, Aiea, HI 96701
| | - Seongjin Kim
- Department of Chemistry, PanThera Biopharma LLC, Aiea, HI 96701
| | - April Thai
- Department of Chemistry, PanThera Biopharma LLC, Aiea, HI 96701
| | | | | | - Alan T. Johnson
- Department of Chemistry, PanThera Biopharma LLC, Aiea, HI 96701
| | - Gye Won Han
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Sean O’Malley
- Department of Chemistry, PanThera Biopharma LLC, Aiea, HI 96701
| | - Raymond C. Stevens
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037,Address correspondence to: The Scripps Research Institute, 10550 North Torrey Pines Rd., GAC-1200, La Jolla, CA 92037. Tel.: 858-784-9416; Fax: 858-784-9483;
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17
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Li B, Peet NP, Butler MM, Burnett JC, Moir DT, Bowlin TL. Small molecule inhibitors as countermeasures for botulinum neurotoxin intoxication. Molecules 2010; 16:202-20. [PMID: 21193845 PMCID: PMC6259422 DOI: 10.3390/molecules16010202] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 12/20/2010] [Accepted: 12/29/2010] [Indexed: 11/18/2022] Open
Abstract
Botulinum neurotoxins (BoNTs) are the most potent of known toxins and are listed as category A biothreat agents by the U.S. CDC. The BoNT-mediated proteolysis of SNARE proteins inhibits the exocytosis of acetylcholine into neuromuscular junctions, leading to life-threatening flaccid paralysis. Currently, the only therapy for BoNT intoxication (which results in the disease state botulism) includes experimental preventative antibodies and long-term supportive care. Therefore, there is an urgent need to identify and develop inhibitors that will serve as both prophylactic agents and post-exposure ‘rescue’ therapeutics. This review focuses on recent progress to discover and develop small molecule inhibitors as therapeutic countermeasures for BoNT intoxication.
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Affiliation(s)
- Bing Li
- Microbiotix, Inc., One Innovation Drive, Worcester, MA 01605, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-508-757-2800; Fax: +1-508-757-1999
| | - Norton P. Peet
- Microbiotix, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | | | - James C. Burnett
- Target, Structure-Based Drug Discovery Group, SAIC-Frederick, Inc., National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD 21702, USA; E-Mail: (J.C.B.)
| | - Donald T. Moir
- Microbiotix, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | - Terry L. Bowlin
- Microbiotix, Inc., One Innovation Drive, Worcester, MA 01605, USA
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18
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Chang TW, Blank M, Janardhanan P, Singh BR, Mello C, Blind M, Cai S. In vitro selection of RNA aptamers that inhibit the activity of type A botulinum neurotoxin. Biochem Biophys Res Commun 2010; 396:854-60. [PMID: 20452328 DOI: 10.1016/j.bbrc.2010.05.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 05/03/2010] [Indexed: 10/19/2022]
Abstract
The category A agent, botulinum neurotoxin (BoNT), is the most toxic molecule known to mankind. The endopeptidase activity of light chain domain of BoNT is the cause for the inhibition of the neurotransmitter release and the flaccid paralysis that leads to lethality in botulism. Currently, antidotes are not available to reverse the flaccid paralysis caused by BoNT. In the present study, we have identified three RNA aptamers through SELEX-process, which bind strongly to the light chain of type A BoNT (BoNT/A) and inhibit the endopeptidase activity, with IC(50) in low nM range. Inhibition kinetic studies reveal low nM K(I) and non-competitive nature of their inhibition. Aptamers are unique group of molecules as therapeutics, and this is first report of their development as an antidote against botulism. These data on K(I) and IC(50) strongly suggest that the aptamers have strong potential as antidotes that can reverse the symptom caused by BoNT/A.
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Affiliation(s)
- Tzuu-Wang Chang
- Department of Chemistry and Biochemistry, and Botulinum Research Center, University of Massachusetts Dartmouth, North Dartmouth, MA 02747, USA
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19
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Cai S, Lindo P, Park JB, Vasa K, Singh BR. The identification and biochemical characterization of drug-like compounds that inhibit botulinum neurotoxin serotype A endopeptidase activity. Toxicon 2009; 55:818-26. [PMID: 20003913 DOI: 10.1016/j.toxicon.2009.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Revised: 10/17/2009] [Accepted: 11/17/2009] [Indexed: 10/20/2022]
Abstract
A robust, high-throughput, two-tiered assay for screening small molecule inhibitors against botulinum neurotoxin serotype A was developed and employed to screen 16,544 compounds. Thirty-four compounds were identified as potent hits employing the first-tier assay. Subsequently, nine were confirmed as actives by our second-tier confirmatory assay. Of these, one displayed potent inhibitory efficacy, possessing an IC(50)=16 microM (+/-1.6 microM) in our in vitro assay. This inhibitor (0831-1035) is highly water-soluble, and possesses an IC(50)=47 microM (+/-7.0 microM) in our primary cell culture assay (with virtually no cytotoxicity up to 500 microM), suggesting that this inhibitor is a good candidate for further development as a therapeutic countermeasure to treat botulism resulting from botulinum neurotoxin serotype A intoxication. An enzyme kinetics study indicated that this inhibitor exhibits mixed non-competitive inhibition, with a K(I)=9 microM.
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Affiliation(s)
- Shuowei Cai
- Botulinum Research Center, and Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, MA 02747, USA
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20
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Identification and biochemical characterization of small-molecule inhibitors of Clostridium botulinum neurotoxin serotype A. Antimicrob Agents Chemother 2009; 53:3478-86. [PMID: 19528275 DOI: 10.1128/aac.00141-09] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An integrated strategy that combined in silico screening and tiered biochemical assays (enzymatic, in vitro, and ex vivo) was used to identify and characterize effective small-molecule inhibitors of Clostridium botulinum neurotoxin serotype A (BoNT/A). Virtual screening was initially performed by computationally docking compounds of the National Cancer Institute (NCI) database into the active site of BoNT/A light chain (LC). A total of 100 high-scoring compounds were evaluated in a high-performance liquid chromatography (HPLC)-based protease assay using recombinant full-length BoNT/A LC. Seven compounds that significantly inhibited the BoNT/A protease activity were selected. Database search queries of the best candidate hit [7-((4-nitro-anilino)(phenyl)methyl)-8-quinolinol (NSC 1010)] were performed to mine its nontoxic analogs. Fifty-five analogs of NSC 1010 were synthesized and examined by the HPLC-based assay. Of these, five quinolinol derivatives that potently inhibited both full-length BoNT/A LC and truncated BoNT/A LC (residues 1 to 425) were selected for further inhibition studies in neuroblastoma (N2a) cell-based and tissue-based mouse phrenic nerve hemidiaphragm assays. Consistent with enzymatic assays, in vitro and ex vivo studies revealed that these five quinolinol-based analogs effectively neutralized BoNT/A toxicity, with CB 7969312 exhibiting ex vivo protection at 0.5 microM. To date, this is the most potent BoNT/A small-molecule inhibitor that showed activity in an ex vivo assay. The reduced toxicity and high potency demonstrated by these five compounds at the biochemical, cellular, and tissue levels are distinctive among the BoNT/A small-molecule inhibitors reported thus far. This study demonstrates the utility of a multidisciplinary approach (in silico screening coupled with biochemical testing) for identifying promising small-molecule BoNT/A inhibitors.
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21
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Hermone AR, Burnett JC, Nuss JE, Tressler LE, Nguyen TL, Solaja BA, Vennerstrom JL, Schmidt JJ, Wipf P, Bavari S, Gussio R. Three-dimensional database mining identifies a unique chemotype that unites structurally diverse botulinum neurotoxin serotype A inhibitors in a three-zone pharmacophore. ChemMedChem 2009; 3:1905-12. [PMID: 19006141 DOI: 10.1002/cmdc.200800241] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A search query consisting of two aromatic centers and two cationic centers was defined based on previously identified small molecule inhibitors of the botulinum neurotoxin serotype A light chain (BoNT/A LC) and used to mine the National Cancer Institute Open Repository. Ten small molecule hits were identified, and upon testing, three demonstrated inhibitory activity. Of these, one was structurally unique, possessing a rigid diazachrysene scaffold. The steric limitations of the diazachrysene imposed a separation between the overlaps of previously identified inhibitors, revealing an extended binding mode. As a result, the pharmacophore for BoNT/A LC inhibition has been modified to encompass three zones. To demonstrate the utility of this model, a novel three-zone inhibitor was mined and its activity was confirmed.
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Affiliation(s)
- Ann R Hermone
- Target Structure-Based Drug Discovery Group, SAIC-Frederick, Inc. National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
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22
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Wipf P, Wang C, Widom J, Petronijevic F, C. Burnett J, E. Nuss J, Bavari S, Gussio R. Synthesis and Biological Evaluation of Inhibitors of Botulinum Neurotoxin Metalloprotease. HETEROCYCLES 2009. [DOI: 10.3987/com-08-s(d)8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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23
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Eapen BR. Molecular biology of botulinum neurotoxin serotype A: a cosmetic perspective. J Cosmet Dermatol 2008; 7:221-5. [PMID: 18789058 DOI: 10.1111/j.1473-2165.2008.00392.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cosmetic use of botulinum neurotoxin serotype A (BoNT/A) involves low doses of toxin administered for facial wrinkles and hyperhidrosis. The structural and functional properties of BoNT/A can affect the degree and duration of effect. Actively using the injected muscle is favorable as it exposes more receptors to BoNT/A. Divided doses of BoNT/A at an interval of more than 3 days may be longer lasting than single dose by blocking nascent neuronal sprouts. Antibodies are unlikely to be effective in BoNT/A neutralization because of the large area of receptor interaction. Several commonly used drugs including zinc and chloroquine can interact with BoNT/A, necessitating dosage adjustment for optimum effect. Serotype E (BoNT/E) can emerge as an antidote for BoNT/A for cosmetic use.
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24
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Agarwal R, Swaminathan S. SNAP-25 substrate peptide (residues 180-183) binds to but bypasses cleavage by catalytically active Clostridium botulinum neurotoxin E. J Biol Chem 2008; 283:25944-51. [PMID: 18658150 DOI: 10.1074/jbc.m803756200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clostridium botulinum neurotoxins are the most potent toxins to humans. The recognition and cleavage of SNAREs are prime evente in exhibiting their toxicity. We report here the crystal structure of the catalytically active full-length botulinum serotype E catalytic domain (BoNT E) in complex with SNAP-25 (a SNARE protein) substrate peptide Arg(180)-Ile(181)-Met(182)-Glu(183) (P1-P3'). It is remarkable that the peptide spanning the scissile bond binds to but bypasses cleavage by the enzyme and inhibits the catalysis fairly with K(i) approximately 69 microm. The inhibitory peptide occupies the active site of BoNT E and shows well defined electron density. The catalytic zinc and the conserved key residue Tyr(350) of the enzyme facilitate the docking of Arg(180) (P1) by interacting with its carbonyl oxygen that displaces the nucleophilic water. The general base Glu(212) side chain interacts with the main chain amino group of P1 and P1'. Conserved Arg(347) of BoNT E stabilizes the proper docking of the Ile(181) (P1') main chain, whereas the hydrophobic pockets stabilize the side chains of Ile(181) (P1') and Met(182) (P2'), and the 250 loop stabilizes Glu(183) (P3'). Structural and functional analysis revealed an important role for the P1' residue and S1' pocket in driving substrate recognition and docking at the active site. This study is the first of its kind and rationalizes the substrate cleavage strategy of BoNT E. Also, our complex structure opens up an excellent opportunity of structure-based drug design for this fast acting and extremely toxic high priority BoNT E.
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Affiliation(s)
- Rakhi Agarwal
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
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25
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Hines HB, Kim AD, Stafford RG, Badie SS, Brueggeman EE, Newman DJ, Schmidt JJ. Use of a recombinant fluorescent substrate with cleavage sites for all botulinum neurotoxins in high-throughput screening of natural product extracts for inhibitors of serotypes A, B, and E. Appl Environ Microbiol 2008; 74:653-9. [PMID: 18083881 PMCID: PMC2227718 DOI: 10.1128/aem.01690-07] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Accepted: 11/26/2007] [Indexed: 11/20/2022] Open
Abstract
The seven serotypes of botulinum neurotoxin (BoNTs) are zinc metalloproteases that cleave and inactivate proteins critical for neurotransmission. The synaptosomal protein of 25 kDa (SNAP-25) is cleaved by BoNTs A, C, and E, while vesicle-associated membrane protein (VAMP) is the substrate for BoNTs B, D, F, and G. BoNTs not only are medically useful drugs but also are potential bioterrorist and biowarfare threat agents. Because BoNT protease activity is required for toxicity, inhibitors of that activity might be effective for antibotulinum therapy. To expedite inhibitor discovery, we constructed a hybrid gene encoding (from the N terminus to the C terminus, with respect to the expressed product) green fluorescent protein, then a SNAP-25 fragment encompassing residues Met-127 to Gly-206, and then VAMP residues Met-1 to Lys-94. Cysteine was added as the C terminus. The expressed product, which contained the protease cleavage sites for all seven botulinum serotypes, was purified and coupled covalently through the C-terminal sulfhydryl group to maleimide-activated 96-well plates. The substrate was readily cleaved by BoNTs A, B, D, E, and F. Using this assay and an automated 96-well pipettor, we screened 528 natural product extracts for inhibitors of BoNT A, B, and E protease activities. Serotype-specific inhibition was found in 30 extracts, while 5 others inhibited two serotypes.
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Affiliation(s)
- Harry B Hines
- Department of Cell Biology and Biochemistry, Integrated Toxicology Division, USAMRIID, Frederick, MD 21702-5011, USA
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26
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Boldt GE, Kennedy JP, Janda KD. Identification of a potent botulinum neurotoxin a protease inhibitor using in situ lead identification chemistry. Org Lett 2007; 8:1729-32. [PMID: 16597152 PMCID: PMC2733786 DOI: 10.1021/ol0603211] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] Botulinum neurotoxins (BoNTs), etiological agents of the deadly food poisoning disease botulism, are the most toxic proteins currently known. By using in situ lead identification chemistry, we have uncovered the first class of inhibitors that displays nanomolar potency. From a 15 microM lead compound, structure-activity relationship studies were performed granting the most potent BoNT/A inhibitor reported to date that displays an inhibition constant of 300 nM.
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27
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Burnett JC, Ruthel G, Stegmann CM, Panchal RG, Nguyen TL, Hermone AR, Stafford RG, Lane DJ, Kenny TA, McGrath CF, Wipf P, Stahl AM, Schmidt JJ, Gussio R, Brunger AT, Bavari S. Inhibition of metalloprotease botulinum serotype A from a pseudo-peptide binding mode to a small molecule that is active in primary neurons. J Biol Chem 2006; 282:5004-5014. [PMID: 17092934 DOI: 10.1074/jbc.m608166200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An efficient research strategy integrating empirically guided, structure-based modeling and chemoinformatics was used to discover potent small molecule inhibitors of the botulinum neurotoxin serotype A light chain. First, a modeled binding mode for inhibitor 2-mercapto-3-phenylpropionyl-RATKML (K(i) = 330 nM) was generated, and required the use of a molecular dynamic conformer of the enzyme displaying the reorientation of surface loops bordering the substrate binding cleft. These flexible loops are conformationally variable in x-ray crystal structures, and the model predicted that they were pivotal for providing complementary binding surfaces and solvent shielding for the pseudo-peptide. The docked conformation of 2-mercapto-3-phenylpropionyl-RATKML was then used to refine our pharmacophore for botulinum serotype A light chain inhibition. Data base search queries derived from the pharmacophore were employed to mine small molecule (non-peptidic) inhibitors from the National Cancer Institute's Open Repository. Four of the inhibitors possess K(i) values ranging from 3.0 to 10.0 microM. Of these, NSC 240898 is a promising lead for therapeutic development, as it readily enters neurons, exhibits no neuronal toxicity, and elicits dose-dependent protection of synaptosomal-associated protein (of 25 kDa) in a primary culture of embryonic chicken neurons. Isothermal titration calorimetry showed that the interaction between NSC 240898 and the botulinum A light chain is largely entropy-driven, and occurs with a 1:1 stoichiometry and a dissociation constant of 4.6 microM.
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Affiliation(s)
- James C Burnett
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Gordon Ruthel
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702
| | - Christian M Stegmann
- Howard Hughes Medical Institute (HHMI) and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and the Stanford Synchrotron Radiation Laboratory, Stanford University, School of Medicine, Stanford, California 94305, and the
| | - Rekha G Panchal
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Tam L Nguyen
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Ann R Hermone
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Robert G Stafford
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702
| | - Douglas J Lane
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Tara A Kenny
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Connor F McGrath
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Peter Wipf
- Combinatorial Chemistry Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Andrea M Stahl
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702
| | - James J Schmidt
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702
| | - Rick Gussio
- Information Technology Branch, Developmental Therapeutics Program, National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Axel T Brunger
- Howard Hughes Medical Institute (HHMI) and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and the Stanford Synchrotron Radiation Laboratory, Stanford University, School of Medicine, Stanford, California 94305, and the.
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702.
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Boldt GE, Kennedy JP, Hixon MS, McAllister LA, Barbieri JT, Tzipori S, Janda KD. Synthesis, characterization and development of a high-throughput methodology for the discovery of botulinum neurotoxin a inhibitors. ACTA ACUST UNITED AC 2006; 8:513-21. [PMID: 16827563 PMCID: PMC2644723 DOI: 10.1021/cc060010h] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Botulinum neurotoxins (BoNTs), etiological agents of the deadly food poisoning disease botulism, are the most toxic proteins currently known. Although only a few hundred cases of botulism are reported in the United States annually, there is growing interest in BoNTs attributable to their potential use as biological warfare agents. Neurotoxicity results from cleavage of the soluble NSF-attachment protein receptor complex proteins of the presynaptic vesicles by the BoNT light chain subunit, a Zn endopeptidase. Few effective inhibitors of BoNT/A LC (light chain) activity are known, and the discovery process is hampered by the lack of an efficient high-throughput assay for screening compound libraries. To alleviate this bottleneck, we have synthesized the peptide SNAPtide and have developed a robust assay for the high-throughput evaluation of BoNT/A LC inhibitors. Key aspects for the development of this optimized assay include the addition of a series of detergents, cosolvents, and salts, including 0.01% w/v Tween 20 to increase BoNT/A LC catalysis, stability, and ease of small molecule screening. To evaluate the effectiveness of the assay, a series of hydroxamate-based small molecules were synthesized and examined with BoNT/A LC. The methodology described is superior to other assays reported to date for the high-throughput identification of BoNT/A inhibitors.
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Affiliation(s)
- Grant E. Boldt
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, and Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jack P. Kennedy
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, and Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mark S. Hixon
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, and Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Laura A. McAllister
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, and Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Joseph T. Barbieri
- The Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Saul Tzipori
- The Division of Infectious Diseases, Department of Biomedical Sciences, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Kim D. Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, and Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- To whom correspondence should be addressed. Tel.: +1-858-784-2516; fax: +1-858-784-2595; e-mail:
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29
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Singh BR. Botulinum neurotoxin structure, engineering, and novel cellular trafficking and targeting. Neurotox Res 2006; 9:73-92. [PMID: 16785103 DOI: 10.1007/bf03033925] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Botulinum neurotoxins are multifaceted molecules, which are truly unique not only in their mode of action, but also their utility as a drug carrier either across the gut wall or to the nerve terminals. The molecule is divided in clear functional domains that can operate independently. This feature can be used to employ them as cargo carrier by linking other drugs or vaccines with the binding and translocation domains of BoNT. While the domain structures are largely independent of each other, the dynamic structure of these domains, especially that of the enzymatic domain (L chain), is quite different from the reported crystal structures for several BoNT serotypes and their enzymatic domain. This review discusses the comparative structures of BoNT in crystal and solution for their relevance to the molecular mechanism of BoNT action, especially in view of our recent discovery that the enzymatically active structure of the BoNT exists as a molten-globule and that of the endopeptidase domain as a novel PRIME conformation. Finally, a non-exhaustive discussion has been included to explain the long-lasting biological effects of certain serotypes of BoNT, based on the current knowledge of the structure-function of different serotypes of botulinum neurotoxins.
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Affiliation(s)
- B R Singh
- Botulinum Research Center, and Department of Chemistry and Biochemistry, University of Massachusetts, Dartmouth, 02747, USA.
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30
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Boldt GE, Eubanks LM, Janda KD. Identification of a botulinum neurotoxin A protease inhibitor displaying efficacy in a cellular model. Chem Commun (Camb) 2006:3063-5. [PMID: 16855686 DOI: 10.1039/b603099h] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we describe a small-molecule, non-peptidic, inhibitor for botulinum neurotoxin A protease, that displays for the first time efficacy in a cell-based assay.
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Affiliation(s)
- Grant E Boldt
- Department of Chemistry and Immunology, Skaggs Institute for Chemical Biology, Worm Institute for Research Medicine (WIRM), Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Breidenbach MA, Brunger AT. New insights into clostridial neurotoxin-SNARE interactions. Trends Mol Med 2005; 11:377-81. [PMID: 16006188 DOI: 10.1016/j.molmed.2005.06.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Revised: 06/10/2005] [Accepted: 06/27/2005] [Indexed: 11/29/2022]
Abstract
Botulinum neurotoxin serotype A (BoNT/A) has achieved a dichotomous status in modern medicine; it is both a versatile treatment for several neurological disorders and a lethal poison responsible for causing the neuroparalytic syndrome botulism. The extent of paralysis largely depends on the dosage of toxin received. The toxins block neurotransmitter release by delivering their Zn(2+)-dependent protease components to the presynaptic side of chemical synapses. These highly specialized enzymes exclusively hydrolyze peptide bonds within SNARE (soluble N-ethylmaleiamide-sensitive factor attachment protein receptor) proteins. Recently, the structural basis for the highly specific interaction between BoNT/A and its target SNARE, SNAP-25 (synaptosomal-associated protein of 25kDa), was elucidated. New details regarding the nature of the toxin-SNARE interactions could be exploited for novel inhibitor design.
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Affiliation(s)
- Mark A Breidenbach
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
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Burnett JC, Henchal EA, Schmaljohn AL, Bavari S. The evolving field of biodefence: therapeutic developments and diagnostics. Nat Rev Drug Discov 2005; 4:281-97. [PMID: 15803193 PMCID: PMC7096857 DOI: 10.1038/nrd1694] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bioweapons are a clear threat to both military and civilian populations. Here, the latest advances in the pursuit of inhibitors against biothreat threat toxins, current therapeutic strategies for treating biodefence related pathogens, and strategies for improving detection and exposure survivability are covered. There are numerous lead therapeutics that have emerged from drug discovery efforts. However, many of these are toxic and/or fail to possess conventional drug-like properties. One clear advantage of small (non-peptidic) molecules is that they possess scaffolds that are inherently more likely to evolve into real therapeutics. One of the major obstacles impeding the translation of these lead therapeutics into viable drugs is the lack of involvement of the pharmaceutical industry, which has been discovering leads and translating them into drugs for decades. The expertise of the pharmaceutical industry therefore needs to be more effectively engaged in developing drugs against biothreat agents. New methods for rapidly detecting and diagnosing biothreat agents are also in development. The detection and diagnosis of biothreats is inherently linked with treatment. The means for detecting the release of bioweapons are being deployed, and new technologies are shortening the timeframe between initial sample collection and conclusive agent determination. However, the organization of this process is imperfect. At present, a unifying entity that orchestrates the biodefence response is clearly needed to reduce the time-to-drug process and redundancies in drug development efforts. Such a central entity could formulate and implement plans to coordinate all participants, including academic institutions, government agencies and the private sector. This could accelerate the development of countermeasures against high probability biothreat agents.
The threat of bioterrorism and the potential use of biological weapons against both military and civilian populations has become a major concern for governments around the world. For example, in 2001 anthrax-tainted letters resulted in several deaths, caused widespread public panic and exerted a heavy economic toll. If such a small-scale act of bioterrorism could have such a huge impact, then the effects of a large-scale attack would be catastrophic. This review covers recent progress in developing therapeutic countermeasures against, and diagnostics for, such agents.
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Affiliation(s)
- James C. Burnett
- Developmental Therapeutics Program, Target Structure-Based Drug Discovery Group, National Cancer Institute-SAIC, Frederick, 21702 Maryland USA
| | - Erik A. Henchal
- United States Army Medical Research Institute of Infectious Diseases, Frederick, 21702 Maryland USA
| | - Alan L. Schmaljohn
- United States Army Medical Research Institute of Infectious Diseases, Frederick, 21702 Maryland USA
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Frederick, 21702 Maryland USA
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